Contacts of the strand formed by residues 111 - 116 (chain A) in PDB entry 3VI4
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 SER 111 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107A ALA* 3.3 5.7 - - - +
108A HIS 3.0 36.7 + - - +
109A GLY 4.1 0.2 - - - +
110A SER* 1.3 81.4 + - - +
112A ILE* 1.3 59.9 + - - +
113A LEU 4.3 0.2 - - - -
137A LEU* 4.0 7.2 - - - -
138A SER 3.2 8.1 - - - -
139A THR* 3.7 11.3 - - - +
140A ASP 4.5 1.4 + - - -
172A PHE* 4.3 4.2 - - - -
197A GLN* 2.7 40.9 + - - -
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Residues in contact with ILE 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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26A TYR* 3.7 42.6 - - + -
36A LEU* 3.8 33.0 - - + -
55A VAL* 5.6 0.2 - - + -
70A ILE* 4.3 6.1 - - + -
72A PHE* 3.5 22.6 - - + -
105A VAL* 4.9 4.9 - - + -
106A ARG 3.5 7.6 - - - +
107A ALA* 4.1 0.9 - - + -
110A SER 4.5 0.7 - - - +
111A SER* 1.3 78.3 - - - +
113A LEU* 1.3 66.4 + - - +
114A ALA* 5.0 0.4 - - + -
136A TYR 3.5 2.3 - - - +
137A LEU* 3.4 6.8 - - - +
138A SER* 2.9 39.8 + - - +
142A PHE* 3.7 19.3 - - + -
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Residues in contact with LEU 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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104A THR* 3.9 1.0 - - + +
105A VAL* 3.5 2.6 - - - -
106A ARG* 2.6 47.3 + - + +
112A ILE* 1.3 74.9 - - - +
114A ALA* 1.3 62.9 + - - +
115A CYS* 4.0 9.4 - - - -
135A CYS* 3.8 23.6 - - + -
136A TYR 3.7 5.2 - - - +
137A LEU* 4.5 14.6 - - + -
148A TYR* 5.2 4.5 - - + -
170A ALA* 3.8 29.2 - - + -
171A GLU* 5.1 3.8 - - - +
172A PHE* 3.6 22.7 - - + -
178A VAL* 4.0 33.4 - - + -
180A LEU* 4.2 1.1 - - + -
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Residues in contact with ALA 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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55A VAL* 3.8 21.5 - - + -
72A PHE* 4.1 12.6 - - + -
101A PHE* 3.2 30.9 - - + -
104A THR 3.3 7.2 - - - +
105A VAL* 4.5 2.2 - - + -
112A ILE* 5.0 1.3 - - + -
113A LEU* 1.3 78.0 - - - +
115A CYS* 1.3 60.7 + - - +
135A CYS* 3.3 0.2 - - - -
136A TYR 2.7 37.6 + - - +
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Residues in contact with CYS 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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100A TRP 3.4 2.6 - - - +
101A PHE* 3.8 2.7 - - - -
102A GLY 3.0 24.6 + - - -
103A ALA 3.7 4.9 + - - -
104A THR* 3.0 16.8 + - - +
113A LEU* 4.0 18.2 - - - -
114A ALA* 1.3 76.5 - - - +
116A ALA* 1.3 61.4 + - - +
117A PRO* 3.7 2.6 - - + +
134A THR 3.4 3.6 - - - +
135A CYS* 2.1 46.0 - - - -
167A GLY* 3.8 27.8 - - - +
170A ALA* 4.4 4.3 - - - -
180A LEU* 4.3 2.2 - - - -
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Residues in contact with ALA 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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99A GLN* 3.4 27.4 - - + +
100A TRP 3.3 4.5 - - - -
101A PHE* 3.6 24.2 - - + +
115A CYS* 1.3 76.3 - - - +
117A PRO* 1.4 58.5 - - - +
118A LEU 3.2 9.6 + - - -
119A TYR* 3.2 6.8 + - + -
133A GLY* 3.2 3.5 - - - -
134A THR* 2.7 36.1 + - + +
166A GLY 5.1 0.7 - - - -
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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