Contacts of the strand formed by residues 112 - 119 (chain A) in PDB entry 4OQZ
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 THR 112 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A ARG 2.8 13.0 + - - +
87A VAL* 3.4 26.0 - - + +
88A LEU* 2.7 34.7 + - - +
106A VAL* 3.9 3.1 - - - +
107A ALA* 6.1 0.2 - - - -
110A GLY 5.7 0.4 - - - +
111A GLY* 1.4 78.7 - - - +
113A HIS* 1.3 56.6 + - - +
137A PRO* 4.6 16.2 - - + -
140A ALA* 3.4 19.3 - - + +
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Residues in contact with HIS 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A TYR* 4.1 5.5 - + - -
72A MET* 4.9 1.8 - - - +
88A LEU* 3.4 8.0 + - - +
90A ASN* 3.5 32.4 + - + +
99A ALA 3.8 6.3 + - - -
102A ALA* 3.9 23.6 - - + +
103A ALA* 3.5 41.7 + - + +
106A VAL* 3.9 20.4 - - + +
107A ALA* 6.3 0.2 - - - +
111A GLY 4.3 0.2 + - - -
112A THR* 1.3 72.6 - - - +
114A LEU* 1.3 62.5 + - - +
115A THR* 2.9 32.4 + - - -
136A GLY* 4.1 3.6 - - - -
137A PRO* 3.2 23.7 - - - +
162A PRO* 4.8 2.1 - - + +
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Residues in contact with LEU 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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87A VAL* 4.0 24.0 - - + -
88A LEU 2.9 9.5 + - - +
89A VAL* 3.5 21.1 - - + -
90A ASN* 2.9 27.4 + - - -
112A THR 4.1 0.2 + - - -
113A HIS* 1.3 80.7 + - - +
115A THR* 1.3 61.5 + - - +
134A TYR* 4.7 7.2 - - + -
135A SER 3.6 13.2 - - - +
136A GLY 4.4 1.1 - - - -
137A PRO* 3.8 27.4 - - + +
140A ALA* 4.0 7.2 - - + +
141A TYR* 3.9 35.4 - - + +
144A HIS* 5.3 1.6 - - + -
148A LEU* 4.3 14.8 - - + -
157A TYR* 5.2 0.4 - - + -
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Residues in contact with THR 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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69A TYR* 3.3 23.1 - - - +
90A ASN 3.9 2.7 - - - -
99A ALA* 4.0 6.6 - - + +
113A HIS* 2.9 24.0 + - - -
114A LEU* 1.3 72.2 - - - +
116A GLY* 1.3 63.3 + - - +
134A TYR* 3.2 9.8 - - - -
135A SER* 2.8 36.9 + - - -
162A PRO* 2.9 33.6 + - - +
165A ALA* 3.5 12.1 - - + +
166A ALA* 4.1 9.6 - - + +
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Residues in contact with GLY 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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69A TYR* 4.9 1.7 + - - -
90A ASN 3.0 17.9 + - - +
91A LEU* 3.8 35.2 - - - +
92A SER 5.0 2.3 - - - +
93A SER* 5.3 2.6 + - - -
114A LEU 3.9 0.6 + - - -
115A THR* 1.3 78.6 - - - +
117A GLY* 1.3 57.2 - - - -
118A VAL 4.0 2.0 - - - -
132A THR* 4.3 0.2 - - - -
133A PHE 3.2 7.0 - - - -
134A TYR* 3.9 6.9 - - - -
165A ALA* 4.4 3.8 - - - -
166A ALA* 5.7 0.7 + - - -
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Residues in contact with GLY 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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91A LEU 5.6 0.2 - - - -
93A SER* 6.2 1.1 - - - -
116A GLY* 1.3 72.8 - - - -
118A VAL* 1.4 60.4 + - - -
119A LEU* 3.5 2.8 + - - +
132A THR* 3.4 5.3 - - - +
133A PHE* 2.8 42.5 + - - -
165A ALA* 4.2 5.9 - - - +
166A ALA* 5.9 0.2 - - - -
169A TYR* 3.7 30.1 - - - -
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Residues in contact with VAL 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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13A MET* 3.9 13.0 - - + +
17A MET* 4.2 12.6 - - + -
91A LEU* 3.8 42.2 + - + +
116A GLY 4.0 0.4 + - - -
117A GLY* 1.4 67.4 - - - -
119A LEU* 1.3 59.0 + - - +
120A SER* 3.1 14.9 + - - +
125A ILE* 3.8 27.8 - - + -
132A THR* 3.7 21.5 - - + +
151A ILE* 4.3 3.4 - - + -
152A THR* 3.8 10.5 - - + -
169A TYR* 3.4 20.7 + - - -
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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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117A GLY 4.1 3.1 - - - +
118A VAL* 1.3 68.1 - - - +
120A SER* 1.3 60.6 + - - +
121A PRO* 4.9 0.2 - - - -
130A MET* 3.6 15.1 - - - +
131A SER* 2.9 36.2 + - - +
133A PHE* 3.5 35.4 - - + -
169A TYR* 4.0 25.4 - - + -
172A ASN* 3.7 41.1 - - + +
173A MET* 5.6 0.4 - - - -
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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