Contacts of the helix formed by residues 20 - 31 (chain G) in PDB entry 1HNW
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 20 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15G ASP* 2.8 25.1 + - - +
18G TYR 2.8 10.3 + - - +
19G GLY* 1.3 77.7 - - - +
21G VAL* 1.3 79.7 + - - +
22G LEU* 3.0 30.1 + - - +
23G VAL* 3.7 21.4 + - + +
59G LEU* 4.7 7.0 - - + -
62G PHE* 5.0 0.3 - - - -
63G LYS* 3.3 35.0 + - - +
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Residues in contact with VAL 21 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12G LEU* 4.0 28.1 - - + +
14G PRO* 3.9 27.1 - - + -
19G GLY 4.7 0.7 - - - +
20G ASP* 1.3 78.7 + - - +
22G LEU* 1.3 70.2 + - + +
23G VAL 2.7 5.8 + - - -
24G THR* 2.7 29.6 + - - -
25G ALA* 3.2 8.8 + - - +
97G GLN* 6.2 0.2 - - - +
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Residues in contact with LEU 22 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20G ASP* 3.0 18.8 + - - +
21G VAL* 1.3 84.3 - - + +
23G VAL* 1.3 59.2 + - - +
25G ALA* 3.6 6.0 - - + +
26G PHE* 3.3 20.1 + - - +
62G PHE* 3.8 20.4 - - + -
63G LYS* 4.6 16.6 - - + +
66G VAL* 4.5 18.8 - - + -
97G GLN* 3.4 40.8 - - + +
101G LEU* 4.0 14.4 - - + -
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Residues in contact with VAL 23 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15G ASP* 2.7 29.8 - - - +
18G TYR* 4.6 2.0 - - + -
20G ASP* 3.7 24.7 - - + +
21G VAL 2.7 5.3 + - - -
22G LEU* 1.3 73.1 - - - +
24G THR* 1.3 58.2 + - - +
25G ALA 3.1 1.1 - - - -
26G PHE* 3.2 5.4 + - - +
27G ILE* 2.8 37.9 + - + +
43G PHE* 3.2 34.5 - - + -
59G LEU* 4.0 23.6 - - + -
62G PHE* 4.3 11.4 - - + -
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Residues in contact with THR 24 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1374A A 5.8 0.7 - - - +
12G LEU* 4.6 13.7 - - + -
13G GLN* 3.2 27.0 + - + +
14G PRO* 3.5 15.6 + - - +
15G ASP* 3.6 2.7 + - - +
16G LEU* 6.2 2.5 - - + -
21G VAL* 2.7 17.1 + - - -
23G VAL* 1.3 74.2 - - - +
25G ALA* 1.3 50.2 + - - -
27G ILE* 3.1 11.7 + - + +
28G ASN* 2.6 55.0 + - - +
36G LYS* 4.2 19.5 - - - +
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Residues in contact with ALA 25 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1375A A 4.8 2.5 - - - +
12G LEU* 4.5 13.1 - - + +
21G VAL 3.2 4.2 + - - +
22G LEU* 3.6 16.4 - - - +
24G THR* 1.3 78.7 - - - +
26G PHE* 1.3 64.7 + - - +
28G ASN* 2.9 23.4 + - - +
29G LYS* 3.1 14.1 + - - +
97G GLN* 4.3 11.2 - - - +
101G LEU* 3.7 22.2 - - + -
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Residues in contact with PHE 26 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22G LEU 3.3 2.9 + - - +
23G VAL* 3.2 7.0 + - - +
25G ALA* 1.3 79.8 - - - +
27G ILE* 1.3 62.0 + - - +
29G LYS* 3.2 12.5 + - - +
30G ILE* 3.2 51.1 + - + +
43G PHE* 3.6 22.2 - + + -
62G PHE* 3.6 29.6 - + + -
101G LEU* 3.7 27.1 - - + +
104G LEU* 3.7 33.7 - - + -
105G VAL* 3.8 17.9 - - + -
120G ILE* 3.5 33.4 - - + -
124G LEU* 4.7 5.6 - - + -
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Residues in contact with ILE 27 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G ASP* 4.4 1.1 - - - +
23G VAL* 2.8 46.2 + - + +
24G THR* 3.5 11.7 - - + +
26G PHE* 1.3 75.4 - - + +
28G ASN* 1.3 65.0 + - - +
30G ILE* 2.9 11.2 + - - +
31G MET* 2.9 20.6 + - - +
36G LYS* 4.8 14.4 - - + +
39G ALA* 3.8 26.2 - - + +
40G ALA* 3.8 14.6 - - + +
43G PHE* 4.1 20.2 - - + -
44G TYR* 4.1 22.9 - - + +
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Residues in contact with ASN 28 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1374A A 3.5 47.0 + - - +
1375A A 3.3 20.5 + - - +
12G LEU* 3.6 9.5 - - - +
24G THR* 2.6 41.2 + - - +
25G ALA* 2.9 7.9 + - - +
27G ILE* 1.3 73.1 - - - +
29G LYS* 1.3 62.1 + - - +
31G MET* 3.1 29.3 + - - +
36G LYS* 2.6 28.7 + - - +
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Residues in contact with LYS 29 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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939A G 3.7 1.0 + - - -
940A C 2.8 37.1 + - - -
1375A A 3.2 44.4 + - - -
1376A U 4.9 2.7 - - - -
25G ALA 3.1 12.6 + - - +
26G PHE* 3.6 10.5 - - - +
27G ILE 3.2 0.4 - - - -
28G ASN* 1.3 77.1 - - - +
30G ILE* 1.3 60.5 + - - +
31G MET 3.8 4.3 - - - +
98G SER* 4.8 4.0 - - - +
101G LEU* 4.5 9.6 - - + +
102G ARG* 3.8 36.8 - - + +
105G VAL* 3.7 27.9 - - + +
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Residues in contact with ILE 30 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1240A U 2.7 55.2 + - + +
26G PHE* 3.2 42.0 - - + +
27G ILE* 2.9 14.2 + - - +
29G LYS* 1.3 77.6 - - - +
31G MET* 1.3 64.9 + - - +
32G ARG* 4.1 3.5 + - - -
39G ALA* 4.5 7.6 - - + +
42G ILE* 4.1 22.0 - - + -
43G PHE* 4.0 18.2 - - + +
105G VAL* 3.7 12.3 - - + -
120G ILE* 3.2 19.5 - - + -
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Residues in contact with MET 31 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1240A U 4.6 0.4 - - - -
1349A A 5.5 0.9 - - - +
1373A G 3.8 11.7 - - - +
1374A A 3.5 49.1 - - - +
27G ILE 2.9 8.8 + - - +
28G ASN* 3.1 24.9 + - - +
29G LYS 3.8 4.2 - - - +
30G ILE* 1.3 80.9 - - - +
32G ARG* 1.3 64.6 + - - +
34G GLY* 3.6 18.6 - - - +
35G LYS 3.9 5.4 - - - +
36G LYS* 3.5 42.6 - - + +
39G ALA* 3.4 21.7 - - + +
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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