Contacts of the helix formed by residues 24 - 37 (chain C) in PDB entry 6QY3
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 ASP 24 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22C ILE* 3.2 4.0 - - - +
23C GLU* 1.3 78.1 - - - +
25C VAL* 1.3 60.3 + - - +
26C SER* 4.5 2.7 - - - +
27C VAL* 3.8 23.6 - - + +
28C PHE* 2.9 30.2 + - - +
208C LEU 4.7 1.0 + - - -
209C ASP 5.5 1.3 - - - +
210C LYS* 4.8 17.5 - - + +
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Residues in contact with VAL 25 (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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23C GLU 4.1 2.0 + - - -
24C ASP* 1.3 73.6 - - - +
26C SER* 1.3 57.8 + - - +
28C PHE* 3.8 5.5 - - - +
29C ALA* 2.9 32.2 + - - +
171D SER 4.6 10.1 - - - +
172D TYR 3.7 17.7 - - - +
173D PHE 4.9 2.5 - - - +
174D SER* 4.9 17.5 - - - +
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Residues in contact with SER 26 (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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24C ASP* 3.3 3.0 - - - +
25C VAL* 1.3 80.3 - - - +
27C VAL* 1.3 56.8 + - - +
29C ALA* 4.3 3.0 - - - +
30C GLN* 2.9 32.7 + - - +
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Residues in contact with VAL 27 (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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7C LEU* 6.1 4.5 - - + -
22C ILE* 5.1 5.4 - - + -
24C ASP* 3.4 22.9 + - + +
25C VAL 3.4 0.4 - - - -
26C SER* 1.3 77.4 - - - +
28C PHE* 1.3 59.1 + - - +
30C GLN* 4.2 4.4 - - - +
31C LEU* 2.9 29.1 + - - +
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Residues in contact with PHE 28 (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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22C ILE* 4.0 22.2 - - + +
24C ASP 2.9 20.2 + - - +
25C VAL* 3.8 7.0 - - - +
26C SER 3.2 0.2 - - - -
27C VAL* 1.3 76.3 - - - +
29C ALA* 1.3 60.4 + - - +
31C LEU* 3.1 6.5 + - - +
32C VAL* 2.9 29.1 + - - +
196C GLU 6.2 0.7 - - - -
197C PRO* 5.4 9.0 - - + -
171D SER 5.9 2.2 - - - +
172D TYR* 6.0 2.2 - - - -
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Residues in contact with ALA 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C VAL 2.9 17.6 + - - +
26C SER* 4.3 3.6 - - - +
28C PHE* 1.3 76.3 - - - +
30C GLN* 1.3 58.0 + - - +
32C VAL* 3.4 5.6 + - - +
33C LYS* 2.9 28.4 + - - +
144D VAL* 5.0 16.5 + - + +
172D TYR* 3.9 30.2 + - + +
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Residues in contact with GLN 30 (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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26C SER 2.9 21.3 + - - +
27C VAL* 4.2 4.0 - - - +
29C ALA* 1.3 76.5 - - - +
31C LEU* 1.3 57.8 + - - +
33C LYS* 3.5 8.0 + - - +
34C GLU* 2.9 27.2 + - - +
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Residues in contact with LEU 31 (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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27C VAL 2.9 21.5 + - - +
28C PHE* 3.1 7.8 + - - +
30C GLN* 1.3 76.1 - - - +
32C VAL* 1.3 59.8 + - - +
34C GLU* 3.2 8.8 + - - +
35C PHE* 2.9 26.0 + - - +
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Residues in contact with VAL 32 (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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28C PHE 2.9 16.8 + - - +
29C ALA* 3.9 6.7 - - - +
31C LEU* 1.3 72.4 - - - +
33C LYS* 1.3 61.1 + - - +
35C PHE* 2.9 10.1 + - - +
36C TYR* 2.9 28.9 + - - +
167C VAL* 5.6 11.0 - - + -
144D VAL* 6.4 2.0 - - + -
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Residues in contact with LYS 33 (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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29C ALA 2.9 18.5 + - - +
30C GLN* 3.7 9.6 - - - +
32C VAL* 1.3 77.2 - - - +
34C GLU* 1.3 55.7 + - - +
36C TYR* 3.9 4.7 - - - +
37C GLN* 2.9 34.9 + - + +
142D CYS 5.4 3.1 - - - +
143D THR* 5.3 14.6 - - - -
144D VAL* 5.4 4.3 - - + +
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Residues in contact with GLU 34 (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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30C GLN 2.9 18.5 + - - +
31C LEU* 3.2 9.2 + - - +
33C LYS* 1.3 75.7 - - - +
35C PHE* 1.3 57.4 + - - +
37C GLN* 4.5 3.6 - - - +
38C TYR* 3.0 28.5 + - - +
41C GLN* 5.3 9.9 - - + +
43C ASN* 5.8 3.1 - - + -
44C LEU* 4.1 28.9 - - + +
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Residues in contact with PHE 35 (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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31C LEU 2.9 11.8 + - - +
32C VAL* 2.9 14.7 + - - +
34C GLU* 1.3 76.3 - - - +
36C TYR* 1.3 64.4 + - - +
38C TYR* 3.5 17.0 - - - +
61C LEU* 5.4 14.5 - - + +
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Residues in contact with TYR 36 (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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32C VAL 2.9 14.4 + - - +
33C LYS* 4.2 4.5 - - - +
35C PHE* 1.3 76.2 - - - +
37C GLN* 1.3 58.5 + - + +
38C TYR 3.3 1.2 + - - -
39C ASP* 4.9 2.4 + - - +
66D LEU* 4.3 24.2 - - + +
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Residues in contact with GLN 37 (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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33C LYS 2.9 20.0 + - - +
34C GLU* 3.8 2.2 - - - -
36C TYR* 1.3 74.5 - - - +
38C TYR* 1.3 51.0 + - - +
39C ASP* 3.1 3.6 - - - -
40C GLU* 2.6 38.9 + - + +
41C GLN* 2.7 26.9 + - + -
140D LYS 4.8 12.8 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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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