Contacts of the strand formed by residues 114 - 120 (chain B) in PDB entry 2H1R
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 CYS 114 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16B ALA 4.3 5.8 - - - -
17B ALA* 3.8 33.7 - - - -
87B ASP 3.3 2.0 + - - -
88B VAL* 3.2 13.9 - - + +
89B CYS 3.0 21.5 + - - -
112B PHE* 3.5 10.4 - - - -
113B LYS* 1.3 88.1 - - + +
115B ALA* 1.3 62.1 + - - +
116B VAL* 4.2 11.2 - - - -
172B LYS* 4.4 8.1 - - - -
173B LEU 3.2 12.8 - - - +
174B ILE* 4.2 10.5 - - + -
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Residues in contact with ALA 115 (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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89B CYS* 3.2 20.6 - - + +
105B LEU* 4.6 2.9 - - + -
112B PHE* 3.6 21.1 - - + -
114B CYS* 1.3 74.3 - - - +
116B VAL* 1.3 63.4 + - - +
117B LEU* 4.0 23.1 - - + -
171B VAL 3.8 0.7 - - - +
172B LYS* 3.4 4.0 - - - +
173B LEU* 2.8 39.3 + - + +
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Residues in contact with VAL 116 (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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13B ILE* 4.1 31.9 - - + +
16B ALA* 4.1 14.4 - - + -
17B ALA* 3.9 35.4 - - + +
88B VAL* 5.4 0.4 - - + -
89B CYS 2.8 11.7 + - - +
90B THR* 3.2 9.1 + - - +
91B ALA 3.1 21.7 + - - +
114B CYS* 4.2 7.4 - - - -
115B ALA* 1.3 76.3 - - - +
117B LEU* 1.3 59.4 + - - +
152B VAL* 4.5 0.9 - - + -
170B ILE* 3.4 25.6 - - + -
171B VAL 3.4 4.9 - - - +
172B LYS* 4.4 5.2 - - + -
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Residues in contact with LEU 117 (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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89B CYS* 4.2 9.9 - - - -
91B ALA* 3.6 29.6 - - + +
93B ILE* 4.9 0.2 - - + -
101B LEU* 4.6 3.6 - - + -
102B ILE* 4.3 1.6 - - + -
105B LEU* 3.7 26.7 - - + -
115B ALA* 4.0 18.2 - - + +
116B VAL* 1.3 78.6 - - - +
118B MET* 1.3 60.8 + - - +
119B PHE* 3.5 36.0 + - + -
169B VAL 3.8 0.7 - - - +
170B ILE* 3.3 4.4 - - - -
171B VAL* 2.9 37.3 + - + +
173B LEU* 3.9 27.6 - - + -
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Residues in contact with MET 118 (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 LEU* 3.7 27.6 - - + -
9B ILE* 4.2 0.4 - - + -
13B ILE* 4.2 6.7 - - + -
91B ALA 2.9 17.4 + - - +
92B ASN* 3.6 20.7 - - - +
93B ILE* 3.3 29.6 + - - +
117B LEU* 1.3 71.2 - - - +
119B PHE* 1.3 62.7 + - - +
155B VAL* 3.9 9.0 - - + -
160B PHE* 3.6 30.7 - - - -
168B SER* 3.9 17.7 - - - +
169B VAL 3.5 3.6 - - - +
170B ILE* 3.4 36.3 - - + +
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Residues in contact with PHE 119 (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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93B ILE* 3.6 24.2 - - + -
98B SER* 3.6 29.8 - - - -
101B LEU* 4.4 4.5 - - + -
102B ILE* 3.8 21.1 - - + -
117B LEU* 3.5 32.3 - - + -
118B MET* 1.3 77.0 - - - +
120B GLN* 1.3 68.9 + - - +
123B PHE* 3.7 23.6 - + + -
124B ALA* 4.1 9.4 - - + -
127B MET* 3.5 27.6 - - + -
168B SER* 3.2 7.4 - - - -
169B VAL* 2.8 33.4 + - - +
171B VAL* 3.9 15.0 - - + -
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Residues in contact with GLN 120 (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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93B ILE 5.3 3.4 + - - -
95B TYR* 3.2 34.6 - - + +
98B SER* 5.5 2.2 + - - +
119B PHE* 1.3 73.4 - - - +
121B LYS* 1.3 67.5 + - - +
122B GLU* 3.3 11.3 + - - +
123B PHE* 3.1 13.9 + - + +
124B ALA 3.0 18.7 + - - -
166B VAL* 3.6 35.1 - - + +
167B ASP 3.8 5.8 - - - +
168B SER* 4.1 5.7 + - - +
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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