Contacts of the helix formed by residues 359 - 380 (chain C) in PDB entry 3CMM
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ILE 359 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C THR* 4.0 2.7 - - - -
156C THR* 4.7 3.6 - - - +
158C GLY* 3.9 26.3 + - - +
159C LEU* 4.1 8.3 - - + +
357C GLY 4.1 0.4 - - - -
358C ASP* 1.3 81.1 + - - +
360C PRO* 1.3 68.6 - - - +
361C GLY 4.1 5.2 - - - +
362C VAL* 2.9 35.4 + - + +
363C VAL* 3.0 12.1 + - - +
419C ASN 4.0 0.7 - - - +
420C GLN* 3.8 23.6 - - + -
423C VAL* 4.0 12.3 - - + -
424C PHE* 3.5 25.8 - - + -
879C LEU* 4.3 0.9 - - + -
882C TYR* 3.4 34.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 360 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C SER 3.9 9.2 - - - +
78C THR* 3.7 9.6 - - - +
358C ASP 3.5 8.5 - - - +
359C ILE* 1.3 88.0 - - + +
361C GLY* 1.3 63.6 + - - +
363C VAL* 3.1 4.9 + - + +
364C ALA* 2.9 24.4 + - - +
420C GLN* 3.5 30.1 - - + +
452C ASN* 3.6 18.3 - - - +
455C LEU* 4.1 20.9 - - + -
456C LEU* 3.7 18.8 - - + -
878C ASN* 6.0 0.4 - - + -
882C TYR* 4.1 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 361 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359C ILE* 3.2 4.2 + - - +
360C PRO* 1.3 80.1 - - - +
362C VAL* 1.3 55.9 + - - +
364C ALA 3.5 0.3 + - - -
365C PHE* 2.9 27.2 + - - +
452C ASN* 3.9 4.2 + - - -
456C LEU* 5.5 0.4 - - - +
875C GLY* 3.5 30.1 - - - -
878C ASN* 4.4 8.3 - - - +
879C LEU* 3.9 16.6 - - - -
882C TYR* 5.1 2.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 362 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156C THR* 3.7 18.4 - - + +
158C GLY 3.5 19.5 - - - +
159C LEU* 3.8 17.7 - - + +
160C PHE 3.8 21.1 - - - +
359C ILE* 2.9 24.9 + - + +
361C GLY* 1.3 72.1 - - - +
363C VAL* 1.3 56.7 + - - +
365C PHE* 3.2 6.9 + - - +
366C PHE* 3.0 41.6 + - + +
391C PHE* 4.7 7.2 - - + -
393C SER* 5.5 0.2 - - - -
879C LEU* 4.0 18.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 363 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C GLY 3.6 5.4 - - - +
47C LEU* 3.6 29.3 - - + +
50C GLU* 4.1 11.1 - - + +
78C THR* 3.4 35.7 - - + +
156C THR* 3.8 25.8 - - + +
358C ASP* 3.7 13.7 - - - +
359C ILE 3.0 11.0 + - - +
360C PRO* 3.1 6.7 + - + +
362C VAL* 1.3 73.2 - - - +
364C ALA* 1.3 56.3 + - - +
366C PHE 3.4 0.2 + - - -
367C GLY* 2.8 33.8 + - - -
455C LEU* 6.4 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 364 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C GLU* 4.3 12.6 - - + -
360C PRO 2.9 16.7 + - - +
363C VAL* 1.3 73.2 - - - +
365C PHE* 1.3 69.1 + - - +
368C GLY 3.1 16.3 + - - -
451C LYS* 4.5 8.7 - - - +
452C ASN* 4.1 17.7 - - - +
871C SER* 3.6 28.0 + - - +
872C LEU* 3.8 1.2 - - - -
875C GLY* 3.6 14.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 365 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281C SER* 5.2 0.9 - - - -
361C GLY 2.9 14.8 + - - +
362C VAL* 3.2 10.7 + - - +
364C ALA* 1.3 79.8 - - - +
366C PHE* 1.3 91.6 + + - +
369C LEU* 3.3 7.1 + - + +
389C MET* 4.5 7.0 - - + -
391C PHE* 3.8 39.7 - + + -
872C LEU* 3.2 63.5 - - + +
875C GLY* 4.1 1.5 - - - -
876C LEU* 3.5 30.5 - - + -
