Contacts of the strand formed by residues 134 - 139 (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 THR 134 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A LYS* 6.6 0.2 - - - -
99A GLN* 4.8 2.9 - - - +
101A PHE* 5.0 0.9 - - - -
115A CYS* 3.4 0.9 - - - +
116A ALA* 2.7 43.6 + - + +
119A TYR* 3.6 31.0 - - + -
133A GLY* 1.3 75.5 - - - -
135A CYS* 1.3 70.8 + - - +
136A TYR* 4.5 13.9 - - + -
147A GLU* 2.9 32.7 + - - +
148A TYR 4.1 0.7 - - - -
149A ALA* 3.5 15.8 - - - +
166A GLY 3.9 3.7 + - - -
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Residues in contact with CYS 135 (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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113A LEU* 3.8 15.3 - - + -
114A ALA 3.3 5.2 - - - +
115A CYS* 2.1 45.3 - - - -
134A THR* 1.3 82.9 + - - +
136A TYR* 1.3 64.1 + - - +
147A GLU* 3.4 5.5 - - - +
148A TYR* 3.0 38.9 + - + +
166A GLY 4.3 1.1 - - - -
167A GLY* 4.1 4.9 - - - -
180A LEU* 3.8 30.1 - - - -
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Residues in contact with TYR 136 (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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72A PHE* 3.6 40.4 - - + -
73A ASP* 3.5 32.2 + - + -
78A ARG* 4.8 4.5 + - - -
96A LYS* 4.5 8.6 + - - -
99A GLN* 6.0 3.4 - - - -
101A PHE* 4.1 19.7 - + + -
112A ILE 3.5 4.5 - - - +
113A LEU* 4.6 2.2 - - - -
114A ALA 2.7 33.2 + - - +
134A THR* 4.5 9.4 - - + -
135A CYS* 1.3 75.4 - - - +
137A LEU* 1.3 61.3 + - - +
145A ILE* 4.1 13.2 - - + -
146A LEU 3.3 5.6 - - - -
147A GLU* 3.4 51.8 + - + +
204A TYR* 5.0 4.5 - - - -
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Residues in contact with LEU 137 (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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72A PHE* 4.6 1.1 - - - -
111A SER* 4.0 15.5 - - - -
112A ILE 3.4 21.3 - - - +
113A LEU* 4.4 12.0 - - + +
135A CYS 4.2 0.8 - - - -
136A TYR* 1.3 72.5 - - - +
138A SER* 1.3 69.1 + - - +
139A THR* 3.8 13.7 - - + -
144A ARG 4.1 0.2 - - - +
145A ILE* 3.4 3.5 - - - +
146A LEU* 2.5 62.2 + - + +
148A TYR* 5.1 3.5 - - + +
172A PHE* 4.4 8.5 - - + -
178A VAL* 4.4 6.7 - - + -
197A GLN* 4.2 22.2 - - + +
200A ILE* 4.0 29.4 - - + -
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Residues in contact with SER 138 (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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72A PHE* 3.7 16.2 - - - -
110A SER 3.8 1.8 + - - +
111A SER* 3.2 5.2 - - - -
112A ILE* 2.9 46.6 + - - +
136A TYR 3.9 0.4 + - - -
137A LEU* 1.3 74.0 - - - +
139A THR* 1.3 61.1 + - - +
142A PHE* 3.5 27.5 + - - -
144A ARG 3.5 4.5 - - - -
145A ILE* 3.9 18.4 - - - -
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Residues in contact with THR 139 (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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111A SER* 3.7 5.8 - - - +
137A LEU* 3.8 17.9 - - + -
138A SER* 1.3 77.1 - - - +
140A ASP* 1.3 81.3 + - - +
141A ASN 3.5 1.6 - - - -
142A PHE 3.2 2.1 + - - -
143A THR 3.0 19.8 + - - -
144A ARG* 2.9 32.1 + - - +
146A LEU* 4.5 12.4 - - + +
197A GLN* 3.5 27.1 - - + +
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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