Contacts of the helix formed by residues 38 - 42 (chain S) in PDB entry 2K6M
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 LEU 38 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24S LEU* 3.7 11.0 - - + +
29S LEU* 5.7 2.5 - - + -
34S ASP 2.6 31.6 - - - +
35S PRO* 3.1 24.2 - - + +
37S LYS* 1.3 68.8 - - - +
39S GLU* 1.3 54.1 - - - +
40S ILE 2.7 5.4 + - - -
41S TYR* 2.6 72.0 + - + +
42S LEU* 3.1 7.7 - - + +
75S LEU* 2.8 39.3 - - + +
76S PHE* 3.3 22.8 - - + +
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Residues in contact with GLU 39 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38S LEU* 1.3 77.8 - - - +
40S ILE* 1.3 73.0 + - + +
42S LEU* 3.2 20.4 + - - +
47S PHE* 2.7 46.4 - - + -
51S LEU* 3.3 25.8 - - + +
55S ARG* 5.1 2.9 - - - +
58S TYR* 3.2 21.6 - - - +
59S ASN* 4.9 2.4 + - - +
66S GLN* 2.9 22.5 + - - +
70S LYS* 2.6 35.5 + - - +
76S PHE* 3.9 7.1 - - + -
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Residues in contact with ILE 40 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16S LYS* 5.5 8.5 - - - +
18S ILE* 5.3 3.8 - - - +
32S GLY 5.4 1.1 - - - +
34S ASP* 4.8 4.3 - - - +
37S LYS* 2.9 72.2 - - + +
38S LEU 2.7 5.1 + - - -
39S GLU* 1.3 91.4 - - + +
41S TYR* 1.3 69.7 + - + +
42S LEU 3.5 1.2 + - - -
55S ARG* 4.5 34.8 + - - +
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Residues in contact with TYR 41 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17S THR 5.2 4.7 - - - +
18S ILE* 3.2 10.5 - - - +
19S TYR* 3.2 29.9 + - + +
24S LEU* 2.9 55.2 - - + +
29S LEU* 4.5 0.9 - - - +
32S GLY 4.4 3.8 - - - +
33S VAL* 3.1 40.9 - - + +
34S ASP 3.3 27.6 - - - -
37S LYS 3.5 7.6 - - - -
38S LEU* 2.6 61.0 + - - +
40S ILE* 1.3 82.4 - - + +
42S LEU* 1.3 55.2 + - - +
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Residues in contact with LEU 42 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18S ILE* 3.4 7.5 - - - +
24S LEU* 3.3 23.1 - - + -
38S LEU 3.1 20.2 - - - +
39S GLU* 3.2 20.0 - - - +
40S ILE 3.5 2.7 + - - -
41S TYR* 1.3 76.6 - - - +
43S THR* 1.3 55.6 + - - +
46S ASP* 2.9 26.2 - - - +
47S PHE* 2.7 91.1 - - + -
51S LEU* 4.1 4.0 - - + -
55S ARG* 5.0 1.9 - - - +
75S LEU* 3.8 17.0 - - + -
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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
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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