Contacts of the helix formed by residues 6 - 18 (chain B) in PDB entry 2H1R
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 6 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B LEU* 4.0 5.2 - - + +
5B LYS* 1.3 77.7 - - - +
7B PRO* 1.4 71.7 - - - +
8B GLY* 3.1 16.8 + - - -
9B ILE* 3.1 35.9 + - + +
10B LEU* 3.4 17.4 + - - +
34B ASN* 6.1 0.4 - - - +
159B SER* 2.8 31.1 + - - +
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Residues in contact with PRO 7 (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 LYS 4.4 1.6 - - - -
6B ASN* 1.4 86.7 - - - +
8B GLY* 1.3 62.0 + - - +
10B LEU* 3.2 16.2 + - + +
11B ASP* 3.2 28.3 + - - +
34B ASN* 6.1 2.7 - - - +
38B LYS* 5.2 0.3 + - - -
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Residues in contact with GLY 8 (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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6B ASN* 3.1 8.8 + - - -
7B PRO* 1.3 79.9 - - - +
9B ILE* 1.3 62.8 + - - +
11B ASP* 3.4 13.0 + - - +
12B LYS* 3.2 24.0 + - - +
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Residues in contact with ILE 9 (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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4B LEU* 4.2 20.0 - - + -
6B ASN* 3.1 36.8 + - + +
8B GLY* 1.3 73.5 - - - +
10B LEU* 1.3 66.4 + - - +
12B LYS* 3.1 10.7 + - + +
13B ILE* 3.0 21.9 + - + +
118B MET* 4.2 2.7 - - + -
153B CYS* 4.4 9.2 - - - -
154B ASN 4.1 20.2 - - - +
155B VAL* 4.3 15.9 - - + -
159B SER* 5.1 0.7 - - - +
170B ILE* 3.5 28.5 - - + -
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Residues in contact with LEU 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B LEU* 3.6 32.5 - - + +
6B ASN 3.7 13.5 - - - +
7B PRO* 3.2 14.2 + - + +
9B ILE* 1.3 75.9 - - - +
11B ASP* 1.3 63.4 + - - +
13B ILE* 3.2 11.1 + - + +
14B ILE* 3.0 27.9 + - - +
34B ASN* 3.8 45.1 - - + +
35B LEU* 3.9 22.6 - - + +
38B LYS* 4.0 18.4 - - + -
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Residues in contact with ASP 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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7B PRO* 3.2 15.7 + - - +
8B GLY* 3.5 12.9 - - - +
10B LEU* 1.3 78.4 - - - +
12B LYS* 1.3 57.2 + - - +
14B ILE* 3.5 6.1 + - - +
15B TYR* 3.0 27.7 + - - +
38B LYS* 2.7 32.4 + - - -
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Residues in contact with LYS 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B GLY 3.2 12.9 + - - +
9B ILE* 3.1 16.6 + - + +
11B ASP* 1.3 74.2 - - - +
13B ILE* 1.3 65.1 + - - +
15B TYR* 3.5 13.9 + - - +
16B ALA* 3.0 24.9 + - - +
152B VAL* 3.2 42.4 + - + +
153B CYS* 3.7 26.5 - - + -
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Residues in contact with ILE 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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4B LEU* 4.4 2.0 - - + -
9B ILE* 3.0 20.1 + - + +
10B LEU* 3.5 24.0 - - + +
12B LYS* 1.3 72.3 - - - +
14B ILE* 1.3 69.1 + - + +
16B ALA* 3.2 4.0 + - - +
17B ALA* 3.0 24.7 + - + +
35B LEU* 4.2 21.1 - - + -
39B LEU* 5.7 1.3 - - + -
90B THR* 3.5 26.2 - - - +
116B VAL* 4.1 21.1 - - + +
118B MET* 4.2 13.5 - - + -
152B VAL* 5.3 0.4 - - - -
170B ILE* 3.7 29.6 - - + -
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Residues in contact with ILE 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 LEU 3.0 20.2 + - - +
11B ASP* 3.8 5.6 - - - +
13B ILE* 1.3 76.9 - - + +
15B TYR* 1.3 65.9 + - - +
17B ALA* 3.3 12.9 + - + +
18B LYS* 3.5 9.2 + - - -
19B ILE* 4.6 3.8 + - + +
35B LEU* 3.8 13.5 - - + -
38B LYS* 3.8 31.0 - - + +
39B LEU* 3.5 32.1 - - + -
42B LEU* 3.5 30.5 - - + +
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Residues in contact with TYR 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 ASP 3.0 18.8 + - - +
12B LYS* 3.7 14.1 - - - +
14B ILE* 1.3 78.3 - - - +
16B ALA* 1.3 62.4 + - + +
18B LYS* 3.0 48.8 + - - +
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Residues in contact with ALA 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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12B LYS 3.0 17.7 + - - +
13B ILE 3.2 3.3 + - - +
15B TYR* 1.3 80.4 - - + +
17B ALA* 1.3 62.9 + - - +
18B LYS* 3.4 15.5 + - - +
114B CYS* 4.3 2.8 - - - -
116B VAL* 4.1 11.7 - - + -
152B VAL* 3.9 29.6 - - + -
172B LYS* 3.5 25.8 - - + +
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Residues in contact with ALA 17 (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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13B ILE* 3.0 20.3 + - + +
14B ILE* 3.3 4.9 + - + +
16B ALA* 1.3 77.5 - - - +
18B LYS* 1.3 68.6 + - - +
19B ILE* 3.3 29.4 + - + -
39B LEU* 5.8 0.4 - - + -
88B VAL* 4.0 19.1 - - + +
90B THR* 6.1 2.0 - - - -
114B CYS* 3.8 16.2 - - - -
116B VAL* 3.9 15.0 - - + -
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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
----------------------------------------------------------
14B ILE 3.5 7.8 + - - -
15B TYR* 3.0 54.2 + - - +
16B ALA* 4.0 11.9 + - - +
17B ALA* 1.3 79.1 - - - +
19B ILE* 1.3 64.1 + - - +
20B LYS* 3.6 17.3 + - - +
23B ASP* 4.3 3.1 - - - +
88B VAL* 5.3 0.5 - - - +
172B LYS* 4.7 13.2 - - - +
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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