Contacts of the helix formed by residues 31 - 40 (chain B) in PDB entry 2C2L
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 31 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B ALA 3.3 10.5 + - - +
28B GLN* 4.1 18.2 + - - +
29B GLU 2.4 10.3 + - - -
30B LEU* 1.3 70.5 - - - +
32B GLU* 1.3 74.2 + - - +
33B GLN 3.2 0.2 - - - -
34B GLY* 3.1 7.8 + - - -
35B ASN* 2.6 30.9 + - - +
50B TYR* 3.6 22.2 - - + -
53B ALA* 5.1 0.9 - - - -
62B VAL* 4.3 10.6 - - + +
63B TYR* 3.6 28.3 - - + -
66B ASN* 4.2 13.0 - - - +
59C LEU* 3.9 24.4 - - - +
509F ASP* 5.3 4.2 + - - +
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Residues in contact with GLU 32 (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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28B GLN 3.0 21.8 - - - +
29B GLU* 2.6 17.3 + - - +
31B LYS* 1.3 88.3 - - - +
33B GLN* 1.3 56.6 + - - +
34B GLY 3.0 4.9 - - - -
35B ASN* 3.0 32.3 + - + +
36B ARG* 3.1 21.9 + - - +
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Residues in contact with GLN 33 (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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25B PRO* 5.9 2.2 - - - +
29B GLU 3.4 2.9 + - - +
30B LEU* 4.0 20.1 - - - +
32B GLU* 1.3 78.7 - - - +
34B GLY* 1.3 58.7 + - - +
36B ARG* 3.3 50.6 - - - +
37B LEU* 3.5 14.2 + - + +
49B CYS* 3.2 20.3 - - - +
52B ARG* 2.6 32.7 + - - +
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Residues in contact with GLY 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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30B LEU 3.4 1.0 + - - -
31B LYS 3.1 8.1 + - - -
32B GLU 3.0 1.0 - - - -
33B GLN* 1.3 78.4 - - - +
35B ASN* 1.3 59.0 + - - +
36B ARG 3.2 0.4 - - - -
38B PHE* 3.0 29.8 + - - +
46B ALA* 3.4 7.6 - - - +
49B CYS* 3.0 22.8 - - - -
50B TYR* 3.5 22.6 - - - -
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Residues in contact with ASN 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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31B LYS* 2.6 28.2 - - - +
32B GLU* 3.2 21.1 + - + +
34B GLY* 1.3 76.4 - - - +
36B ARG* 1.3 68.6 + - - +
38B PHE* 4.0 7.0 - - + -
39B VAL* 3.1 31.6 + - + +
50B TYR* 2.6 22.5 + - - -
508F VAL* 4.1 19.8 + - - +
509F ASP* 5.0 5.1 + - - +
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Residues in contact with ARG 36 (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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29B GLU 5.6 0.4 + - - -
32B GLU* 3.1 14.2 + - - +
33B GLN* 3.3 53.9 - - + +
35B ASN* 1.3 80.0 - - - +
37B LEU* 1.3 67.3 + - + +
39B VAL* 4.0 1.8 - - - +
40B GLY* 2.9 17.5 + - - -
42B LYS* 5.3 1.7 + - - -
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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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33B GLN* 3.5 13.2 + - + +
34B GLY 4.1 0.4 - - - +
36B ARG* 1.3 79.3 - - + +
38B PHE* 1.3 67.3 + - - +
40B GLY 3.0 5.5 + - - -
42B LYS* 2.8 65.5 + - + +
45B GLU* 3.3 20.2 - - + +
46B ALA* 3.1 39.5 - - + +
49B CYS* 3.9 11.9 - - + -
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Residues in contact with PHE 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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34B GLY 3.0 21.3 + - - +
35B ASN* 3.4 7.6 - - + +
36B ARG 3.1 0.2 + - - -
37B LEU* 1.3 73.6 - - - +
39B VAL* 1.3 80.8 + - + +
40B GLY 2.5 0.4 + - - -
41B ARG 2.5 30.7 + - - -
43B TYR* 2.9 38.5 - + - -
46B ALA* 3.5 3.5 - - - +
50B TYR* 4.8 2.0 - - - +
69B LEU* 4.1 9.4 - - + -
70B CYS* 3.2 28.3 - - - -
73B LYS* 4.5 11.0 - - + -
506F GLU 3.9 20.6 - - - -
507F GLU* 4.6 3.4 - - + -
508F VAL* 3.7 39.0 - - + -
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Residues in contact with VAL 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 ASN* 3.1 21.2 + - + +
36B ARG* 4.1 1.1 - - - +
38B PHE* 1.3 99.5 - - + +
40B GLY* 1.3 55.2 + - - +
41B ARG* 3.2 18.0 + - - -
43B TYR* 4.9 2.6 + - - -
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Residues in contact with GLY 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 ARG 2.9 12.1 + - - -
37B LEU 3.1 4.3 - - - -
38B PHE 2.5 6.1 + - - -
39B VAL* 1.3 73.2 - - - +
41B ARG* 1.3 63.6 + - - +
42B LYS* 2.9 40.1 + - - +
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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