879C LEU* 5.3 0.7 - - + -
906C PHE* 3.8 29.2 - + + -
908C PHE* 5.1 2.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 366 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C LEU* 3.9 17.0 - - + -
154C SER* 3.8 8.5 - - - +
156C THR* 4.2 6.7 - - - +
161C GLY* 3.3 36.3 - - - -
162C ASN 3.4 27.8 - - - -
163C THR* 3.7 7.2 - - + -
362C VAL* 3.0 22.8 + - + +
365C PHE* 1.3 94.9 - + - +
367C GLY* 1.3 53.8 + - - +
369C LEU* 3.2 20.0 + - + -
370C VAL* 2.7 40.5 + - + +
389C MET* 3.4 28.9 - - + -
391C PHE* 3.6 17.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 367 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C LEU* 3.8 3.6 - - - +
50C GLU* 4.0 13.2 - - - -
51C ILE* 3.8 22.0 - - - -
54C ASN* 3.4 9.6 + - - -
363C VAL 2.8 22.3 + - - -
364C ALA 4.0 0.7 - - - -
366C PHE* 1.3 68.2 - - - +
368C GLY* 1.3 63.5 + - - +
371C ALA* 3.1 25.3 + - - +
871C SER* 4.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 368 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C ASN* 3.9 3.8 - - - -
364C ALA 3.1 13.2 + - - -
365C PHE 3.8 2.9 - - - -
367C GLY* 1.3 75.7 - - - +
369C LEU* 1.3 64.1 + - - +
372C GLN* 3.0 20.5 + - - +
868C THR* 3.4 24.7 + - - -
871C SER* 3.5 18.6 + - - -
872C LEU* 4.3 4.5 - - - -
901C LEU* 4.8 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 369 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163C THR* 3.4 28.3 - - + +
365C PHE* 3.3 8.1 + - + +
366C PHE* 3.2 26.8 + - + +
368C GLY* 1.3 74.9 - - - +
370C VAL* 1.3 68.9 + - + +
372C GLN* 3.3 10.3 + - + +
373C GLU* 3.0 46.3 + - + +
385C LEU* 4.1 11.9 - - + -
389C MET* 5.2 2.0 - - - -
872C LEU* 3.6 23.2 - - + +
901C LEU* 4.6 7.0 - - + -
904C PRO* 5.2 0.2 - - + -
906C PHE* 3.6 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 370 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C ILE* 3.9 27.4 - - + -
127C VAL* 4.0 11.4 - - + -
152C ILE* 3.7 22.7 - - + -
154C SER* 3.7 29.6 - - - +
163C THR* 3.8 15.0 - - - +
366C PHE* 2.7 25.0 + - + +
369C LEU* 1.3 77.5 - - + +
371C ALA* 1.3 65.9 + - - +
373C GLU* 3.1 8.3 + - - +
374C VAL* 2.9 23.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 371 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C ILE* 4.0 7.8 - - - +
54C ASN* 3.4 29.4 - - + -
55C VAL* 3.9 20.3 - - + +
367C GLY 3.1 22.6 + - - +
368C GLY 3.5 3.4 - - - +
370C VAL* 1.3 75.2 - - - +
372C GLN* 1.3 63.1 + - - +
374C VAL* 3.1 14.0 + - - +
375C LEU* 3.1 17.5 + - + +
868C THR* 3.9 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 372 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C LEU* 4.7 0.9 - - - +
368C GLY 3.0 9.9 + - - +
369C LEU* 3.3 10.1 - - - +
371C ALA* 1.3 76.1 - - - +
373C GLU* 1.3 62.4 + - + +
375C LEU* 3.1 13.7 + - - +
376C LYS* 3.0 32.6 + - - +
382C PHE* 3.6 30.1 - - - -
571C THR* 4.5 8.3 - - - +
866C ILE* 3.6 17.5 - - - +
868C THR* 3.0 39.6 + - + +
901C LEU* 3.4 28.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 373 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C ILE* 3.8 15.9 - - + +
163C THR* 5.5 2.0 - - - +
165C VAL* 4.3 19.2 - - + +
167C LEU* 5.3 2.4 - - - +
369C LEU* 3.0 34.9 + - + +
370C VAL* 3.1 10.7 + - - +
