Contacts of the strand formed by residues 114 - 120 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A ALA 4.4 4.0 - - - -
17A ALA* 3.7 35.0 - - - -
87A ASP 3.4 1.4 + - - -
88A VAL* 3.3 15.0 - - - +
89A CYS 3.0 21.1 + - - -
112A PHE* 3.6 9.2 - - - -
113A LYS* 1.3 86.1 - - + +
115A ALA* 1.3 63.9 + - - +
116A VAL* 4.1 11.4 - - - -
172A LYS* 4.5 2.0 - - - -
173A LEU 3.3 6.1 - - - +
174A ILE* 3.4 25.4 - - + -
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Residues in contact with ALA 115 (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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89A CYS* 3.2 20.4 - - + +
105A LEU* 4.7 2.7 - - + -
112A PHE* 3.8 20.6 - - + -
114A CYS* 1.3 75.5 - - - +
116A VAL* 1.3 63.9 + - - +
117A LEU* 4.0 23.7 + - + -
171A VAL 3.8 0.7 - - - +
172A LYS* 3.3 5.0 - - - +
173A LEU* 2.9 37.0 + - + +
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Residues in contact with VAL 116 (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 ILE* 4.2 20.6 - - + +
16A ALA* 4.1 18.6 - - + +
17A ALA* 3.7 38.1 - - + +
89A CYS 2.8 11.9 + - - +
90A THR* 3.2 14.1 + - - +
91A ALA 3.2 22.2 + - - +
114A CYS* 4.1 7.9 - - - -
115A ALA* 1.3 75.7 - - - +
117A LEU* 1.3 59.8 + - - +
152A VAL* 4.4 1.3 - - + -
170A ILE* 3.4 26.5 - - + -
171A VAL 3.4 4.7 - - - +
172A LYS* 4.5 4.5 - - + -
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Residues in contact with LEU 117 (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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89A CYS* 4.2 10.8 - - - -
91A ALA* 3.6 28.3 - - + +
93A ILE* 5.0 1.1 - - + -
101A LEU* 4.2 9.4 - - + -
102A ILE* 4.3 1.8 - - + -
105A LEU* 3.6 24.9 - - + -
115A ALA* 4.0 17.9 - - + +
116A VAL* 1.3 79.7 - - - +
118A MET* 1.3 60.9 + - - +
119A PHE* 3.5 32.9 + - + -
169A VAL 3.7 0.9 - - - +
170A ILE* 3.3 4.2 - - - -
171A VAL* 2.8 43.9 + - + +
173A LEU* 3.8 24.7 - - + -
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Residues in contact with MET 118 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A LEU* 4.5 18.8 - - + -
13A ILE* 5.8 3.1 - - + -
91A ALA 2.9 15.5 + - - +
92A ASN* 3.1 44.1 - - + +
93A ILE* 3.1 29.3 + - - +
117A LEU* 1.3 72.6 - - - +
119A PHE* 1.3 65.5 + - - +
155A VAL* 4.0 21.8 - - - -
160A PHE* 3.6 30.3 - - + -
168A SER* 3.8 16.4 - - - +
169A VAL 3.4 6.1 - - - +
170A ILE* 3.7 17.0 - - + -
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Residues in contact with PHE 119 (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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93A ILE* 3.9 23.8 - - + -
98A SER* 3.7 23.3 - - - -
101A LEU* 4.2 5.4 - - + -
102A ILE* 3.7 22.4 - - + -
117A LEU* 3.5 33.0 - - + -
118A MET* 1.3 77.8 - - - +
120A GLN* 1.3 72.7 + - - +
121A LYS* 4.2 0.2 - - - -
123A PHE* 3.6 30.3 - + + -
124A ALA* 4.2 9.9 - - + +
127A MET* 3.6 24.7 - - + -
168A SER* 3.3 6.5 - - - -
169A VAL* 2.9 29.2 + - - +
171A VAL* 3.9 15.7 - - + -
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Residues in contact with GLN 120 (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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93A ILE 4.9 4.9 + - - -
95A TYR* 3.3 57.7 - - + +
98A SER* 5.5 0.8 + - - -
119A PHE* 1.3 75.9 - - - +
121A LYS* 1.3 67.1 + - - +
122A GLU* 2.6 29.3 + - - +
123A PHE* 3.1 12.2 + - - +
124A ALA 3.2 7.3 + - - -
166A VAL* 3.7 34.7 - - + +
167A ASP 3.7 11.0 - - - +
168A SER* 4.0 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