Contacts of the strand formed by residues 27 - 37 (chain B) 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 27 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18B VAL* 2.6 41.2 + - - +
25B VAL* 3.4 18.6 + - + +
26B CYS* 1.3 72.7 - - - +
28B THR* 1.3 62.2 + - - +
29B VAL* 3.9 10.3 - - + -
67B ILE* 3.4 29.4 - - + -
68B ARG 5.0 0.2 - - - +
69B LEU* 3.7 12.3 - - + -
70B PRO* 3.4 36.6 - - + -
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Residues in contact with THR 28 (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 THR* 4.2 17.4 + - - +
16B LEU 3.3 9.9 - - - -
17B ALA* 4.1 5.4 - - + +
26B CYS 4.2 2.9 - - - +
27B ILE* 1.3 77.2 - - - +
29B VAL* 1.3 62.3 + - - +
30B ASN* 3.7 7.6 + - - -
108B LEU 5.8 0.9 - - - -
110B CYS* 3.5 26.7 - - - +
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Residues in contact with VAL 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B THR* 3.0 9.5 - - - -
16B LEU* 2.7 46.7 + - + +
18B VAL* 3.4 21.5 - - + -
27B ILE* 3.4 5.6 + - + -
28B THR* 1.3 71.2 - - - +
30B ASN* 1.3 70.2 + - - +
31B THR* 4.8 0.2 - - - -
67B ILE* 3.8 26.0 - - + -
82B TYR* 3.6 49.6 - - + +
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Residues in contact with ASN 30 (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 ALA 3.7 5.2 - - - +
15B THR* 3.6 19.4 - - - +
28B THR* 3.7 10.3 + - - -
29B VAL* 1.3 83.6 + - - +
31B THR* 1.3 63.7 + - - +
65B GLU* 5.3 0.5 - - - +
82B TYR* 3.8 15.8 + - - -
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Residues in contact with THR 31 (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 ASN* 3.4 7.7 - - - +
14B ALA 2.9 28.8 + - - +
16B LEU* 3.6 37.2 - - + -
30B ASN* 1.3 77.8 - - - +
32B THR* 1.3 69.6 + - - +
33B ILE* 3.6 15.3 - - + -
82B TYR* 3.9 9.9 - - - -
83B ALA 2.7 23.5 + - - +
84B VAL* 3.3 16.0 - - - +
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Residues in contact with THR 32 (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 PRO* 4.4 5.6 - - + -
12B ILE 3.0 15.7 - - - +
13B ASN* 3.1 26.7 - - - +
31B THR* 1.3 84.7 + - - +
33B ILE* 1.3 66.9 + - - +
59B TYR* 4.0 5.9 + - - -
83B ALA 4.4 0.7 - - - +
84B VAL* 3.4 11.9 - - + +
85B ALA* 3.0 57.2 + - - +
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Residues in contact with ILE 33 (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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35A ARG* 5.0 5.6 - - + +
36A ALA 3.5 8.1 - - - +
37A TYR* 3.2 31.6 - - + -
38A PRO* 3.8 13.9 - - + -
11B PRO* 3.3 7.1 - - - +
12B ILE* 2.8 43.6 + - + -
14B ALA* 4.1 16.4 - - + -
16B LEU* 3.9 2.5 - - + -
31B THR* 3.6 26.9 - - + -
32B THR* 1.3 74.1 - - - +
34B CYS* 1.3 74.2 + - - +
35B ALA* 4.7 1.1 - - + -
59B TYR* 4.3 2.9 - - - -
85B ALA* 3.9 1.9 - - - +
108B LEU* 3.6 23.3 - - + -
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Residues in contact with CYS 34 (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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35A ARG* 3.0 4.3 - - - +
36A ALA* 2.7 55.4 + - + +
33B ILE* 1.3 72.5 - - - +
35B ALA* 1.3 63.0 + - - +
57B CYS* 3.8 8.7 - - - -
58B ASN 3.6 10.3 - - - -
59B TYR* 3.6 20.4 - - - -
85B ALA* 3.8 12.3 - - - -
88B CYS* 2.0 50.3 - - + -
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Residues in contact with ALA 35 (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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33A PHE* 3.8 21.8 - - + -
34A SER 3.3 7.0 - - - +
35A ARG* 4.0 4.9 - - + -
10B ARG* 2.7 42.1 + - - +
12B ILE* 3.7 30.0 - - + +
33B ILE* 4.1 1.1 - - + -
34B CYS* 1.3 77.4 - - - +
36B GLY* 1.3 59.2 + - - +
57B CYS* 3.6 6.8 - - - -
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Residues in contact with GLY 36 (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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33A PHE* 3.1 11.2 - - - -
34A SER* 2.9 33.9 + - - +
7B PRO 3.1 13.5 - - - -
9B CYS* 3.8 7.6 - - - -
10B ARG* 3.2 8.1 - - - -
35B ALA* 1.3 78.4 - - - +
37B TYR* 1.3 66.5 + - - -
57B CYS* 3.9 0.6 - - - -
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Residues in contact with TYR 37 (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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7A CYS* 3.7 19.8 - - + -
31A CYS* 3.6 6.5 - - + -
32A CYS* 3.0 41.3 - - - -
33A PHE* 3.7 21.4 - + + +
84A CYS* 5.6 2.0 - - - -
5B LEU 3.9 6.9 + - - -
6B ARG* 3.3 44.4 - - + -
7B PRO* 2.7 30.3 + - + +
8B ARG* 3.1 15.1 - - - +
9B CYS 3.1 17.3 + - - +
36B GLY* 1.3 77.4 - - - -
38B CYS* 1.3 64.3 + - - +
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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