Contacts of the helix formed by residues 432 - 448 (chain C) in PDB entry 1JZ3
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 TRP 432 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C PRO* 3.8 38.3 - - + +
111C PRO* 4.1 22.7 - - + +
112C PRO* 4.5 4.5 - - + -
193C ASP* 3.7 28.5 - - + -
196C TYR* 3.8 16.2 - + + -
197C LEU* 3.9 38.4 - - + -
426C LEU* 3.5 46.6 - - + +
429C ASP* 2.9 24.4 + - + -
431C ARG* 1.3 84.1 - - + +
433C LEU* 1.3 64.3 + - - +
434C PRO 3.3 2.5 - - - -
435C ALA* 3.5 8.1 + - + +
436C MET* 3.1 27.5 + - - +
467C ASN* 3.6 3.4 - - - +
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Residues in contact with LEU 433 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433B LEU* 5.7 6.1 - - + -
434B PRO* 6.4 0.2 - - + -
437B SER* 3.9 27.4 - - - +
441B THR* 4.8 6.1 - - + -
471B LEU* 4.6 8.3 - - + -
474B TRP* 4.4 18.6 - - + +
430C PRO* 3.0 14.0 + - + +
432C TRP* 1.3 78.2 - - - +
434C PRO* 1.3 57.5 - - + +
436C MET* 3.2 1.6 + - - -
437C SER* 2.6 50.1 + - - -
467C ASN* 3.3 42.7 - - + +
470C ALA* 4.6 7.6 - - + -
471C LEU* 4.3 15.0 - - + -
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Residues in contact with PRO 434 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B PRO* 3.6 36.7 - - + +
437B SER* 4.8 5.2 - - - +
438B GLU* 5.0 12.3 - - + +
19C PRO 5.0 6.3 - - - +
20C GLY* 5.8 6.7 - - - +
22C THR* 5.4 0.4 - - + -
430C PRO 3.5 9.2 - - - +
431C ARG* 3.7 11.2 - - - +
432C TRP 3.5 2.9 - - - -
433C LEU* 1.3 96.5 - - + +
435C ALA* 1.3 63.7 + - - +
437C SER* 3.2 10.3 + - - +
438C GLU* 3.1 27.7 + - - +
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Residues in contact with ALA 435 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C PRO* 3.9 13.6 + - + +
22C THR* 3.8 28.8 - - + +
193C ASP* 5.7 0.9 - - - +
197C LEU* 3.9 19.3 - - + -
432C TRP* 3.5 17.1 + - + +
433C LEU 3.4 0.6 - - - -
434C PRO* 1.3 83.0 - - - +
436C MET* 1.3 64.8 + - - +
438C GLU* 3.4 10.5 + - - +
439C ARG* 3.5 19.5 + - - +
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Residues in contact with MET 436 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197C LEU* 4.3 17.0 - - + -
415C ILE* 3.7 31.4 - - + +
426C LEU 4.5 2.2 - - - +
427C THR* 3.6 36.1 - - + -
432C TRP* 3.1 15.2 + - + +
433C LEU* 3.6 3.8 - - - +
435C ALA* 1.3 80.3 - - - +
437C SER* 1.3 65.5 + - - +
439C ARG* 3.0 17.2 + - - +
440C VAL 3.2 9.0 + - - -
467C ASN* 3.5 40.6 - - + -
468C HIS* 4.0 18.8 - - + +
471C LEU* 3.8 15.6 - - + +
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Residues in contact with SER 437 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430B PRO 5.1 1.6 + - - -
433B LEU* 3.9 23.7 - - - +
434B PRO* 4.4 8.8 - - - +
433C LEU* 2.6 26.4 + - - -
434C PRO* 3.2 10.3 + - - +
435C ALA 3.1 0.2 - - - -
436C MET* 1.3 75.5 - - - +
438C GLU* 1.3 55.0 + - - +
440C VAL* 3.1 2.1 + - - +
441C THR* 2.7 41.7 + - - +
471C LEU* 3.7 27.4 - - - -
