Contacts of the strand formed by residues 25 - 32 (chain A) in PDB entry 1HCN
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 ILE 25 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A GLN 3.6 0.3 - - - +
14A GLU* 3.7 1.6 - - - -
15A ASN* 2.7 36.2 + - + +
18A PHE* 3.4 38.4 - - + +
19A SER* 2.6 11.2 + - - +
24A PRO* 1.3 70.8 - - - +
26A LEU* 1.3 57.7 + - - +
68A VAL* 4.2 4.3 - - + -
70A VAL* 4.7 2.2 - - + -
76A VAL* 4.0 22.4 - - + -
77A GLU 4.0 9.0 - - - +
78A ASN* 3.3 19.7 - - + +
94A NAG 3.5 29.6 - - + -
44B VAL* 3.8 30.1 - - + -
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Residues in contact with LEU 26 (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 LEU* 4.2 23.3 - - + -
13A GLN 3.1 14.6 - - - +
14A GLU* 3.1 27.8 - - - +
24A PRO* 4.2 8.7 - - + +
25A ILE* 1.3 73.0 - - - +
27A GLN* 1.3 61.4 + - - +
78A ASN* 2.6 14.8 + - - +
79A HIS* 2.8 46.0 + - - +
94A NAG 3.9 31.0 - - - -
44B VAL* 3.5 9.8 - - - +
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Residues in contact with GLN 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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12A LEU* 4.2 1.1 - - - -
13A GLN* 2.6 47.4 + - + +
15A ASN* 3.8 24.1 + - + +
25A ILE 4.0 0.2 + - - -
26A LEU* 1.3 75.6 - - - +
28A CYS* 1.3 68.0 + - - +
29A MET* 3.9 8.9 - - + +
79A HIS* 3.3 7.4 - - - +
41B MET* 3.5 34.5 - - - +
42B THR 2.7 30.6 + - - +
43B ARG* 3.8 2.8 - - - +
44B VAL* 3.6 26.4 - - + +
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Residues in contact with CYS 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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11A THR 3.6 0.2 - - - -
12A LEU* 3.8 4.9 - - - -
27A GLN* 1.3 72.2 - - - +
29A MET* 1.3 64.9 + - - +
60A CYS* 3.8 6.5 - - - +
61A VAL* 4.0 5.2 - - - -
62A ALA* 3.5 25.4 - - - +
79A HIS* 2.8 17.7 + - + +
81A ALA 3.3 17.5 - - - -
82A CYS* 2.0 54.1 - - + -
41B MET* 3.4 14.2 - - - +
42B THR* 4.1 5.6 + - - +
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Residues in contact with MET 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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9A GLU 3.4 2.8 - - - +
11A THR* 2.8 29.2 + - - +
13A GLN* 3.3 35.9 + - + +
14A GLU 6.1 0.4 - - - +
27A GLN* 3.7 17.3 - - - +
28A CYS* 1.3 81.5 - - - +
30A GLY* 1.3 59.2 + - - +
60A CYS* 3.1 7.5 - - - -
40B THR 4.5 0.2 - - - +
41B MET* 3.4 43.7 - - + -
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Residues in contact with GLY 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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8A PRO* 3.3 8.1 - - - -
9A GLU 3.3 13.5 - - - -
10A CYS* 3.3 4.3 - - - -
29A MET* 1.3 77.1 - - - +
31A CYS* 1.3 65.7 + - - -
60A CYS* 3.1 11.8 - - - +
38B CYS 3.7 0.2 - - - +
39B PRO* 3.5 1.7 - - - +
40B THR* 2.9 32.5 + - - +
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Residues in contact with CYS 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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7A CYS* 2.0 55.6 - - + +
8A PRO* 2.6 34.6 + - - +
10A CYS 3.6 11.0 + - - +
30A GLY* 1.3 78.1 - - - -
32A CYS* 1.3 68.5 + - - +
84A CYS* 3.8 3.6 - - - -
6B ARG* 4.5 4.3 - - + -
37B TYR* 3.6 17.9 - - + -
38B CYS 3.3 6.1 - - - +
39B PRO* 3.7 6.7 - - - -
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Residues in contact with CYS 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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10A CYS* 3.9 3.4 - - - -
30A GLY 4.3 0.2 + - - -
31A CYS* 1.3 76.3 - - - +
33A PHE* 1.3 58.9 + - - +
34A SER* 3.9 0.9 + - - -
58A THR* 2.9 33.2 - - - +
59A CYS* 4.2 1.8 - - - +
60A CYS* 3.7 22.9 - - - -
84A CYS* 2.0 54.5 - - - -
37B TYR* 3.0 31.6 - - - -
38B CYS* 3.4 10.0 + - - +
40B THR* 4.9 0.6 + - - +
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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