Contacts of the strand formed by residues 339 - 352 (chain C) in PDB entry 1AF6
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 LYS 339 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330C ASN* 3.7 30.5 - - - +
331C VAL 3.2 4.0 - - - +
332C GLU* 2.6 40.2 + - + +
337C GLY 4.1 7.0 + - - +
338C ASP* 1.3 79.7 - - - +
340C ASN* 1.3 68.5 + - - +
341C ASN* 4.2 3.3 - - - +
373C ASP 4.1 3.1 - - - +
375C LYS* 3.3 26.4 + - + +
376C TRP* 3.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 340 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C THR* 3.9 12.0 - - + +
26C THR* 3.0 36.0 + - - +
329C ASP 4.0 0.2 - - - +
330C ASN* 3.3 2.5 + - - -
331C VAL* 2.7 41.8 + - + +
339C LYS* 1.3 72.1 - - - +
341C ASN* 1.3 62.8 + - - +
373C ASP 3.6 3.1 - - - -
374C GLU* 3.1 13.1 - - + -
375C LYS 2.9 25.1 + - - -
376C TRP* 3.0 48.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 341 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C THR* 4.5 2.9 - - - -
328C TYR* 4.0 13.9 - - + +
329C ASP 3.1 12.6 - - - +
330C ASN* 3.7 17.7 + - - +
339C LYS* 5.4 3.3 - - - +
340C ASN* 1.3 76.8 - - - +
342C GLN* 1.3 68.7 + - - +
343C TYR* 5.1 4.9 - - - +
371C LYS* 4.9 3.8 + - - +
372C TRP* 3.3 4.8 - - - +
373C ASP* 2.9 61.1 + - - +
374C GLU* 4.7 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 342 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C PHE* 3.3 34.5 + - - +
24C GLN* 4.1 1.6 - - - +
25C THR* 3.2 21.4 + - - +
31C LYS* 5.8 0.4 - - - +
32C TYR* 6.3 0.2 - - - -
327C GLY 3.8 0.5 - - - +
328C TYR* 3.3 6.8 - - - -
329C ASP* 2.8 41.7 + - + +
341C ASN* 1.3 79.1 - - - +
343C TYR* 1.3 73.3 + - - +
344C LYS* 4.5 12.3 - - - +
370C ALA* 4.4 3.1 - - - -
371C LYS 3.3 16.8 - - - +
372C TRP* 3.8 8.3 - - + +
405C ARG* 2.9 38.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 343 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326C ILE* 5.9 4.5 - - + -
327C GLY 3.2 8.3 - - - +
328C TYR* 4.2 16.4 - + + -
341C ASN* 5.5 5.2 - - - -
342C GLN* 1.3 78.7 - - - +
344C LYS* 1.3 62.5 + - - +
345C ILE* 3.9 30.7 - - + -
369C TYR* 4.0 20.9 + + - -
370C ALA* 3.4 2.4 - - - -
371C LYS* 3.0 67.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 344 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C PHE* 5.1 0.9 - - + -
32C TYR* 3.1 34.1 + - + +
34C LEU 2.7 24.0 + - - -
36C ASN* 3.7 18.2 - - - +
325C GLU* 2.6 32.5 + - - +
326C ILE* 3.3 5.5 - - - +
327C GLY 2.7 35.1 + - - +
342C GLN* 4.3 14.6 - - - +
343C TYR* 1.3 76.0 - - - +
345C ILE* 1.3 66.2 + - - +
346C THR* 3.0 17.4 + - - +
368C THR* 3.9 13.7 - - + -
369C TYR 3.4 9.6 - - - +
370C ALA* 4.3 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 345 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324C MET* 5.2 10.3 - - + -
325C GLU 3.4 6.1 - - - +
326C ILE* 4.4 22.4 - - + -
343C TYR* 3.9 29.8 - - + -
344C LYS* 1.3 79.4 - - - +
346C THR* 1.3 69.6 + - - +
347C LEU* 6.1 0.7 - - + -
367C ALA 4.0 0.3 - - - +
368C THR* 3.4 1.9 - - - -
