Contacts of the strand formed by residues 110 - 116 (chain A) in PDB entry 2RAP
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 110 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A GLN 3.4 20.4 - - - +
77A GLY* 3.3 3.1 - - - -
78A PHE* 2.9 26.3 + - - +
106A TYR* 4.7 5.8 - - - +
108A LYS 3.8 5.4 - - - +
109A VAL* 1.3 80.8 - - + +
111A VAL* 1.3 60.8 + - - +
159A ILE* 3.9 3.8 - - + +
162A GLN* 3.6 39.5 - - + +
163A MET* 3.9 21.8 - - + -
166A ALA* 3.7 19.3 - - + -
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Residues in contact with VAL 111 (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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78A PHE* 3.1 28.5 - - + +
80A LEU* 4.2 13.5 - - + -
97A ARG* 4.6 22.4 - - + +
100A ILE* 4.1 16.8 - - + -
109A VAL* 3.1 18.7 + - + +
110A PRO* 1.3 79.3 - - - +
112A ILE* 1.3 67.9 + - - +
137A TRP* 5.0 2.5 - - + +
139A CYS* 3.3 37.6 - - + +
140A PRO* 3.5 6.4 - - - +
159A ILE* 4.6 0.9 - - - -
162A GLN* 4.5 4.5 + - - +
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Residues in contact with ILE 112 (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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78A PHE 3.1 6.9 + - - +
79A ILE* 3.8 4.0 - - + -
80A LEU* 2.9 28.1 + - - +
111A VAL* 1.3 79.2 - - - +
113A LEU* 1.3 70.2 + - - +
114A VAL* 3.9 14.8 + - + +
139A CYS* 4.4 1.8 - - - -
140A PRO* 3.7 28.5 - - + +
142A MET* 4.7 9.4 - - + -
155A LEU* 3.9 20.4 - - + +
158A GLU* 3.6 30.7 - - + +
159A ILE* 3.7 30.3 - - + +
162A GLN* 4.4 3.1 - - + -
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Residues in contact with LEU 113 (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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80A LEU* 3.5 16.2 - - + +
82A TYR* 3.8 20.0 - - + -
93A ILE* 3.7 22.0 - - + -
112A ILE* 1.3 71.8 - - - +
114A VAL* 1.3 60.5 + - - +
130A GLY 3.6 24.5 - - - +
133A LEU* 3.6 18.6 - - + -
134A ALA* 3.6 16.2 - - + +
137A TRP* 3.6 22.7 - - + -
139A CYS* 3.9 11.4 - - - -
140A PRO 2.9 13.6 + - - +
141A PHE* 3.4 10.8 - - + -
142A MET 3.1 22.9 + - - -
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Residues in contact with VAL 114 (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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19A LEU* 4.3 17.3 - - + -
79A ILE* 4.1 12.6 - - + -
80A LEU 2.8 13.4 + - - +
81A VAL* 4.3 7.0 - - + -
82A TYR* 2.8 35.3 + - - +
112A ILE* 4.0 7.6 - - + +
113A LEU* 1.3 78.2 - - - +
115A GLY* 1.3 60.6 + - - +
116A ASN* 4.1 6.7 - - + +
142A MET* 3.3 10.1 - - + +
144A THR* 3.2 29.4 - - + +
155A LEU* 3.5 29.8 - - + -
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Residues in contact with GLY 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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82A TYR* 3.4 33.4 - - - -
84A LEU* 3.7 8.5 - - - +
114A VAL* 1.3 71.9 - - - +
116A ASN* 1.3 62.8 + - - -
141A PHE* 4.2 1.6 - - - -
142A MET 2.8 12.6 + - - -
143A GLU* 3.1 11.4 - - - +
144A THR 2.9 22.2 + - - +
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Residues in contact with ASN 116 (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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14A VAL 2.8 28.0 + - - +
15A GLY* 3.4 10.7 + - - -
19A LEU* 3.7 11.4 - - + +
81A VAL* 4.0 11.0 - - + -
82A TYR 2.8 12.4 + - - +
83A SER* 3.6 0.5 - - - -
84A LEU* 3.0 28.1 + - - +
114A VAL* 3.6 1.2 + - + -
115A GLY* 1.3 74.5 - - - +
117A LYS* 1.3 73.8 + - - +
144A THR* 3.3 17.8 + - - +
146A ALA 3.2 13.0 + - - -
180A GTP 3.2 35.2 + - - +
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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