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Residues in contact with GLU 438 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430B PRO 6.2 0.2 - - - +
434B PRO* 4.9 11.4 - - + +
22C THR* 2.5 33.0 + - - -
23C GLN* 4.7 8.8 + - - +
26C ARG* 3.0 25.5 + - - +
164C ASP* 4.8 2.4 - - + +
167C LEU* 4.5 0.9 - - - +
434C PRO* 3.1 12.1 + - - +
435C ALA* 3.7 8.7 - - - +
436C MET 3.2 0.2 - - - -
437C SER* 1.3 80.7 + - - +
439C ARG* 1.3 63.6 + - + +
441C THR* 3.7 7.4 - - - +
442C ARG* 3.1 42.0 + - - +
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Residues in contact with ARG 439 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C THR* 6.1 1.6 - - - +
163C GLN* 4.7 3.8 - - - +
164C ASP* 3.3 44.4 + - + +
167C LEU* 4.0 5.1 - - - +
194C GLY* 3.5 26.7 - - - -
197C LEU* 3.6 28.1 - - - +
198C GLU* 3.0 34.1 + - - +
413C ALA* 3.6 11.3 - - - +
414C ASN* 2.8 47.7 + - - +
415C ILE* 3.7 17.0 - - + -
435C ALA* 3.5 16.6 + - - +
436C MET 3.0 7.5 + - - +
438C GLU* 1.3 80.8 - - + +
440C VAL* 1.3 59.6 + - - +
443C MET* 3.6 18.2 + - - +
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Residues in contact with VAL 440 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413C ALA* 3.8 21.3 - - + -
415C ILE* 4.1 6.7 - - + -
436C MET 3.2 4.9 + - - +
437C SER 3.1 6.3 + - - +
439C ARG* 1.3 77.5 - - - +
441C THR* 1.4 68.7 + - + +
443C MET* 3.3 8.4 + - + +
444C VAL* 3.2 20.9 + - + +
458C LEU* 4.3 13.7 - - + +
471C LEU* 3.9 37.0 - - + -
474C TRP* 4.4 6.7 - - + -
475C ILE* 3.7 35.2 - - + -
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Residues in contact with THR 441 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430B PRO* 3.8 22.7 + - + +
433B LEU* 4.8 9.6 - - + -
437C SER* 2.7 31.7 + - - +
438C GLU* 3.7 8.0 - - - +
440C VAL* 1.4 72.8 - - + +
442C ARG* 1.4 64.4 + - - +
444C VAL* 3.3 2.8 + - - +
445C GLN* 2.9 35.2 + - - +
471C LEU* 4.9 1.8 - - + -
474C TRP* 3.6 49.7 - - + +
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Residues in contact with ARG 442 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C ARG* 3.2 57.8 - - - +
27C LEU 4.8 5.1 + - - -
29C ALA* 4.0 27.2 - - + +
163C GLN 4.5 4.0 + - - -
164C ASP* 4.4 7.1 + - - +
167C LEU* 3.6 40.2 + - + +
168C PRO 2.8 25.9 + - - -
170C GLU 5.1 0.4 - - - +
438C GLU* 3.1 33.3 + - + +
441C THR* 1.4 82.8 + - - +
443C MET* 1.3 65.0 + - - +
445C GLN* 4.0 11.4 - - - +
446C ARG* 3.2 22.0 + - - +
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Residues in contact with MET 443 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167C LEU* 3.7 14.0 - - - +
393C PRO* 4.0 14.4 - - + -
411C ASP* 3.7 23.6 - - - +
412C GLU 3.4 36.6 - - - +
413C ALA* 3.4 20.4 - - + +
439C ARG 3.6 11.0 - - - +
440C VAL* 3.3 18.9 + - + +
441C THR 3.2 0.6 - - - -
442C ARG* 1.3 76.2 - - - +
444C VAL* 1.3 69.1 + - + +
446C ARG* 3.1 2.1 + - - +
447C ASP* 2.9 25.9 + - - +
456C TRP* 3.8 24.9 - - + -
457C SER 3.9 10.8 - - - +
