Contacts of the strand formed by residues 5 - 15 (chain A) in PDB entry 2HRG
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 VAL 5 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A GLY* 3.3 6.5 + - - -
4A PRO* 1.3 86.4 - - + +
6A ALA* 1.3 67.4 + - - +
43A ARG 4.4 9.0 - - - +
45A GLN* 3.4 41.5 - - + +
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Residues in contact with ALA 6 (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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2A ILE* 4.3 18.4 - - + -
3A GLY* 4.0 18.4 - - - +
4A PRO 4.0 1.0 + - - -
5A VAL* 1.3 79.6 - - - +
7A ASP* 1.3 70.9 + - - +
8A LEU* 3.9 2.1 + - + +
36A ILE* 6.2 0.2 - - + -
45A GLN 3.0 7.0 + - - +
46A LEU* 3.4 13.9 - - + +
47A ASN* 2.9 25.0 + - - +
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Residues in contact with ASP 7 (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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6A ALA* 1.3 77.7 - - - +
8A LEU* 1.3 63.5 + - - +
9A THR* 3.9 5.2 - - - +
28A ASN* 3.1 22.0 + - - +
47A ASN* 3.3 29.3 + - - +
49A ILE* 3.9 22.1 - - + +
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Residues in contact with LEU 8 (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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2A ILE* 3.7 29.4 - - + -
6A ALA* 4.7 4.7 - - + +
7A ASP* 1.3 74.3 - - - +
9A THR* 1.3 62.1 + - - +
10A ILE* 3.7 9.6 + - + +
27A VAL* 4.1 18.4 - - + -
28A ASN* 3.5 6.7 - - - +
34A PRO* 5.0 0.2 - - + -
36A ILE* 3.9 22.9 - - + -
46A LEU* 4.0 14.4 - - + -
47A ASN 2.8 12.6 + - - +
48A VAL* 3.4 13.0 - - + -
49A ILE 2.9 22.8 + - - -
63A ILE* 4.7 2.5 - - + -
65A TRP* 3.7 31.0 - - + -
108A TYR* 4.7 10.1 - - + +
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Residues in contact with THR 9 (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 ASP* 4.7 4.2 - - - +
8A LEU* 1.3 71.1 - - - +
10A ILE* 1.3 66.5 + - - +
11A SER* 3.9 5.4 + - - -
26A LEU 3.6 0.7 - - - +
27A VAL* 3.4 3.6 - - - -
28A ASN* 2.8 47.0 + - - -
29A ASP* 4.5 4.5 + - - +
49A ILE* 3.4 28.5 - - + +
51A ASN* 3.4 30.1 - - + +
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Residues in contact with ILE 10 (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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8A LEU* 3.7 15.0 - - + +
9A THR* 1.3 75.4 - - - +
11A SER* 1.3 63.2 + - - +
25A ILE* 3.6 26.7 - - + -
26A LEU 3.5 2.0 - - - +
27A VAL* 4.0 21.3 - - + -
48A VAL* 3.8 17.9 - - + -
49A ILE 2.8 17.7 + - - +
50A ASP* 4.4 6.7 - - - +
51A ASN* 2.8 34.5 + - - +
52A MET* 3.5 19.0 + - + -
61A THR* 4.5 4.9 - - + -
63A ILE* 4.1 21.3 - - + -
120A LEU* 3.8 14.4 - - + -
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Residues in contact with SER 11 (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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9A THR* 3.9 6.9 + - - -
10A ILE* 1.3 76.2 - - - +
12A ASN* 1.3 63.1 + - - +
25A ILE* 3.4 8.3 - - - +
26A LEU* 2.8 53.1 + - - +
29A ASP* 4.3 12.3 + - - -
51A ASN* 4.4 15.3 - - - -
52A MET* 3.8 7.4 - - - -
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Residues in contact with ASN 12 (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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11A SER* 1.3 80.3 + - - +
13A GLY* 1.3 58.2 + - - +
23A GLN* 4.2 9.0 - - - +
24A ALA 3.4 6.3 + - - +
25A ILE* 4.0 3.4 - - - +
26A LEU* 4.1 7.3 - - - +
51A ASN 5.0 0.6 + - - -
52A MET* 3.5 23.5 - - - +
53A THR* 2.8 36.8 + - - +
54A ASN* 3.0 23.8 + - + +
57A MET* 3.6 23.3 - - + +
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Residues in contact with GLY 13 (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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12A ASN* 1.3 75.4 - - - +
14A ALA* 1.3 62.7 - - - -
15A VAL* 3.8 2.1 + - - +
23A GLN* 3.3 13.1 + - - -
24A ALA* 2.8 31.4 + - - +
26A LEU* 3.9 19.3 - - - +
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Residues in contact with ALA 14 (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 GLY* 1.3 73.0 - - - -
15A VAL* 1.3 65.3 + - - +
16A SER* 5.4 0.2 - - - -
21A SER* 5.2 7.2 - - - -
22A ARG 3.3 14.1 - - - +
23A GLN* 3.7 19.3 - - - +
26A LEU* 4.9 2.8 - - - +
2001A GOL 4.7 2.8 - - - -
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Residues in contact with VAL 15 (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 GLY 4.1 4.0 - - - +
14A ALA* 1.3 79.0 - - - +
16A SER* 1.3 66.1 + - - +
17A PRO* 3.6 5.1 - - + +
20A PHE 3.6 0.7 - - - +
21A SER* 3.1 0.9 - - - -
22A ARG* 2.8 39.1 + - + +
24A ALA* 3.6 11.7 - - + -
26A LEU* 3.7 15.9 - - + -
31A PHE* 3.4 31.6 - - + -
151A TRP* 3.6 31.6 - - + -
2001A GOL 3.7 18.6 - - - +
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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