Contacts of the helix formed by residues 34 - 43 (chain F) 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 LYS 34 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26F LEU* 3.5 24.3 - - + +
27F LEU 3.7 7.0 - - - -
28F GLY* 2.4 48.4 + - - +
29F GLU 3.3 15.7 - - - -
32F VAL* 3.8 10.3 - - + -
33F GLY* 1.3 73.2 - - - +
35F SER* 1.3 66.3 + - - +
36F SER 3.1 1.3 - - - -
37F LEU* 3.3 2.7 + - - +
38F VAL* 3.1 28.4 + - - +
76F ASP* 3.4 14.4 - - - +
77F THR* 3.9 20.4 + - - +
79F GLY* 3.3 20.0 - - - +
100F VAL* 4.3 9.9 - - + -
115F TRP* 6.0 0.2 - - - -
301F GNP 3.1 18.1 + - - +
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Residues in contact with SER 35 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34F LYS* 1.3 77.7 - - - +
36F SER* 1.3 57.5 + - - +
38F VAL* 4.0 2.7 - - - +
39F LEU* 3.1 27.9 + - - +
50F GLN* 3.4 21.8 + - - -
51F GLU 5.4 2.0 - - - -
53F THR* 2.6 6.3 + - - -
76F ASP* 2.6 24.0 + - - -
301F GNP 3.1 9.4 + - - -
302F MG 2.2 30.8 - - - -
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Residues in contact with SER 36 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33F GLY* 4.5 0.7 - - - -
34F LYS 3.1 0.2 - - - -
35F SER* 1.3 76.1 - - - +
37F LEU* 1.3 64.4 + - - +
39F LEU* 3.6 1.6 + - - +
40F ARG* 3.1 23.4 + - - +
45F GLN 4.3 2.3 - - - +
46F PHE* 4.0 9.1 - - - -
47F HIS 4.3 1.6 + - - -
50F GLN* 3.4 22.9 + - - -
165F ALA* 3.8 10.0 - - - +
301F GNP 2.7 60.2 + - - -
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Residues in contact with LEU 37 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26F LEU* 4.8 7.2 - - + -
33F GLY 3.2 21.0 + - - +
34F LYS* 3.3 9.0 + - - +
36F SER* 1.3 75.8 - - - +
38F VAL* 1.3 66.0 + - - +
40F ARG* 3.3 5.4 + - - +
41F PHE* 3.0 24.1 + - - +
98F ILE* 5.3 3.6 - - + -
100F VAL* 4.1 22.9 - - + -
132F ALA* 4.8 4.3 - - + -
134F ASN* 3.9 20.9 - - - +
163F THR* 4.3 18.6 - - + +
165F ALA* 4.2 7.2 - - + -
171F VAL* 3.7 39.2 - - + +
174F ILE* 6.0 2.9 - - + -
175F PHE* 5.0 7.6 - - + -
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Residues in contact with VAL 38 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26F LEU* 3.6 21.5 - - + -
34F LYS 3.1 16.2 + - - +
35F SER* 4.0 5.4 - - - +
37F LEU* 1.3 75.5 - - - +
39F LEU* 1.3 53.1 + - - +
41F PHE* 3.1 6.4 + - - -
42F VAL* 2.7 47.3 + - + +
59F LEU* 3.9 28.3 - - + -
74F ILE* 3.8 31.9 - - + -
76F ASP* 4.3 10.5 - - + +
175F PHE* 5.0 5.6 - - + -
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Residues in contact with LEU 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35F SER 3.1 19.7 + - - +
36F SER 3.6 3.8 - - - +
38F VAL* 1.3 77.5 - - - +
40F ARG* 1.3 57.3 + - - +
42F VAL* 4.7 1.8 - - - -
43F LYS* 2.7 57.3 + - + +
44F GLY 3.1 4.0 + - - -
45F GLN* 3.4 31.0 - - + +
46F PHE* 3.8 3.6 - - - -
47F HIS* 3.5 26.9 - - + +
50F GLN* 3.2 23.6 - - - +
59F LEU* 6.4 0.7 - - - -
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Residues in contact with ARG 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36F SER 3.1 14.7 + - - +
37F LEU* 3.6 4.9 - - - +
39F LEU* 1.3 78.8 - - - +
41F PHE* 1.3 60.5 + - - +
44F GLY* 3.2 38.9 + - - -
45F GLN* 3.2 13.4 + - - +
46F PHE* 3.9 15.4 - - - +
165F ALA* 3.4 28.9 + - + +
166F LYS 4.4 11.9 + - - -
167F THR* 5.2 0.8 - - - +
168F ALA* 3.8 27.8 - - + +
171F VAL* 3.6 23.1 - - + -
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Residues in contact with PHE 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F LEU 3.0 17.0 + - - +
38F VAL 3.6 2.5 - - - +
40F ARG* 1.3 79.3 - - - +
42F VAL* 1.3 62.0 + - + +
44F GLY 4.7 0.2 - - - -
61F GLN* 3.7 28.6 - - + +
63F VAL* 3.7 27.8 - - + -
72F PHE* 4.2 13.2 - + - -
74F ILE* 3.9 19.3 - - + -
171F VAL* 4.7 4.9 - - + -
172F ASN* 3.4 31.6 - - - +
175F PHE* 3.4 62.4 - + + -
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Residues in contact with VAL 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38F VAL* 2.7 38.0 + - + +
39F LEU* 4.1 2.0 - - - +
41F PHE* 1.3 79.0 - - + +
43F LYS* 1.3 74.6 + - + +
44F GLY 3.4 2.5 + - - -
59F LEU* 3.8 27.4 - - + -
60F THR 4.7 4.3 - - - +
61F GLN* 2.9 48.7 + - + +
74F ILE* 4.2 11.4 - - + -
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Residues in contact with LYS 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F LEU* 2.7 35.8 + - + +
42F VAL* 1.3 87.8 - - + +
44F GLY* 1.3 62.1 + - - -
45F GLN* 3.1 23.5 + - - +
59F LEU* 5.2 9.6 - - + -
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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