Contacts of the strand formed by residues 134 - 139 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C GLN* 4.6 2.2 - - - +
101C PHE* 5.3 0.8 - - + -
115C CYS* 3.3 2.3 - - - +
116C ALA* 2.6 45.7 + - + -
119C TYR* 3.6 33.7 - - + -
133C GLY* 1.3 75.1 - - - -
135C CYS* 1.3 61.0 + - - +
136C TYR* 4.4 15.5 - - + -
147C GLU* 2.8 31.6 + - - +
148C TYR 3.8 4.9 - - - -
149C ALA* 3.3 14.8 - - - +
150C PRO* 5.9 0.2 - - - -
166C GLY 3.6 5.0 + - - -
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Residues in contact with CYS 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C LEU* 3.6 15.9 - - + -
114C ALA 3.3 5.4 - - - -
115C CYS* 2.1 44.9 - - - -
134C THR* 1.3 75.0 - - - +
136C TYR* 1.3 62.0 + - - +
147C GLU* 3.4 9.7 - - - +
148C TYR* 2.7 41.5 + - + +
166C GLY 4.2 0.9 - - - -
167C GLY* 4.0 4.7 - - - -
180C LEU* 3.8 31.9 - - - -
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Residues in contact with TYR 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C PHE* 3.9 32.0 - - + -
73C ASP* 2.9 40.3 + - + -
78C ARG* 4.4 4.3 + - - -
96C LYS* 4.4 6.3 + - - -
99C GLN* 6.1 0.4 - - - -
101C PHE* 4.0 18.6 - + + -
112C ILE 3.5 4.2 - - - +
113C LEU* 3.7 2.2 - - - -
114C ALA 2.8 34.2 + - - +
134C THR* 4.4 11.7 - - + -
135C CYS* 1.3 77.7 - - - +
137C LEU* 1.3 59.9 + - - +
138C SER 4.0 0.4 + - - -
145C ILE* 3.9 16.4 - - + -
146C LEU 3.3 14.4 - - - +
147C GLU* 3.5 42.4 + - + -
204C TYR* 5.0 6.3 - - - -
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Residues in contact with LEU 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C SER* 3.5 25.4 - - - +
112C ILE 3.3 11.4 - - - +
113C LEU* 4.3 10.8 - - + -
135C CYS 4.2 0.6 - - - -
136C TYR* 1.3 70.9 - - - +
138C SER* 1.3 57.9 + - - +
139C THR* 3.8 7.0 + - + -
145C ILE* 3.6 2.0 - - - -
146C LEU* 2.6 53.4 + - + +
147C GLU* 4.8 0.2 - - - +
148C TYR* 5.2 4.5 - - + -
172C PHE* 4.1 17.5 - - + -
178C VAL* 4.1 5.8 - - + -
197C GLN* 3.8 22.2 - - + +
200C ILE* 3.5 40.8 - - + -
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Residues in contact with SER 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C PHE* 3.8 22.6 - - - -
110C SER 4.9 2.5 + - - -
111C SER* 3.0 8.5 + - - -
112C ILE* 2.8 42.5 + - - +
136C TYR 4.0 1.4 - - - -
137C LEU* 1.3 71.8 - - - +
139C THR* 1.3 61.2 + - - +
142C PHE* 3.1 38.2 + - - -
144C ARG 3.5 5.7 + - - -
145C ILE* 3.9 13.0 - - - +
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Residues in contact with THR 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C SER 4.4 0.7 - - - -
111C SER* 3.4 19.7 - - - +
137C LEU* 4.2 15.0 - - + +
138C SER* 1.3 74.6 - - - +
140C ASP* 1.3 81.2 + - - +
141C ASN 3.7 1.1 - - - -
142C PHE 3.3 3.8 + - - -
143C THR* 3.1 17.2 + - - -
144C ARG* 2.8 36.0 + - - +
146C LEU* 4.5 14.0 - - + +
197C GLN* 3.8 15.0 - - + +
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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