Contacts of the helix formed by residues 9 - 21 (chain B) in PDB entry 2HQR
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 9 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7B GLU* 3.3 15.5 - - + +
8B LYS* 1.3 86.5 - - - +
10B SER* 1.3 64.4 + - - +
11B VAL* 3.1 5.8 + - + +
12B LEU* 3.5 32.8 + - + +
13B GLY* 3.3 14.7 + - - -
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Residues in contact with SER 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B GLU 5.5 1.1 - - - -
8B LYS 3.1 8.7 + - - -
9B ASN* 1.3 70.9 - - - +
11B VAL* 1.3 60.8 + - - +
13B GLY* 3.5 3.2 - - - +
14B GLY* 2.7 28.6 + - - -
29B VAL* 5.5 8.2 - - - +
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Residues in contact with VAL 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ASN* 3.1 4.4 - - + -
10B SER* 1.3 78.6 - - - +
12B LEU* 1.3 72.9 + - + +
14B GLY* 3.0 11.1 + - - -
15B GLU* 3.3 15.8 + - - +
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Residues in contact with LEU 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B GLU* 4.0 17.5 - - + +
9B ASN* 3.5 33.7 + - + +
10B SER 3.3 0.2 - - - -
11B VAL* 1.3 83.8 - - + +
13B GLY* 1.3 59.5 + - - +
15B GLU* 2.9 46.4 - - - +
16B ILE* 3.3 13.5 - - - +
97B LYS* 2.9 33.0 - - - +
99B TYR* 4.3 13.0 - - + +
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Residues in contact with GLY 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B LEU* 4.7 5.8 - - - +
7B GLU* 5.1 7.1 - - - +
9B ASN 3.3 7.8 + - - -
10B SER 3.2 7.0 + - - -
12B LEU* 1.3 80.4 - - - +
14B GLY* 1.3 57.9 + - - +
16B ILE* 4.1 6.0 - - - +
17B GLU* 2.9 30.1 + - - +
29B VAL* 3.8 27.1 - - - +
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Residues in contact with GLY 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B SER 2.7 14.2 + - - -
11B VAL* 3.0 5.3 + - - -
13B GLY* 1.3 75.7 - - - +
15B GLU* 1.3 66.0 + - - +
17B GLU* 3.1 23.2 + - - +
18B LYS* 3.1 21.2 + - - +
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Residues in contact with GLU 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B VAL* 3.3 9.2 + - - +
12B LEU* 2.9 53.6 - - - +
14B GLY* 1.3 71.8 - - - +
16B ILE* 1.3 69.3 + - + +
18B LYS* 3.1 8.0 + - - +
19B GLY* 2.8 19.2 + - - -
99B TYR* 4.2 10.9 - - - -
102B ILE* 4.1 27.3 - - + +
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Residues in contact with ILE 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B VAL* 6.0 0.2 - - + -
5B LEU* 3.5 39.9 - - + -
12B LEU 3.3 17.2 + - - +
13B GLY* 4.1 2.0 - - - +
14B GLY 3.3 0.6 - - - -
15B GLU* 1.3 79.3 - - + +
17B GLU* 1.3 65.7 + - - +
19B GLY* 2.8 13.2 + - - +
20B LEU* 3.0 25.8 + - + +
49B MET* 5.7 0.4 - - + -
99B TYR* 4.6 15.3 - - + +
102B ILE* 4.1 31.2 - - + -
105B LEU* 3.7 30.3 - - + -
106B VAL* 5.4 5.8 - - + -
109B ILE* 6.4 2.0 - - + -
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Residues in contact with GLU 17 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13B GLY 2.9 20.2 + - - +
14B GLY* 3.2 14.2 - - - +
16B ILE* 1.3 77.5 - - - +
18B LYS* 1.3 58.4 + - + +
20B LEU* 2.9 11.3 - - - +
21B ASN* 2.6 44.6 + - - +
27B ALA* 3.9 24.1 - - + +
29B VAL* 5.6 8.7 - - + +
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Residues in contact with LYS 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B GLY* 3.1 11.8 + - - +
15B GLU* 3.1 9.4 + - - +
17B GLU* 1.3 84.8 - - + +
19B GLY* 1.3 61.9 + - - +
21B ASN* 3.4 21.5 - - - +
22B VAL* 4.2 9.9 - - - +
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Residues in contact with GLY 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B GLU 2.8 9.8 + - - -
16B ILE* 2.8 10.4 + - - -
18B LYS* 1.3 79.0 - - - +
20B LEU* 1.3 61.5 + - - -
21B ASN 3.2 1.7 + - - -
22B VAL* 3.5 19.2 + - - +
23B LYS* 5.0 0.9 - - - +
102B ILE* 4.4 17.3 - - - -
103B LYS* 6.0 5.8 - - - -
106B VAL* 4.0 13.9 - - - +
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Residues in contact with LEU 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B VAL* 3.6 27.1 - - + -
5B LEU* 5.4 1.3 - - + -
16B ILE* 3.0 26.2 + - + +
17B GLU 2.9 29.2 - - - +
19B GLY* 1.3 71.7 - - - +
21B ASN* 1.3 66.7 + - - +
22B VAL 3.0 3.4 - - - -
23B LYS* 2.7 24.4 + - + +
24B GLY 3.3 5.9 + - - -
25B PHE* 3.5 19.7 + - + +
26B MET 3.5 25.1 - - - +
27B ALA* 3.5 22.0 - - + -
106B VAL* 3.9 25.5 - - + +
109B ILE* 6.0 4.5 - - + -
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Residues in contact with ASN 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B GLU* 2.6 39.8 + - - +
18B LYS* 3.4 19.4 - - - +
19B GLY 3.2 0.4 - - - -
20B LEU* 1.3 80.7 - - - +
22B VAL* 1.3 58.7 + - + +
24B GLY* 2.8 20.1 + - - -
25B PHE 3.6 17.5 - - - +
26B MET* 5.2 0.3 - - - -
27B ALA 5.0 2.1 + - - -
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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