Contacts of the strand formed by residues 101 - 109 (chain A) in PDB entry 3WJG
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 VAL 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A ILE 3.3 11.7 - - - +
95A ALA* 4.3 12.6 - - + -
96A CYS* 5.4 0.2 - - - -
99A GLY 5.2 1.8 - - - +
100A LEU* 1.3 78.8 - - - +
102A GLU* 1.4 66.9 + - - +
103A VAL* 6.2 0.4 - - + -
121A LEU* 4.3 10.8 - - + -
122A VAL* 3.4 5.9 - - - +
123A GLY* 2.8 49.3 + - - +
124A ASN* 5.7 1.3 - - + -
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Residues in contact with GLU 102 (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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92A VAL 3.9 0.3 - - - +
93A VAL* 3.4 5.9 - - - +
94A ILE* 2.8 39.6 + - + +
96A CYS* 4.2 11.3 - - - -
100A LEU* 5.3 3.1 - - + +
101A VAL* 1.4 81.8 - - - +
103A VAL* 1.4 64.5 + - - +
104A GLN* 2.9 33.1 + - + +
121A LEU* 3.5 8.3 - - - +
122A VAL* 4.9 1.8 - - + -
131A ILE* 3.6 32.8 - - + +
133A ARG* 2.8 45.7 + - - -
148A TRP* 5.4 0.9 + - - -
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Residues in contact with VAL 103 (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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91A GLU* 5.4 4.3 - - + +
92A VAL 3.7 3.4 - - - +
93A VAL* 4.4 19.3 - - + -
101A VAL* 6.2 0.4 - - + -
102A GLU* 1.4 74.6 - - - +
104A GLN* 1.3 58.8 - - - +
105A LYS* 3.9 27.4 - - - -
119A SER* 3.2 5.2 - - - -
120A ASP* 2.8 36.7 + - + +
121A LEU* 2.9 40.7 + - + +
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Residues in contact with GLN 104 (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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91A GLU* 3.2 5.0 - - - +
92A VAL* 2.8 55.8 + - + +
94A ILE* 5.0 1.6 - - + -
102A GLU* 2.9 34.0 + - + +
103A VAL* 1.3 73.8 - - - +
105A LYS* 1.3 66.2 + - - +
117A LEU* 3.3 18.4 - - + +
118A LYS* 2.8 32.9 + - - -
119A SER* 3.7 7.9 - - - -
131A ILE* 3.0 30.7 + - - +
133A ARG* 4.1 13.3 - - - +
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Residues in contact with LYS 105 (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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90A ILE 3.5 7.9 - - - +
91A GLU* 4.0 23.5 + - + -
103A VAL* 3.9 16.6 - - + -
104A GLN* 1.3 80.3 - - - +
106A GLY* 1.3 58.2 + - - +
117A LEU* 4.0 5.4 - - - -
118A LYS* 2.9 34.3 + - - +
120A ASP* 3.3 39.3 + - - +
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Residues in contact with GLY 106 (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 SER* 3.4 6.1 - - - -
90A ILE* 2.9 30.8 + - - +
105A LYS* 1.3 75.7 - - - +
107A THR* 1.3 70.9 + - - +
116A LYS 3.2 12.6 - - - -
117A LEU* 3.9 2.1 - - - +
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Residues in contact with THR 107 (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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88A GLY 3.1 13.0 - - - +
89A SER* 4.7 4.3 - - - -
90A ILE* 3.6 7.9 - - - +
106A GLY* 1.3 79.9 - - - +
108A TYR* 1.3 64.2 + - - +
115A ILE* 3.5 1.7 - - - -
116A LYS* 2.9 41.2 + - - +
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Residues in contact with TYR 108 (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 PHE 4.7 1.7 + - - -
22A PRO* 3.7 28.7 - - + +
23A LEU* 3.9 18.8 - - + -
84A PRO* 3.9 20.9 - - + -
85A ARG 3.1 30.8 + - - -
86A PRO* 4.1 7.4 + - - +
88A GLY* 2.9 35.5 + - - +
89A SER 3.7 10.3 - - - -
90A ILE* 4.3 6.1 - - + -
107A THR* 1.3 78.8 - - - +
109A ASN* 1.3 62.5 + - - +
110A VAL* 3.7 28.7 + - + -
114A SER 3.2 12.8 - - - +
115A ILE* 4.0 16.2 - - + -
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Residues in contact with ASN 109 (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 TYR* 1.3 74.7 - - - +
110A VAL* 1.3 59.2 + - - +
111A ASP* 3.0 12.6 + - - +
112A GLU* 3.0 42.0 + - - +
113A GLN* 2.9 26.0 + - - -
114A SER* 2.9 29.7 + - - +
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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