Contacts of the strand formed by residues 112 - 120 (chain A) in PDB entry 2W8B
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 TYR 112 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A TRP* 3.8 17.9 - + - -
51A PRO* 3.5 28.3 - - + +
104A VAL* 4.2 8.7 - - + -
105A THR 3.4 15.9 - - - +
106A PRO* 3.9 10.5 - - + -
107A ASN* 3.5 7.7 + - - +
110A GLY 3.7 7.4 - - - -
111A SER* 1.3 77.2 - - - +
113A ASN* 1.3 62.9 + - - +
114A VAL 4.1 0.2 - - - -
134A TYR 3.5 0.3 - - - +
135A LYS* 3.2 4.7 - - - -
136A VAL* 2.8 40.3 + - + +
138A LYS* 3.2 62.8 + - + +
141A LEU* 4.0 22.0 - - + -
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Residues in contact with ASN 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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103A GLN 3.8 1.1 - - - +
104A VAL* 3.3 7.3 - - - +
105A THR* 2.9 50.3 + - - +
106A PRO 4.4 1.0 + - - -
107A ASN* 2.5 40.1 + - - +
112A TYR* 1.3 74.2 - - - +
114A VAL* 1.3 62.8 + - - +
115A ALA* 4.1 1.3 - - + -
133A SER* 4.3 12.5 + - - +
134A TYR 3.3 4.8 - - - +
135A LYS* 4.0 12.6 + - - +
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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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42A PHE* 4.5 6.1 - - + -
54A ILE* 3.9 36.6 - - + -
103A GLN 3.7 2.7 - - - -
104A VAL* 4.3 10.8 - - + -
112A TYR* 4.9 0.2 - - + -
113A ASN* 1.3 74.4 - - - +
115A ALA* 1.3 62.1 + - - +
133A SER* 3.3 1.3 - - - -
134A TYR* 2.7 51.4 + - + +
136A VAL* 4.4 4.3 - - + -
141A LEU* 3.8 28.5 - - + -
144A ALA* 4.0 26.7 - - + +
148A ALA* 5.6 2.5 - - + -
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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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42A PHE* 3.4 5.9 - - - -
102A GLY* 3.0 3.0 - - - -
103A GLN* 2.9 51.8 + - + +
113A ASN* 4.1 1.5 - - + -
114A VAL* 1.3 75.9 - - - +
116A TYR* 1.3 61.0 + - - +
117A GLN* 4.1 5.6 - - - +
132A ASN 3.2 13.9 - - - +
133A SER* 3.7 15.3 - - - +
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Residues in contact with TYR 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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42A PHE* 3.8 17.5 - - + -
100A VAL* 4.4 4.7 - - + -
101A VAL 3.2 11.9 - - - +
102A GLY* 3.9 0.2 - - - -
115A ALA* 1.3 74.4 - - - +
117A GLN* 1.4 82.4 + - - +
118A LEU* 3.9 3.6 - - + -
130A ALA* 3.4 33.5 - - + +
131A GLN* 3.4 7.5 + - - -
132A ASN* 3.1 37.8 + - + +
134A TYR* 3.4 25.4 - + - -
148A ALA* 3.6 25.6 - - + -
151A GLU* 2.7 32.8 + - + +
152A VAL* 3.8 25.1 - - + -
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Residues in contact with GLN 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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82A SER* 4.4 0.5 - - - -
83A ALA* 4.1 21.3 + - + -
99A VAL 3.7 0.5 - - - +
100A VAL* 3.6 2.1 - - - -
101A VAL* 2.9 50.5 + - + +
103A GLN* 3.1 40.1 + - - -
115A ALA* 4.1 4.9 - - - +
116A TYR* 1.4 94.0 + - - +
118A LEU* 1.3 60.8 + - - +
119A VAL* 4.0 1.5 + - + -
128A VAL* 4.2 11.4 - - + -
130A ALA 3.5 7.4 - - - +
131A GLN* 3.8 21.9 + - + +
132A ASN 4.9 0.6 + - - -
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Residues in contact with LEU 118 (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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98A ALA* 3.8 24.5 - - + -
99A VAL 3.6 13.7 - - - +
100A VAL* 4.1 14.8 - - + +
116A TYR* 3.9 11.2 - - + -
117A GLN* 1.3 72.4 - - - +
119A VAL* 1.3 57.9 + - - +
128A VAL* 3.5 4.5 - - - -
129A LEU* 2.8 41.2 + - + +
130A ALA* 2.8 20.6 + - + +
152A VAL* 4.2 15.0 - - + +
155A LYS* 3.8 25.1 - - + -
156A LEU* 3.7 35.0 - - + -
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Residues in contact with VAL 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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83A ALA* 3.7 35.0 - - + +
86A VAL* 4.1 31.6 - - + -
98A ALA* 3.4 3.8 - - - -
99A VAL* 2.9 36.0 + - + +
101A VAL* 4.5 2.7 - - + -
117A GLN* 4.2 12.6 - - + +
118A LEU* 1.3 77.6 - - - +
120A ASP* 1.3 72.0 + - - +
121A THR* 3.4 1.6 + - - +
126A GLY* 3.8 20.6 - - - +
127A THR 3.4 9.0 - - - +
128A VAL* 4.5 2.7 - - + -
129A LEU* 4.5 2.2 - - - -
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Residues in contact with ASP 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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97A ASP 3.7 8.3 - - - -
119A VAL* 1.3 71.3 - - - +
121A THR* 1.3 61.7 + - - +
122A GLY* 2.8 28.9 + - - -
123A GLY 3.4 3.5 + - - -
124A ALA* 3.0 45.5 + - - +
125A PRO* 3.4 0.7 - - - +
126A GLY* 2.8 29.5 + - - -
127A THR* 2.8 15.3 + - - +
129A LEU* 3.7 32.3 - - + +
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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