372C GLN* 1.3 76.1 - - - +
374C VAL* 1.3 62.3 + - - +
376C LYS* 2.6 39.1 + - - +
377C ALA* 3.0 22.9 + - - +
384C PRO* 3.4 4.5 - - - +
385C LEU* 2.8 38.9 + - + +
901C LEU* 6.1 0.2 - - - +
904C PRO* 3.8 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 374 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C VAL* 4.1 25.4 - - + -
51C ILE* 4.7 1.6 - - + -
55C VAL* 4.1 24.5 - - + -
125C VAL* 4.0 13.7 - - + -
127C VAL* 3.5 29.2 - - + -
152C ILE* 3.7 14.6 - - + -
370C VAL* 2.9 22.3 + - + +
371C ALA 3.1 8.0 + - - +
373C GLU* 1.3 76.8 - - - +
375C LEU* 1.3 62.4 + - + +
377C ALA* 3.1 5.9 + - - +
378C CYS* 3.1 24.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 375 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C LEU* 4.5 11.9 - - + -
34C MET* 4.2 19.6 - - + +
54C ASN 5.4 1.3 - - - +
55C VAL* 4.5 20.2 - - + -
58C ALA* 3.7 34.1 - - + -
60C VAL* 4.5 8.5 - - + -
371C ALA* 3.1 14.7 + - + +
372C GLN* 3.1 28.8 + - - +
374C VAL* 1.3 76.0 - - + +
376C LYS* 1.3 56.2 + - - +
378C CYS* 3.2 13.5 + - - +
379C SER* 2.7 27.1 + - - -
866C ILE* 3.9 14.1 - - + -
868C THR* 4.7 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 376 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167C LEU* 5.6 0.2 - - + -
171C PHE* 3.4 9.4 - - + -
372C GLN* 3.0 29.2 + - - +
373C GLU* 2.6 48.2 + - - +
375C LEU* 1.3 74.1 - - - +
377C ALA* 1.3 62.3 + - - +
379C SER* 3.1 0.6 + - - -
380C GLY* 3.0 28.1 + - - -
381C LYS 3.4 24.5 - - - +
382C PHE* 4.0 13.5 - - + +
383C THR 2.8 25.0 + - - +
384C PRO* 3.8 19.3 - - + -
901C LEU 2.9 26.7 + - - -
904C PRO* 4.0 4.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 377 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C VAL* 4.0 15.7 - - + -
150C ARG* 3.1 33.7 + - + -
152C ILE* 4.5 3.6 - - + -
167C LEU* 3.8 26.9 - - + +
171C PHE* 3.5 18.1 - - - -
373C GLU 3.0 14.0 + - - +
374C VAL* 3.1 10.9 + - - +
376C LYS* 1.3 75.6 - - - +
378C CYS* 1.3 59.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 378 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C LYS* 3.4 18.8 - - - +
34C MET* 3.8 15.3 - - + -
37C SER* 3.4 38.3 + - - +
39C VAL* 4.3 11.4 - - - -
60C VAL* 4.3 9.9 - - - -
125C VAL* 3.8 15.3 - - - -
150C ARG* 4.3 6.8 + - - +
374C VAL* 3.1 19.7 + - - -
375C LEU* 3.4 10.1 - - - +
376C LYS 3.1 0.6 - - - -
377C ALA* 1.3 79.6 - - - +
379C SER* 1.3 56.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 379 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C LEU* 5.9 0.9 - - - +
30C ALA* 3.7 37.6 - - - +
33C LYS* 3.3 26.4 - - - +
34C MET* 4.4 5.5 - - - -
174C LEU* 4.0 8.0 - - - +
375C LEU 2.7 22.4 + - - -
376C LYS* 3.1 2.1 + - - -
378C CYS* 1.3 80.8 - - - +
380C GLY* 1.3 62.6 + - - +
381C LYS* 3.2 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 380 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C PHE* 4.0 11.1 - - - -
172C THR 3.5 21.1 - - - -
173C VAL* 3.5 5.5 - - - +
174C LEU* 2.6 37.8 + - - +
175C ASP 3.5 2.4 + - - -
376C LYS 3.0 12.1 + - - -
379C SER* 1.3 78.2 - - - +
381C LYS* 1.3 58.8 + - - +
382C PHE 4.5 2.2 - - - -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il