Contacts of the strand formed by residues 18 - 24 (chain B) in PDB entry 2HP4
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 VAL 18 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B TRP* 3.7 25.1 - - + +
17B THR* 1.3 74.4 - - - +
19B GLU* 1.3 61.2 + - - +
20B LEU* 3.7 30.2 - - + +
79B LEU* 3.6 1.7 - - - +
80B THR* 3.4 2.9 - - - -
81B LEU* 2.8 55.2 + - + +
84B PHE* 3.7 41.1 - - + -
92B TYR* 5.7 2.9 - - + -
110B VAL* 3.9 17.3 - - + -
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Residues in contact with GLU 19 (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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7B PRO* 3.3 23.0 - - - +
12B TRP* 4.4 4.3 - - - +
17B THR* 4.0 10.9 + - + +
18B VAL* 1.3 74.2 - - - +
20B LEU* 1.3 61.3 + - - +
21B LYS* 4.8 14.0 - - + +
71B LYS* 4.4 14.0 + - - -
78B VAL* 3.4 31.4 - - + +
79B LEU 3.3 3.6 - - - +
80B THR* 3.1 21.0 + - - +
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Residues in contact with LEU 20 (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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6B SER 3.4 4.9 - - - +
7B PRO* 3.7 10.8 - - + -
12B TRP* 3.9 4.5 - - + -
18B VAL* 3.7 25.4 - - + -
19B GLU* 1.3 77.4 - - - +
21B LYS* 1.3 63.8 + - - +
35B TRP* 3.7 17.2 - - + -
78B VAL* 3.3 6.8 - - - +
79B LEU* 2.8 42.7 + - + +
92B TYR* 3.3 44.2 - - + -
108B VAL* 3.6 26.2 - - + -
110B VAL* 3.9 11.0 - - + -
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Residues in contact with LYS 21 (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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4B ARG 4.5 0.4 - - - -
5B VAL* 3.3 7.7 - - - +
6B SER* 2.8 48.3 + - - +
7B PRO* 6.1 0.2 - - + -
19B GLU* 4.8 15.9 - - + +
20B LEU* 1.3 80.5 - - - +
22B CYS* 1.3 63.1 + - - +
23B GLN 4.2 0.7 - - - -
35B TRP* 3.8 4.6 - - - -
73B LEU* 5.6 6.2 - - - +
76B THR* 3.8 19.1 - - + -
77B PHE 3.4 3.8 - - - -
78B VAL* 4.0 20.9 - - + -
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Residues in contact with CYS 22 (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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3B PHE* 4.7 8.1 - - + -
4B ARG 3.6 3.4 - - - -
5B VAL* 4.1 12.8 - - + -
21B LYS* 1.3 75.7 - - - +
23B GLN* 1.3 65.1 + - - +
24B VAL 3.6 2.1 + - - -
33B ALA* 4.2 5.8 - - - -
35B TRP* 3.7 7.2 - - + -
76B THR* 3.4 2.0 - - - -
77B PHE* 2.9 51.8 + - - -
94B CYS* 2.0 53.4 - - + -
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Residues in contact with GLN 23 (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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3B PHE* 3.0 9.9 - - - +
4B ARG* 2.9 57.3 + - - +
21B LYS 4.2 0.4 - - - -
22B CYS* 1.3 71.3 - - - +
24B VAL* 1.3 64.6 + - - +
25B LEU* 3.6 22.7 + - + +
75B ASP* 3.5 8.7 - - + +
76B THR* 3.7 22.1 + - + +
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Residues in contact with VAL 24 (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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2B GLN 3.9 3.8 - - - +
3B PHE* 3.8 22.4 - - + -
22B CYS* 4.3 1.3 - - - +
23B GLN* 1.3 72.4 - - - +
25B LEU* 1.3 65.4 + - - +
26B LEU* 3.7 33.5 - - + +
29B PRO* 4.4 15.0 - - + -
32B GLY 5.9 0.4 - - - -
33B ALA* 4.4 6.5 - - + +
75B ASP* 2.8 35.3 + - + +
77B PHE* 3.4 33.2 - - + -
96B ALA* 4.8 5.2 - - + -
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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