Contacts of the helix formed by residues 33 - 42 (chain B) in PDB entry 4KYI
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 GLY 33 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32B VAL* 1.3 80.7 - - - +
34B LYS* 1.3 62.6 + - - +
36B SER* 3.2 1.9 + - - -
37B LEU* 2.9 39.3 + - - +
100B VAL* 4.9 0.4 - - - -
134B ASN* 3.9 1.8 - - - -
301B GNP 3.2 40.1 + - - -
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Residues in contact with LYS 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B LEU* 3.6 26.0 - - + +
27B LEU 3.3 33.7 - - - +
28B GLY* 3.4 11.3 + - - +
29B GLU 2.6 27.1 + - - -
32B VAL* 3.4 9.8 - - + +
33B GLY* 1.3 78.7 - - - +
35B SER* 1.3 62.1 + - - +
36B SER 3.3 0.3 + - - -
37B LEU* 3.3 6.9 + - - -
38B VAL* 3.3 21.0 + - - +
76B ASP* 3.3 11.9 - - - +
77B THR* 3.7 15.9 - - - -
79B GLY* 4.2 2.4 - - - +
100B VAL* 3.9 10.5 - - + +
301B GNP 2.5 46.0 + - - +
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Residues in contact with SER 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B LYS* 1.3 74.9 - - - +
36B SER* 1.3 60.8 + - - +
38B VAL 3.8 0.8 + - - -
39B LEU* 3.5 17.8 + - - +
50B GLN* 3.8 17.7 + - - -
51B GLU 5.3 1.8 - - - -
53B THR* 2.5 6.4 + - - -
76B ASP* 2.4 22.7 + - - -
301B GNP 3.0 16.7 + - - -
302B EDO 3.2 21.8 + - - -
304B MG 2.0 30.5 - - - -
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Residues in contact with SER 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B GLY 3.2 4.9 + - - -
35B SER* 1.3 75.8 - - - +
37B LEU* 1.3 58.7 + - - +
38B VAL 3.2 1.8 - - - -
39B LEU* 3.3 3.4 + - - +
40B ARG* 3.0 28.8 + - - +
45B GLN 4.5 1.9 - - - +
46B PHE* 4.1 8.9 - - - -
50B GLN* 2.8 28.7 + - - +
165B ALA* 3.8 17.7 - - - +
301B GNP 3.0 36.9 + - - -
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Residues in contact with LEU 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B LEU* 4.5 10.1 - - + -
33B GLY 2.9 19.3 + - - +
34B LYS 3.3 4.9 + - - +
36B SER* 1.3 78.9 - - - +
38B VAL* 1.3 51.6 + - - +
40B ARG* 3.3 2.8 + - - +
41B PHE* 2.8 36.9 + - - +
98B ILE* 5.4 2.9 - - + -
100B VAL* 4.0 31.0 - - + -
132B ALA* 5.2 2.0 - - + -
134B ASN* 3.2 27.1 - - - +
163B THR* 3.8 14.4 - - + +
165B ALA* 3.8 18.4 - - + +
171B VAL* 3.8 24.2 - - + +
174B ILE* 6.2 2.2 - - + -
175B PHE* 5.0 10.1 - - + -
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Residues in contact with VAL 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B LEU* 3.8 29.4 - - + -
34B LYS 3.3 15.5 + - - +
35B SER 3.9 7.9 - - - +
36B SER 3.2 0.2 - - - -
37B LEU* 1.3 74.5 - - - +
39B LEU* 1.3 60.4 + - - +
41B PHE* 3.7 5.1 - - - -
42B VAL* 2.9 43.1 + - + +
59B LEU* 4.3 14.4 - - + -
74B ILE* 4.4 13.9 - - + -
76B ASP* 4.3 13.2 - - + -
175B PHE* 5.2 4.5 - - + -
302B EDO 3.9 20.9 - - - -
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Residues in contact with LEU 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B SER 3.5 11.5 + - - +
36B SER* 3.3 10.0 + - - +
38B VAL* 1.3 79.7 - - - +
40B ARG* 1.3 51.1 + - - +
42B VAL* 5.0 0.7 - - - -
43B LYS* 2.8 47.4 + - + +
44B GLY 2.6 30.5 + - - -
45B GLN* 3.4 36.5 + - + +
46B PHE* 3.9 6.3 - - - +
47B HIS* 4.5 15.7 - - + +
50B GLN* 3.9 18.4 - - - +
59B LEU* 6.5 0.2 - - - -
302B EDO 6.0 3.8 - - - +
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Residues in contact with ARG 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B SER 3.0 16.4 + - - +
37B LEU 3.7 4.3 - - - +
39B LEU* 1.3 76.9 - - - +
41B PHE* 1.3 61.7 + - - +
44B GLY* 3.2 33.9 + - - -
45B GLN 3.6 15.0 + - - +
46B PHE* 3.9 10.7 - - - +
165B ALA* 2.9 30.8 + - + -
166B LYS 3.6 17.8 + - - -
167B THR 4.4 0.6 - - - -
168B ALA* 3.4 30.8 - - - +
171B VAL* 3.6 31.3 - - + +
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Residues in contact with PHE 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B LEU 2.8 21.9 + - - +
38B VAL* 3.9 3.1 - - - +
39B LEU 3.3 0.2 - - - -
40B ARG* 1.3 74.0 - - - +
42B VAL* 1.3 67.3 + - + +
61B GLN* 3.9 26.2 + - + +
63B VAL* 4.3 24.5 - - + -
72B PHE* 4.5 13.2 - + - -
74B ILE* 4.0 14.4 - - + -
171B VAL* 3.9 9.9 - - + -
172B ASN* 4.1 34.1 + - - +
175B PHE* 3.5 62.4 - + + -
176B MET* 5.2 2.5 - - + -
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Residues in contact with VAL 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B VAL* 2.9 24.1 + - + +
39B LEU* 5.0 0.9 - - - -
41B PHE* 1.3 88.2 - - + +
43B LYS* 1.3 78.0 + - + +
44B GLY* 3.3 1.6 + - - -
59B LEU* 4.0 28.9 - - + -
60B THR 5.7 2.5 - - - +
61B GLN* 3.3 45.3 + - + +
74B ILE* 4.7 3.6 - - + -
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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