Contacts of the strand formed by residues 55 - 59 (chain B) in PDB entry 1HRP
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 55 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A SER* 5.7 0.5 - - - -
57A SER* 5.4 0.2 - - - -
59A CYS* 4.4 7.3 - - - -
38B CYS* 4.5 4.6 - - + +
39B PRO* 3.4 26.7 - - + +
40B THR* 3.6 17.1 - - + +
53B PRO 5.1 3.1 - - - +
54B GLN* 1.3 76.3 - - - +
56B VAL* 1.3 66.2 + - - +
90B CYS* 4.0 19.7 - - - +
91B ALA* 3.5 31.0 - - - +
92B LEU* 4.0 6.7 - - + +
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Residues in contact with VAL 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A SER* 4.2 4.9 - - - -
55A SER* 3.5 22.7 - - - +
57A SER* 3.4 30.7 - - - +
87A CYS* 5.4 2.9 - - - -
88A TYR* 4.1 10.1 - - + +
38B CYS* 4.7 5.4 - - - -
54B GLN 4.7 0.4 - - - +
55B VAL* 1.3 78.4 - - - +
57B CYS* 1.3 69.9 + - - +
58B ASN* 3.3 14.0 + - + +
90B CYS* 3.8 1.2 - - - -
91B ALA 2.9 33.8 + - - +
93B CYS* 3.8 30.7 - - + +
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Residues in contact with CYS 57 (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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34A SER* 2.8 34.0 + - - +
35A ARG 4.3 2.5 + - - +
36A ALA* 3.6 19.6 + - - +
55A SER* 4.5 0.2 + - - -
9B CYS* 2.0 57.0 - - + -
34B CYS* 3.8 5.4 - - - -
35B ALA* 3.6 30.3 - - - -
36B GLY 4.3 2.7 - - - +
38B CYS* 4.2 7.0 - - - -
56B VAL* 1.3 76.8 - - - +
58B ASN* 1.3 58.4 + - - +
89B GLN 4.0 0.7 - - - -
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Residues in contact with ASN 58 (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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36A ALA* 4.0 10.7 - - - +
53A VAL* 4.7 4.9 - - - +
55A SER* 5.8 0.7 - - - -
9B CYS* 3.5 2.0 - - - -
34B CYS* 4.0 6.5 - - - -
56B VAL* 3.8 18.6 - - + +
57B CYS* 1.3 75.7 - - - +
59B TYR* 1.3 94.0 + - - +
88B CYS* 3.5 2.1 - - - -
89B GLN* 2.7 47.8 + - + +
91B ALA* 4.6 7.3 - - + +
92B LEU 3.9 18.2 + - - -
93B CYS* 4.6 2.8 - - - +
94B ARG 5.3 0.6 - - - +
98B THR* 4.4 17.3 + - - +
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Residues in contact with TYR 59 (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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36A ALA* 3.4 22.1 + - + -
37A TYR* 3.3 6.0 - - - -
38A PRO* 3.0 27.7 - - - +
53A VAL* 3.7 30.7 - - + -
32B THR 4.5 2.2 + - - -
33B ILE* 4.1 8.0 - - - +
34B CYS* 3.7 9.5 - - - -
58B ASN* 1.3 92.4 + - - +
60B ARG* 1.3 63.8 + - - +
61B ASP 5.4 0.2 - - - -
62B VAL* 4.8 11.0 - - + -
83B ALA* 4.9 4.6 + - + +
84B VAL 4.8 2.7 - - - -
85B ALA* 3.7 38.8 - - + -
89B GLN* 4.3 7.1 - - - +
1D NAG 3.9 30.4 - - + +
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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