Contacts of the strand formed by residues 11 - 15 (chain B) in PDB entry 2D4H
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 MET 11 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7B MET* 3.7 23.8 - - + -
9B GLY 4.8 0.2 - - - +
10B PRO* 1.3 77.4 - - - +
12B CYS* 1.3 62.7 + - - +
24B ASN* 4.0 16.6 - - - -
26B GLU* 4.0 13.2 - - + +
27B ALA* 3.6 29.2 - - + +
30B ILE* 3.5 32.3 - - + -
79B TRP* 3.6 4.9 - - - -
80B MET* 2.5 51.3 + - + +
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Residues in contact with CYS 12 (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 MET* 1.3 71.4 - - - +
13B LEU* 1.3 60.5 + - - +
14B ILE 4.0 5.4 - - - -
15B GLU* 3.4 49.6 - - - +
24B ASN* 2.9 37.2 + - - +
27B ALA* 3.4 3.3 - - - +
76B LYS 5.2 2.9 - - - -
78B ILE 3.9 3.4 - - - -
79B TRP* 3.4 39.4 - - + -
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Residues in contact with LEU 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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11B MET 3.1 2.4 + - - -
12B CYS* 1.3 73.4 - - - +
14B ILE* 1.3 66.0 + - + +
15B GLU 4.1 0.2 - - - -
23B ALA* 3.5 5.0 - - - +
24B ASN* 3.0 24.9 + - - +
27B ALA* 3.7 12.1 - - + -
28B LEU* 4.1 22.2 - - + -
31B LEU* 4.4 12.6 - - + -
78B ILE* 2.8 22.7 + - + +
80B MET* 3.7 32.3 - - + -
94B VAL* 6.0 0.2 - - + -
96B LEU* 3.7 27.8 - - + -
122B LEU* 4.6 5.8 - - + -
293B LEU* 5.4 3.8 - - + -
297B VAL* 4.2 19.1 - - + -
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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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12B CYS* 4.0 5.2 - - - -
13B LEU* 1.3 83.3 - - + +
15B GLU* 1.3 71.0 + - - +
21B LEU* 4.2 25.4 - - + -
22B MET 3.9 9.4 - - - +
23B ALA* 4.2 3.8 - - + +
76B LYS 3.9 0.2 - - - +
77B GLY* 3.3 5.2 - - - -
78B ILE* 3.0 50.0 + - + +
115B ILE* 4.7 9.6 - - + -
118B LEU* 3.7 30.7 - - + -
122B LEU* 4.4 6.1 - - + -
297B VAL* 4.1 15.5 - - + -
301B VAL* 3.8 18.6 - - + -
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Residues in contact with GLU 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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12B CYS* 3.4 26.3 - - - +
13B LEU 4.1 0.4 - - - -
14B ILE* 1.3 72.4 - - - +
16B ASN* 1.3 59.3 + - - +
17B THR* 3.2 26.3 + - - +
20B ARG 3.6 0.7 - - - +
21B LEU* 3.6 1.9 - - - -
22B MET* 2.8 61.4 + - + +
24B ASN* 4.7 13.6 - - - +
76B LYS 3.8 5.4 - - - +
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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