Contacts of the helix formed by residues 34 - 43 (chain A) in PDB entry 2A7P
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 GLU 34 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A GLU 5.3 0.7 - - - -
29A GLY* 3.4 1.4 - - - -
30A GLY* 2.8 34.9 + - - +
31A ALA 2.8 15.0 + - - +
32A GLU 3.7 10.1 - - - +
33A ASP* 1.3 83.3 - - - +
35A TYR* 1.3 64.7 + - - +
36A GLY 3.1 2.0 - - - +
37A VAL* 3.3 28.9 - - + +
38A LYS* 3.7 7.1 + - - +
167A ARG* 3.0 44.7 + - - +
261A ASP* 3.1 7.7 + - - -
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Residues in contact with TYR 35 (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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33A ASP* 3.3 36.3 + - + -
34A GLU* 1.3 77.9 - - - +
36A GLY* 1.3 59.1 + - - +
38A LYS* 3.4 8.1 + - + +
39A HIS* 2.9 31.1 + - - +
261A ASP* 2.7 23.6 + - - +
262A CYS* 5.4 9.4 - - - -
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Residues in contact with GLY 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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35A TYR* 1.3 79.3 - - - +
37A VAL* 1.3 56.1 + - - +
39A HIS* 3.1 7.1 + - - +
40A ASN* 2.9 37.1 + - - -
254A ASN* 6.2 0.2 - - - -
257A GLY* 4.7 7.4 - - - -
260A LEU 5.3 0.7 - - - -
261A ASP* 2.6 33.7 + - - -
263A ALA 5.3 3.8 - - - -
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Residues in contact with VAL 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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28A GLU 5.1 3.6 - - - +
30A GLY* 4.3 8.1 - - - +
34A GLU* 3.3 34.7 - - + +
36A GLY* 1.3 71.5 - - - +
38A LYS* 1.3 71.0 + - + +
40A ASN* 3.3 17.8 + - - +
41A ARG* 3.3 17.9 + - - +
256A GLY 3.5 25.6 - - - +
257A GLY* 3.8 13.8 + - - +
261A ASP* 4.6 0.2 + - - -
308A ARG* 4.1 15.5 - - - +
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Residues in contact with LYS 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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34A GLU 4.0 9.2 - - - +
35A TYR* 3.4 11.6 + - + +
36A GLY 3.2 0.4 - - - -
37A VAL* 1.3 83.1 - - + +
39A HIS* 1.3 58.4 + - - +
41A ARG* 3.1 11.7 + - + +
42A ASP* 2.7 68.8 + - - +
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Residues in contact with HIS 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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35A TYR 2.9 18.1 + - - +
36A GLY* 3.1 7.6 + - - +
38A LYS* 1.3 78.2 - - - +
40A ASN* 1.3 65.1 + - - +
42A ASP* 4.4 9.4 - - - +
43A VAL* 3.0 39.6 + - + +
46A GLN* 5.0 7.2 - - - -
263A ALA 4.3 11.7 - - - -
264A ILE* 4.7 0.8 - - - -
265A SER* 3.9 17.9 + - - -
268A GLU* 2.6 31.8 + - - -
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Residues in contact with ASN 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 GLY* 2.9 20.6 + - - +
37A VAL* 3.5 10.7 - - - +
38A LYS 3.3 0.2 - - - -
39A HIS* 1.3 76.9 - - - +
41A ARG* 1.3 58.9 + - - +
43A VAL* 3.3 11.0 - - - +
44A PHE* 3.2 25.3 - - - -
254A ASN* 2.8 44.0 - - - +
256A GLY 3.8 3.8 - - - -
257A GLY* 3.5 11.4 + - - -
263A ALA 5.3 0.4 + - - -
265A SER* 3.9 13.8 - - - +
285A SER* 3.8 15.2 + - - +
286A GLY* 3.8 18.0 + - - -
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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 VAL 3.5 13.5 - - - +
38A LYS* 3.1 11.9 + - + +
39A HIS 3.1 0.6 - - - -
40A ASN* 1.3 77.8 - - + +
42A ASP* 1.3 68.9 + - - +
44A PHE* 3.3 25.7 + - - +
45A GLN* 4.5 3.3 + - - +
286A GLY* 2.8 37.3 + - - -
288A ARG* 3.6 36.0 - - - +
289A ARG* 4.8 8.5 - - - +
292A ASP* 3.4 26.3 + - - -
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Residues in contact with ASP 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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38A LYS* 2.7 59.8 + - - +
39A HIS* 3.2 10.7 + - - +
41A ARG* 1.3 73.7 - - - +
43A VAL* 1.3 66.6 + - - +
44A PHE 3.0 2.7 - - - -
45A GLN* 2.9 28.6 + - - +
46A GLN* 4.1 3.2 + - - +
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Residues in contact with VAL 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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39A HIS* 3.0 21.8 + - + +
40A ASN 3.3 20.6 - - - +
42A ASP* 1.3 76.3 - - - +
44A PHE* 1.3 65.3 + - + +
45A GLN 3.2 0.2 - - - -
46A GLN* 3.2 37.8 + - - +
47A TRP* 3.3 22.7 - - + -
265A SER* 3.5 30.5 - - - +
267A MET* 4.1 18.2 - - + -
268A GLU* 4.2 12.8 - - + -
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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