Contacts of the strand formed by residues 107 - 113 (chain A) in PDB entry 4OIB
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 PHE 107 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A LEU* 4.7 2.5 - - + -
98A PRO* 3.9 29.4 - - + -
101A GLN* 3.4 29.2 - - + +
105A GLU 4.2 6.7 - - - -
106A ASN* 1.3 72.6 - - - +
108A THR* 1.3 62.5 + - - +
109A LEU* 3.4 33.0 - - + -
153A THR* 4.7 1.8 - - - -
154A VAL* 2.9 66.7 + - + +
156A ALA* 4.6 9.9 - - + -
165A PHE* 4.4 7.2 - + - -
190A LEU* 3.8 30.7 - - + -
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Residues in contact with THR 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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98A PRO* 5.6 2.1 - - - +
107A PHE* 1.3 79.6 - - - +
109A LEU* 1.3 78.4 + - - +
110A SER* 4.3 4.3 + - - +
151A THR* 4.5 7.8 + - - -
152A ALA 3.7 13.0 + - - -
153A THR* 4.2 16.9 - - - +
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Residues in contact with LEU 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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94A LEU* 5.6 5.8 - - + -
95A MET* 5.9 0.9 - - - +
97A LEU* 3.9 21.8 - - + -
98A PRO* 5.8 0.4 - - + -
107A PHE* 3.4 31.0 - - + -
108A THR* 1.3 84.3 + - - +
110A SER* 1.3 59.7 + - - +
126A LEU* 3.4 20.3 - - + +
133A LEU* 5.4 4.5 - - + -
150A LEU 3.4 3.1 - - - +
151A THR* 3.1 4.0 - - - -
152A ALA* 2.9 39.7 + - + +
154A VAL* 3.8 23.1 - - + -
165A PHE* 4.2 24.9 - - + -
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Residues in contact with SER 110 (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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94A LEU* 3.3 17.5 - - - +
95A MET* 3.3 37.2 + - - +
108A THR* 4.2 4.8 + - - +
109A LEU* 1.3 73.7 - - - +
111A CYS* 1.3 63.4 + - - +
112A ARG* 4.1 3.6 + - - +
126A LEU* 5.1 0.2 - - - -
149A VAL* 3.9 17.8 - - - +
150A LEU 3.5 3.8 - - - -
151A THR* 4.0 12.7 - - - +
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Residues in contact with CYS 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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92A VAL* 5.0 0.9 - - - -
93A GLU 3.3 20.0 - - - -
94A LEU* 4.0 3.4 - - + -
110A SER* 1.3 76.4 + - - +
112A ARG* 1.3 59.3 - - - +
113A VAL* 4.2 12.7 - - - +
124A LEU* 4.8 1.1 - - + +
126A LEU* 3.8 10.1 - - + -
148A ALA 3.9 0.7 - - - +
149A VAL* 3.2 7.4 - - - +
150A LEU* 2.9 37.8 + - + +
167A CYS* 2.0 57.2 - - + -
185A SER* 4.7 1.6 - - - -
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Residues in contact with ARG 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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93A GLU* 3.5 28.9 + - + +
94A LEU* 5.2 0.2 - - - +
95A MET* 5.5 11.3 - - - +
110A SER* 4.1 5.6 + - - +
111A CYS* 1.3 72.1 - - - +
113A VAL* 1.3 61.7 + - - +
114A PRO* 3.2 16.0 - - + +
148A ALA 4.1 2.7 - - - -
149A VAL* 4.2 14.8 - - + -
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Residues in contact with VAL 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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89A PRO* 5.3 6.5 - - + -
91A ARG 3.3 23.3 - - - +
92A VAL* 4.4 18.4 - - + -
93A GLU 5.1 0.2 - - - +
111A CYS* 4.2 19.3 - - - -
112A ARG* 1.3 77.7 - - - +
114A PRO* 1.3 65.0 - - - +
115A GLY 3.5 1.9 + - - -
116A ALA* 3.7 26.5 - - + +
124A LEU* 4.4 13.2 - - + -
148A ALA* 3.1 29.2 + - + +
149A VAL* 4.9 0.4 - - - +
169A ALA* 4.9 13.5 - - + -
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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