Contacts of the strand formed by residues 118 - 123 (chain A) in PDB entry 2XCV
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 LEU 118 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A LEU* 4.1 23.1 - - + -
111A LYS 3.8 3.4 - - - -
112A VAL* 4.6 6.1 - - + -
116A GLY 4.1 3.1 - - - +
117A ASN* 1.3 69.3 - - - +
119A LEU* 1.3 66.7 + - - +
120A VAL 4.8 5.6 - - - +
121A CYS* 4.2 11.7 - - + -
133A THR* 4.5 9.9 - - + -
137A TYR* 3.8 32.5 - - + -
140A LYS* 3.1 30.4 + - + +
141A PHE* 3.7 21.8 - - - +
142A ILE* 3.8 24.9 - - + -
446A ARG* 4.2 9.2 + - - -
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Residues in contact with LEU 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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111A LYS* 2.6 21.0 + - + +
112A VAL 4.0 17.3 - - - +
113A ASP* 3.9 13.9 - - + +
117A ASN 4.1 4.7 - - - +
118A LEU* 1.3 77.0 - - - +
120A VAL* 1.3 66.9 + - + +
443A SER* 4.0 27.3 + - - +
446A ARG* 3.8 66.6 - - + +
447A GLN 4.1 5.8 - - - +
448A THR* 4.1 11.9 - - + -
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Residues in contact with VAL 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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109A LEU 4.5 0.2 - - - -
110A LEU* 3.3 7.3 - - - +
111A LYS* 3.0 54.7 + - + +
118A LEU* 4.8 3.1 - - - +
119A LEU* 1.3 87.6 + - + +
121A CYS* 1.3 65.5 + - - +
127A PHE* 3.7 35.7 - - + -
431A ASP* 5.5 2.5 - - - +
436A MET 5.2 1.8 - - - +
437A MET* 4.0 17.7 - - + +
443A SER* 4.5 9.2 - - - +
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Residues in contact with CYS 121 (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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108A ASN* 3.9 23.1 - - - -
109A LEU 3.6 3.4 - - - -
110A LEU* 3.5 23.1 - - + -
118A LEU* 4.2 6.3 - - + -
120A VAL* 1.3 79.2 - - - +
122A ALA* 1.3 56.4 + - - +
127A PHE* 3.6 4.7 - - - +
128A ILE* 2.8 54.0 + - - +
133A THR* 4.1 22.4 - - + -
136A GLN* 5.5 0.4 - - - -
137A TYR* 4.1 9.6 - - - -
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Residues in contact with ALA 122 (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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95A PHE* 4.9 0.4 - - + -
107A GLY 4.5 0.2 - - - +
108A ASN* 3.4 5.5 - - - -
109A LEU* 3.0 35.8 + - + +
120A VAL* 4.3 0.4 - - - +
121A CYS* 1.3 74.1 - - - +
123A HIS* 1.3 58.2 + - - +
124A GLY 4.0 14.7 + - - +
126A ASN 3.4 7.2 - - - +
127A PHE* 3.9 16.6 - - + -
128A ILE* 4.7 0.2 - - - -
437A MET* 3.2 33.2 - - + -
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Residues in contact with HIS 123 (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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106A TYR 3.4 15.6 + - - -
107A GLY 3.3 8.3 + - - -
108A ASN* 3.0 22.9 + - - +
122A ALA* 1.3 70.3 - - - +
124A GLY* 1.3 62.4 + - - +
125A PHE 3.2 0.3 + - - -
126A ASN* 2.9 31.9 + - + +
128A ILE* 4.1 18.5 - - + +
136A GLN* 5.8 1.7 + - - -
169A VAL* 3.5 17.4 - - + +
173A THR* 4.1 15.6 + - + +
194A TYR* 3.1 31.3 + + - -
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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