Contacts of the helix formed by residues 26 - 38 (chain A) in PDB entry 3G2V
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 ASP 26 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A ARG* 4.0 15.7 - - - +
17A ALA* 4.8 2.2 + - - -
22A ASN* 4.2 21.5 - - - +
24A GLU 3.4 3.2 + - - +
25A LEU* 1.3 70.4 - - - +
27A TRP* 1.3 59.3 + - - +
28A ALA* 3.6 10.9 + - - +
29A SER* 2.6 35.5 + - - -
30A ILE* 2.9 34.0 + - - +
65A GLN* 4.9 0.6 + - - -
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Residues in contact with TRP 27 (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* 3.6 41.2 + - + +
26A ASP* 1.3 69.5 + - - +
28A ALA* 1.3 60.5 + - - +
30A ILE* 3.7 19.5 - - + -
31A ASN* 2.7 58.3 + - - +
68A THR* 4.1 14.1 - - + -
72A THR* 3.7 28.9 - - + -
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Residues in contact with ALA 28 (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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13A ARG* 3.5 11.2 + - - +
16A ARG* 5.9 0.7 - - - +
26A ASP* 3.6 10.0 + - - +
27A TRP* 1.3 75.7 - - - +
29A SER* 1.3 58.4 + - - +
31A ASN* 4.6 1.0 - - - +
32A GLY* 2.8 27.5 + - - -
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Residues in contact with SER 29 (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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13A ARG* 3.8 8.1 - - - +
16A ARG* 2.7 36.4 + - - +
17A ALA* 3.7 26.1 - - - +
26A ASP* 2.6 31.1 + - - -
27A TRP 3.1 0.4 - - - -
28A ALA* 1.3 77.3 - - - +
30A ILE* 1.3 61.4 + - - +
32A GLY 3.8 0.2 - - - -
33A PHE* 2.9 29.1 + - - +
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Residues in contact with ILE 30 (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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17A ALA* 4.0 15.9 - - + +
25A LEU* 4.0 15.3 - - + -
26A ASP 2.9 34.1 + - - +
27A TRP* 3.7 32.3 - - + +
29A SER* 1.3 78.1 - - - +
31A ASN* 1.3 62.0 + - - +
33A PHE* 3.2 10.9 + - - +
34A CYS* 3.2 13.5 + - - -
65A GLN* 5.6 0.4 - - + +
68A THR* 4.3 10.8 - - + -
69A VAL* 4.0 28.1 - - + +
72A THR* 3.7 31.6 - - + +
73A CYS* 4.4 0.3 - - - -
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Residues in contact with ASN 31 (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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27A TRP* 2.7 45.4 + - - +
28A ALA* 4.6 0.7 - - - +
30A ILE* 1.3 74.2 - - - +
32A GLY* 1.3 55.9 + - - +
34A CYS* 3.2 8.1 + - + +
35A GLU* 2.8 35.8 + - + +
72A THR* 3.2 26.3 - - - +
76A SER* 5.2 2.8 + - - -
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Residues in contact with GLY 32 (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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13A ARG* 3.8 26.7 + - - -
28A ALA 2.8 22.3 + - - -
29A SER 3.8 0.2 - - - -
30A ILE 3.2 0.4 - - - -
31A ASN* 1.3 76.6 - - - +
33A PHE* 1.3 55.0 + - - +
35A GLU* 3.4 14.1 + - - +
36A GLN* 3.0 31.0 + - - +
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Residues in contact with PHE 33 (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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10A LEU* 3.6 37.1 - - + +
13A ARG* 3.9 11.3 - - + +
14A ILE* 3.6 31.2 - - + +
17A ALA* 5.3 0.2 - - + -
29A SER 2.9 14.7 + - - +
30A ILE* 3.3 9.6 - - - +
31A ASN 3.2 0.2 - - - -
32A GLY* 1.3 73.6 - - - +
34A CYS* 1.3 66.9 + - - +
36A GLN* 3.2 1.7 + - - -
37A LEU* 3.0 38.1 + - + +
47A ALA* 3.6 30.3 - - + -
50A LEU* 4.3 4.5 - - + -
51A LEU* 3.8 19.7 - - + -
69A VAL* 3.4 28.9 - - + -
73A CYS* 3.7 5.4 - - - -
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Residues in contact with CYS 34 (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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30A ILE* 3.5 12.1 - - - -
31A ASN* 3.2 10.6 + - - +
33A PHE* 1.3 78.8 - - - +
35A GLU* 1.3 63.2 + - - +
36A GLN 3.3 0.3 + - - -
37A LEU* 3.5 4.7 - - - +
38A ASN* 3.3 15.8 + - - +
72A THR* 4.0 13.2 - - - -
73A CYS* 2.1 62.6 - - + -
76A SER* 3.7 16.8 - - - +
77A CYS* 3.4 17.7 - - - -
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Residues in contact with GLU 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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13A ARG* 5.5 1.9 + - - -
31A ASN* 2.8 22.3 + - + +
32A GLY* 3.5 13.8 - - - +
33A PHE 3.2 0.2 - - - -
34A CYS* 1.3 76.9 - - - +
36A GLN* 1.3 63.2 + - - +
38A ASN* 3.6 9.7 + - - +
39A GLU* 3.4 19.6 + - - +
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Residues in contact with GLN 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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7A PRO* 3.5 35.1 - - - +
8A GLU 3.5 23.2 + - - +
9A THR* 4.6 1.0 - - - -
10A LEU* 3.7 25.6 - - + +
13A ARG* 4.6 10.0 - - + +
32A GLY 3.0 17.6 + - - +
33A PHE 3.2 0.2 + - - -
35A GLU* 1.3 75.2 - - - +
37A LEU* 1.3 61.2 + - - +
38A ASN 3.2 1.3 - - - -
39A GLU* 2.9 34.5 + - - +
40A ASP* 2.9 35.1 - - - +
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Residues in contact with LEU 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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10A LEU* 3.4 15.1 - - + +
33A PHE* 3.0 30.0 + - + +
34A CYS* 3.5 13.7 - - - +
36A GLN* 1.3 76.2 - - - +
38A ASN* 1.3 67.8 + - - +
39A GLU 3.3 0.9 + - - -
40A ASP* 3.4 10.5 - - - +
43A GLY* 3.5 7.1 - - - +
44A PRO* 3.3 34.7 - - + +
47A ALA* 3.7 29.4 - - + -
73A CYS* 4.1 8.1 - - + -
77A CYS* 4.1 12.1 - - - -
80A ARG* 3.4 1.4 + - - -
81A PHE* 3.8 34.8 - - + -
149A IOD 4.2 2.0 - - + -
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Residues in contact with ASN 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 CYS 3.3 14.7 + - - +
35A GLU* 3.6 9.4 + - - +
36A GLN 3.2 0.4 - - - -
37A LEU* 1.3 83.6 - - - +
39A GLU* 1.3 61.0 + - - +
77A CYS* 4.3 12.7 - - - +
80A ARG* 3.2 19.8 + - - +
149A IOD 3.5 17.5 - - - +
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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