Contacts of the helix formed by residues 35 - 45 (chain C) in PDB entry 4CQM
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 ASN 35 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12C ARG* 5.8 6.3 - - - +
33C ALA* 3.5 7.4 - - + +
34C ARG* 1.3 76.2 - - - +
36C LEU* 1.3 63.9 + - - +
37C GLU* 3.2 12.9 + - - +
38C GLY* 2.5 35.0 + - - +
39C ALA* 3.1 20.4 + - - +
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Residues in contact with LEU 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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34C ARG 3.2 5.5 + - - -
35C ASN* 1.3 70.2 - - - +
37C GLU* 1.3 61.7 + - - +
39C ALA* 3.0 4.9 + - + +
40C LYS* 2.8 55.8 + - + +
52C ALA 4.4 9.0 - - - +
53C PHE* 4.1 6.5 - - - +
54C SER* 3.9 35.2 - - - +
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Residues in contact with GLU 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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35C ASN* 3.2 12.8 + - - +
36C LEU* 1.3 78.6 - - - +
38C GLY* 1.3 58.5 + - - +
40C LYS* 3.8 8.4 - - - +
41C ALA* 2.9 31.9 + - - +
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Residues in contact with GLY 38 (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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11C SER* 3.5 23.0 - - - +
12C ARG* 6.3 0.4 - - - -
35C ASN* 2.5 23.6 + - - -
36C LEU 3.2 0.2 - - - -
37C GLU* 1.3 70.5 - - - +
39C ALA* 1.3 63.7 + - - +
41C ALA* 3.5 6.5 + - - +
42C ALA* 3.2 18.7 + - - +
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Residues in contact with ALA 39 (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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11C SER* 4.0 2.8 - - - -
31C VAL* 3.4 39.1 - - + +
33C ALA* 4.4 7.2 - - + +
35C ASN 3.1 12.9 + - - +
36C LEU* 3.0 10.9 + - + +
38C GLY* 1.3 78.5 - - - +
40C LYS* 1.3 56.6 + - - +
43C ALA 3.1 20.8 + - - -
52C ALA* 3.3 14.2 - - + +
53C PHE 3.8 14.1 - - - +
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Residues in contact with LYS 40 (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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36C LEU* 2.8 37.0 + - + +
37C GLU* 4.0 8.7 - - - +
39C ALA* 1.3 74.4 - - - +
41C ALA* 1.3 57.8 + - - +
43C ALA* 4.4 1.6 - - - +
44C GLY* 2.6 33.3 + - - -
51C LEU* 5.9 0.2 - - - +
52C ALA* 3.7 33.4 + - + +
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Residues in contact with ALA 41 (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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37C GLU* 2.9 21.5 + - - +
38C GLY* 3.7 9.2 - - - +
39C ALA 3.3 0.2 - - - -
40C LYS* 1.3 79.6 - - - +
42C ALA* 1.3 61.6 + - - +
44C GLY* 4.0 1.1 - - - -
45C ASP* 3.6 17.8 + - - +
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Residues in contact with ALA 42 (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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10C GLY 3.7 23.6 - - - +
11C SER* 4.0 13.0 - - - +
16C ARG* 5.1 4.5 - - + -
19C ALA* 6.1 0.7 - - + -
31C VAL* 4.1 4.7 - - + -
38C GLY 3.2 14.4 + - - +
39C ALA 3.9 3.8 - - - +
41C ALA* 1.3 79.1 - - - +
43C ALA* 1.3 62.3 + - - +
44C GLY 3.3 0.5 + - - -
45C ASP* 3.4 10.9 + - - +
46C LEU* 3.2 22.4 + - + +
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Residues in contact with ALA 43 (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 VAL* 3.7 14.8 - - + +
39C ALA 3.1 16.5 + - - +
40C LYS* 3.6 1.8 - - - +
42C ALA* 1.3 78.0 - - - +
44C GLY* 1.3 62.1 + - - +
45C ASP 3.3 0.2 - - - -
46C LEU* 3.4 26.8 + - + +
47C GLY 4.2 2.8 + - - -
48C GLY 5.4 1.0 + - - +
50C HIS* 3.9 26.0 - - - +
51C LEU 4.1 3.6 - - - +
52C ALA* 4.0 14.1 - - + +
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Residues in contact with GLY 44 (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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40C LYS 2.6 22.8 + - - -
41C ALA* 4.0 2.7 - - - -
42C ALA 3.1 0.8 - - - -
43C ALA* 1.3 75.9 - - - +
45C ASP* 1.3 56.0 + - - +
46C LEU 3.2 2.3 + - - -
47C GLY* 4.1 7.6 + - - -
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Residues in contact with ASP 45 (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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20C GLN* 5.9 5.0 - - - +
41C ALA 3.6 12.2 + - - +
42C ALA* 3.4 8.3 + - - +
43C ALA 3.3 0.4 - - - -
44C GLY* 1.3 74.7 - - - +
46C LEU* 1.3 64.5 + - + +
47C GLY* 3.5 1.3 - - - -
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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