Contacts of the strand formed by residues 15 - 21 (chain A) in PDB entry 2BQY
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 LEU 15 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A SER 3.4 13.5 - - - +
10A HIS* 4.2 6.3 - - - +
11A ASP 2.6 17.3 + - - +
12A ALA* 3.2 26.2 - - - +
14A SER* 1.3 74.8 - - - +
16A CYS* 1.3 55.4 + - - +
17A VAL* 3.8 23.1 - - + -
57A VAL* 4.1 22.0 - - + -
85A LYS* 4.4 1.1 - - - -
86A ALA* 2.7 53.9 + - + +
87A ARG* 3.8 1.8 - - - -
88A LEU* 4.1 16.2 - - + +
104A LEU* 5.9 0.2 - - + -
106A ALA* 5.3 1.3 - - + -
164A LEU* 4.4 15.7 - - + -
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Residues in contact with CYS 16 (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 GLU* 4.4 13.2 - - + -
8A VAL* 4.4 3.1 - - - -
9A SER* 3.5 26.2 + - - +
14A SER 3.9 1.0 + - - -
15A LEU* 1.3 74.8 - - - +
17A VAL* 1.3 61.8 + - - +
57A VAL* 3.8 10.9 - - - +
58A PRO* 3.4 37.4 - - - +
83A VAL* 3.8 23.6 - - + -
84A VAL 3.5 5.8 - - - +
85A LYS* 4.1 13.5 - - + +
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Residues in contact with VAL 17 (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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15A LEU* 3.8 20.6 - - + -
16A CYS* 1.3 79.1 - - - +
18A VAL* 1.3 66.0 + - - +
19A ILE* 3.5 3.1 + - + -
55A GLY* 3.8 12.6 - - - -
56A PHE 3.6 23.8 - - - +
57A VAL* 4.5 1.8 - - + -
70A ALA* 4.2 17.3 - - + +
72A VAL* 3.8 32.1 - - + -
83A VAL* 3.4 4.4 - - - -
84A VAL* 2.9 39.2 + - + +
86A ALA* 4.2 7.0 - - + -
106A ALA* 5.1 1.8 - - + -
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Residues in contact with VAL 18 (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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4A GLU* 5.9 1.6 - - - +
5A LYS* 4.7 9.9 - - + +
7A GLU* 5.2 2.2 - - - +
17A VAL* 1.3 73.6 - - - +
19A ILE* 1.3 65.3 + - - +
20A GLU* 3.3 5.3 + - + +
31A LEU* 3.9 18.8 - - + -
55A GLY* 3.0 22.2 - - - -
56A PHE* 2.8 49.9 + - + +
58A PRO* 4.0 20.0 - - + -
81A GLY* 5.0 6.7 - - - +
82A SER 3.8 8.3 - - - +
83A VAL* 4.5 19.7 - - + +
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Residues in contact with ILE 19 (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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17A VAL* 4.4 3.1 - - + -
18A VAL* 1.3 73.4 - - - +
20A GLU* 1.3 58.6 + - - +
21A ILE 3.3 25.8 - - - +
38A LEU* 5.1 0.2 - - - +
53A ASN* 3.9 22.0 - - + -
54A TYR 3.6 7.2 - - - +
55A GLY* 4.1 0.2 - - - -
72A VAL* 4.0 13.2 - - + -
78A PHE* 3.8 29.8 - - + +
79A GLN 3.9 9.4 - - - +
80A ALA* 4.1 2.0 - - - -
81A GLY* 2.7 33.3 + - - -
82A SER* 2.9 25.2 + - - +
84A VAL* 3.9 27.1 - - + -
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Residues in contact with GLU 20 (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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18A VAL* 3.8 11.7 - - + +
19A ILE* 1.3 75.7 - - - +
21A ILE* 1.3 64.2 + - + +
28A LYS* 5.5 1.9 + - - -
29A TYR* 2.9 51.1 - - - +
30A GLU* 3.3 14.4 - - - +
31A LEU* 2.7 35.0 + - + +
38A LEU* 4.8 4.0 - - + -
54A TYR* 2.7 18.7 + - + +
55A GLY* 4.3 8.5 - - - -
56A PHE* 3.3 33.3 - - + +
69A ASP* 4.8 2.1 - - - +
80A ALA* 3.5 7.7 - - - +
81A GLY 4.7 0.2 - - - +
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Residues in contact with ILE 21 (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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19A ILE* 3.3 11.2 - - - +
20A GLU* 1.3 86.8 - - - +
22A SER* 1.3 68.5 + - - +
25A SER* 4.5 2.0 - - - -
27A ILE 3.6 17.5 - - - +
28A LYS* 3.7 22.7 - - + +
29A TYR* 3.8 15.0 - - - +
50A TYR* 3.6 50.3 - - + +
53A ASN* 3.5 0.9 - - - -
54A TYR* 2.8 62.2 + - + -
80A ALA* 4.7 1.1 - - - -
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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