Contacts of the strand formed by residues 158 - 163 (chain A) in PDB entry 2HR9
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 PRO 158 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A VAL 3.9 0.2 - - - +
33A GLY* 2.8 28.0 + - - -
34A LYS* 3.7 29.8 - - - +
35A MET* 3.7 20.0 - - + +
70A VAL* 3.6 26.8 - - + +
72A ILE* 5.0 0.7 - - - +
149A LEU* 4.2 8.5 - - + +
150A ASP 3.4 6.7 - - - +
151A TYR* 3.6 20.2 - - + -
156A VAL* 2.9 8.7 - - + +
157A THR* 1.3 82.8 - - - +
159A TYR* 1.3 60.2 + - - +
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Residues in contact with TYR 159 (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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30A GLU* 2.8 50.9 + - + +
31A VAL 3.1 16.8 - - - +
32A GLU* 4.1 15.9 - - + -
132A TYR* 3.9 11.3 + - - -
148A LEU 3.5 0.9 - - - +
149A LEU* 3.3 1.4 - - - -
150A ASP* 2.6 100.3 + - + +
151A TYR 3.3 21.9 + - - -
152A ARG* 3.8 13.9 - - + -
157A THR 4.1 1.6 - - - +
158A PRO* 1.3 75.2 - - - +
160A MET* 1.3 60.5 + - - +
161A ILE* 4.2 13.0 - - + +
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Residues in contact with MET 160 (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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29A LEU 3.2 2.3 - - - +
30A GLU* 3.2 5.7 - - - -
31A VAL 2.8 33.4 + - - +
72A ILE* 3.9 13.7 - - + -
78A LEU* 3.1 36.8 - - + -
135A PHE* 3.7 14.4 - - - -
147A ALA* 3.1 22.2 - - + -
148A LEU 3.2 3.6 - - - +
149A LEU* 3.5 34.5 - - + -
159A TYR* 1.3 73.0 - - - +
161A ILE* 1.3 63.1 + - - +
162A PHE* 3.1 39.9 + - + -
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Residues in contact with ILE 161 (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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23A ILE* 4.0 10.5 - - + -
28A CYS* 4.0 27.4 - - + -
29A LEU 3.6 3.1 - - - +
30A GLU* 4.4 8.5 - - + +
121A GLN* 5.0 5.6 - - + -
125A ILE* 4.2 4.0 - - + -
132A TYR* 3.4 38.4 - - + +
146A VAL 3.5 11.1 - - - +
147A ALA* 3.5 3.3 - - - -
148A LEU* 2.6 56.2 + - + +
159A TYR* 4.2 19.1 - - + -
160A MET* 1.3 72.9 - - - +
162A PHE* 1.3 62.8 + - - +
163A PHE* 4.6 3.8 - - + -
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Residues in contact with PHE 162 (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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13A MET* 3.4 44.4 - - + -
14A PHE* 3.1 48.7 - + + -
28A CYS* 3.0 6.6 - - - +
29A LEU* 2.6 46.2 + - + +
31A VAL* 3.3 24.0 - - + -
72A ILE* 5.6 0.9 - - + -
78A LEU* 4.9 0.4 - - + -
145A MET* 3.8 10.1 - - - -
147A ALA* 3.7 13.9 - - + -
160A MET* 3.1 40.2 - - + -
161A ILE* 1.3 75.3 - - - +
163A PHE* 1.3 63.1 + - - +
167A LEU* 4.4 4.5 - - + -
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Residues in contact with PHE 163 (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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27A LEU* 4.1 3.8 - - + +
28A CYS* 3.7 24.0 - - - -
29A LEU* 4.2 0.9 - - - -
88A TYR* 5.4 2.9 - - - -
95A TYR* 2.7 52.3 - + - -
99A ILE* 4.7 0.2 - - + -
114A PHE* 4.6 13.7 - + + -
121A GLN* 5.5 4.9 - - + -
122A ILE* 6.5 0.2 - - + -
125A ILE* 5.7 2.9 - - + -
145A MET* 3.2 25.1 - - + +
146A VAL* 3.5 31.4 - - + -
148A LEU* 4.6 21.5 - - + -
161A ILE* 4.6 3.4 - - + -
162A PHE* 1.3 75.7 - - - +
164A LYS* 1.3 63.6 + - - +
166A GLY* 4.1 10.1 - - - +
167A LEU* 2.9 28.9 + - - +
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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