475C ILE* 5.2 1.3 - - + -
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Residues in contact with VAL 444 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440C VAL 3.2 12.6 + - - +
441C THR 3.7 6.7 - - - +
443C MET* 1.3 78.0 - - + +
445C GLN* 1.3 66.6 + - + +
448C ARG* 3.1 41.9 + - + +
456C TRP* 3.8 42.2 - - + +
474C TRP* 3.9 26.2 - - + -
475C ILE* 4.3 15.7 - - + -
478C VAL* 4.1 13.9 - - + -
479C ASP* 4.8 6.3 - - + -
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Residues in contact with GLN 445 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430B PRO* 3.6 32.6 - - + +
431B ARG* 6.0 2.2 - - - +
8420B DMS 4.6 16.6 + - - +
28C ALA* 5.7 3.2 - - - +
29C ALA* 3.4 44.4 + - + +
30C HIS* 3.6 1.7 - - - -
31C PRO* 3.5 24.8 - - - +
224C ASP* 4.9 10.6 + - - +
226C HIS* 6.2 2.0 - - - +
441C THR 2.9 22.9 + - - +
442C ARG* 4.0 8.1 - - - +
443C MET 3.2 0.4 - - - -
444C VAL* 1.3 80.2 - - + +
446C ARG* 1.3 59.5 + - - +
448C ARG* 4.3 11.7 - - - +
474C TRP* 5.0 4.5 - - + -
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Residues in contact with ARG 446 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C ALA* 5.5 1.3 - - + -
30C HIS 3.6 19.0 - - - +
31C PRO* 3.6 5.4 - - - +
32C PRO* 3.5 29.2 - - + +
144C ASP* 5.4 1.6 + - - +
166C ARG 4.1 5.5 + - - -
167C LEU* 3.7 13.7 - - - +
168C PRO* 3.7 39.1 - - + +
210C ARG* 4.2 4.0 - - - +
393C PRO* 3.4 8.5 - - - +
394C ASN 2.9 29.7 + - - -
396C PRO* 4.3 20.8 - - + +
399C TYR* 3.3 17.2 + - - -
442C ARG 3.2 16.6 + - - +
443C MET 3.1 4.5 + - - +
445C GLN* 1.3 81.5 - - - +
447C ASP* 1.4 91.6 + - - +
448C ARG 3.7 0.6 + - - -
449C ASN 5.1 0.5 + - - -
450C HIS* 4.9 1.2 - - - -
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Residues in contact with ASP 447 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C PRO* 5.7 0.5 - - - +
399C TYR* 3.3 15.1 + - - -
411C ASP* 2.5 31.2 - - - +
443C MET* 2.9 17.0 + - - +
446C ARG* 1.4 129.0 + - - +
448C ARG* 1.3 62.9 + - - +
449C ASN 3.2 3.6 - - - -
450C HIS* 3.1 33.4 + - + +
453C VAL* 4.3 6.1 - - + +
456C TRP* 3.9 7.9 - - + -
482C ARG* 4.1 3.3 + - - -
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Residues in contact with ARG 448 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8420B DMS 4.2 14.1 + - - +
31C PRO* 5.3 2.0 - - + -
226C HIS* 3.4 58.5 + - + +
227C VAL 4.6 2.5 + - - +
444C VAL* 3.1 26.7 + - + +
445C GLN* 4.3 14.2 - - - +
446C ARG 3.7 0.4 - - - -
447C ASP* 1.3 75.0 - - - +
449C ASN* 1.3 70.9 + - - +
450C HIS 3.3 0.7 - - - -
456C TRP* 3.7 10.2 - - + -
478C VAL* 3.6 30.7 + - - +
479C ASP* 4.7 14.1 + - - +
480C PRO* 5.7 0.8 - - - +
482C ARG* 3.0 33.4 + - - +
8401C DMS 3.8 5.0 - - - +
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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) + - + + + + + -
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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