369C TYR* 2.7 57.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 346 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C LEU* 3.0 32.4 + - + +
35C GLY* 4.2 4.5 - - - -
324C MET* 3.1 9.9 - - - +
325C GLU* 2.8 41.6 + - - +
344C LYS* 3.0 27.9 + - - -
345C ILE* 1.3 79.1 - - - +
347C LEU* 1.3 69.2 + - - +
366C PHE* 4.2 5.6 - - + -
367C ALA 3.4 6.7 - - - +
368C THR* 2.7 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 347 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322C THR* 4.0 20.6 - - + -
323C VAL 3.6 8.1 - - - +
324C MET* 3.9 26.5 - - + -
345C ILE* 6.1 0.9 - - + -
346C THR* 1.3 75.5 - - - +
348C ALA* 1.3 65.5 + - - +
365C VAL 4.0 0.2 - - - +
366C PHE* 3.2 2.6 - - - -
367C ALA* 2.9 38.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 348 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C LEU* 4.3 17.9 - - + -
322C THR* 3.4 7.0 - - - +
323C VAL* 2.6 49.9 + - + +
347C LEU* 1.3 77.3 - - - +
349C GLN* 1.3 64.5 + - - +
350C GLN* 5.3 0.9 - - + +
364C ARG* 4.6 13.0 - - + -
365C VAL 3.1 11.2 - - - +
366C PHE* 3.9 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 349 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316C TRP* 3.9 7.8 + - - -
320C MET* 3.8 21.5 - - + +
321C SER 3.4 10.0 - - - +
322C THR* 2.5 36.5 + - - +
348C ALA* 1.3 72.6 - - - +
350C GLN* 1.3 62.3 + - - +
351C TRP* 4.0 29.9 - - + -
363C ILE 3.9 0.3 - - - +
364C ARG* 3.4 2.6 - - - -
365C VAL* 2.8 37.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 350 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C LEU* 5.3 1.4 - - - +
313C MET* 4.1 6.7 - - - +
320C MET* 3.4 6.6 - - - +
321C SER* 2.8 50.8 + - - +
323C VAL* 4.0 23.1 - - + +
348C ALA* 5.0 1.3 - - + +
349C GLN* 1.3 77.5 - - - +
351C TRP* 1.3 71.8 + - - +
352C GLN* 3.0 31.9 + - - +
357C ILE* 5.8 1.8 + - - +
359C SER 5.3 1.2 + - - -
360C ARG* 5.6 3.3 + - - +
362C ALA* 3.8 13.5 - - + +
363C ILE 3.3 11.4 - - - +
364C ARG* 3.3 33.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 351 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B PHE* 4.0 6.4 - - + -
91B LEU* 4.0 35.5 + - + -
92B ILE* 4.2 24.5 - - + +
100B ILE* 3.8 31.9 - - + -
319C ILE* 3.2 9.4 - - + +
320C MET* 3.8 39.9 - - + -
349C GLN* 4.0 30.5 - - + -
350C GLN* 1.3 74.6 - - - +
352C GLN* 1.3 60.7 + - - +
362C ALA* 3.3 1.4 - - - -
363C ILE* 2.8 44.5 + - + +
365C VAL* 4.3 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 352 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B PHE* 3.6 7.6 - - - -
313C MET* 3.7 17.8 - - - +
315C LYS* 6.0 0.8 - - - +
317C THR 4.9 1.2 + - - -
318C PRO 3.4 13.1 + - - -
319C ILE* 2.8 45.1 + - - +
320C MET 4.1 1.0 - - - +
321C SER* 2.9 23.4 + - - -
350C GLN* 3.0 24.0 + - - +
351C TRP* 1.3 75.9 - - - +
353C ALA* 1.3 58.8 + - - +
354C GLY 2.7 33.6 + - - +
355C ASP* 4.3 1.4 - - - +
356C SER 4.2 4.7 - - - +
359C SER* 3.9 17.9 - - - +
361C PRO 3.2 12.6 - - - +
362C ALA* 4.0 5.6 - - + -
----------------------------------------------------------
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