Contacts of the helix formed by residues 35 - 44 (chain A) in PDB entry 3C2B
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 THR 35 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A GLU 5.4 0.2 - - - +
32A LYS 3.5 22.4 - - - +
33A ALA* 3.1 6.9 + - - -
34A LEU* 1.3 77.1 - - - +
36A THR* 1.3 68.5 + - - +
37A SER* 3.9 6.0 + - - -
38A GLY* 2.8 23.8 + - - -
39A LEU* 2.8 26.4 + - - +
57A ARG* 6.0 0.2 - - - +
60A LEU* 6.4 0.4 - - - -
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Residues in contact with THR 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LEU 4.5 0.2 + - - -
35A THR* 1.3 72.7 - - - +
37A SER* 1.3 57.5 + - - +
39A LEU* 3.7 1.7 + - - -
40A ALA* 3.0 26.5 + - - +
47A LYS* 3.5 34.6 - - + +
50A LEU* 3.9 18.3 - - - +
57A ARG* 6.1 4.0 - - + +
60A LEU* 5.9 6.9 - - - +
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Residues in contact with SER 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A THR* 3.1 6.3 + - - -
36A THR* 1.3 77.4 + - - +
38A GLY* 1.3 65.6 + - - +
39A LEU 3.2 0.2 - - - -
40A ALA* 3.7 7.9 - - - +
41A ARG* 3.1 43.3 + - - +
47A LYS* 5.8 3.0 - - - +
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Residues in contact with GLY 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A LEU* 3.9 13.4 - - - +
33A ALA 4.7 4.7 - - - -
35A THR* 2.8 24.7 + - - -
37A SER* 1.3 71.4 - - - +
39A LEU* 1.3 57.3 + - - +
41A ARG* 3.2 13.6 + - - +
42A ALA* 2.9 28.4 + - - +
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Residues in contact with LEU 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A VAL* 3.8 26.7 - - + +
21A GLN* 3.7 18.2 - - + -
22A ALA* 3.5 42.4 - - + +
25A LEU* 3.7 14.0 - - + +
34A LEU* 5.0 4.9 - - + -
35A THR 2.8 14.8 + - - +
36A THR* 4.2 3.6 - - - +
38A GLY* 1.3 74.1 - - - +
40A ALA* 1.3 62.5 + - - +
42A ALA* 4.3 1.8 - - + -
43A ALA* 3.1 20.2 + - + +
45A CYS* 4.0 3.0 - - - -
50A LEU* 3.7 26.7 - - + -
60A LEU* 5.4 10.1 - - + -
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Residues in contact with ALA 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A THR 3.0 18.4 + - - +
37A SER* 3.7 9.6 - - - +
39A LEU* 1.3 77.0 - - - +
41A ARG* 1.3 57.0 + - + +
44A ASN* 3.0 26.2 + - - -
45A CYS* 3.3 34.8 + - - +
46A SER 4.7 1.3 - - - +
47A LYS* 4.7 13.2 - - + +
50A LEU* 4.5 0.6 - - - +
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Residues in contact with ARG 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A SER* 3.1 32.9 + - - +
38A GLY* 3.4 10.7 - - - +
40A ALA* 1.3 78.9 - - + +
42A ALA* 1.3 63.6 + - - +
43A ALA 3.5 0.3 + - - -
44A ASN* 3.8 12.6 + - - +
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Residues in contact with ALA 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A GLN* 3.8 33.4 + - + +
25A LEU* 4.3 24.2 - - + -
38A GLY 2.9 18.7 + - - +
39A LEU* 4.2 3.1 - - - +
40A ALA 3.5 0.2 - - - -
41A ARG* 1.3 75.4 - - - +
43A ALA* 1.3 57.5 + - - +
44A ASN* 4.0 3.6 + - - +
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Residues in contact with ALA 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ARG* 2.9 25.7 + - - +
17A ALA 5.5 0.4 - - - -
18A VAL* 4.0 25.1 - - + -
21A GLN* 3.8 24.5 - - + -
39A LEU* 3.1 22.0 + - + +
42A ALA* 1.3 74.8 - - - +
44A ASN* 1.3 68.9 + - - +
45A CYS* 3.3 3.1 - - - -
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Residues in contact with ASN 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ARG* 2.8 14.9 + - - +
40A ALA 3.0 10.6 + - - -
41A ARG 3.9 11.0 - - - +
42A ALA 3.6 3.7 + - - -
43A ALA* 1.3 79.2 - - - +
45A CYS* 1.3 59.3 + - - +
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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