Contacts of the strand formed by residues 194 - 197 (chain C) in PDB entry 3BSQ
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 PRO 194 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29C TRP* 4.5 8.1 - - + +
30C GLN* 3.2 37.2 - - - +
43C GLY 4.0 9.9 - - - +
44C VAL* 3.7 23.1 - - + -
131C THR 3.9 1.7 - - - +
132C VAL* 3.4 23.6 - - - +
133C SER* 3.4 10.6 + - - +
192C GLY 4.0 0.2 - - - -
193C GLY* 1.3 85.2 - - - +
195C LEU* 1.3 63.0 + - - +
196C VAL* 4.0 13.5 - - + -
201C LEU* 3.7 15.0 - - + -
203C GLY 3.8 0.7 - - - +
204C LEU* 5.0 0.4 - - + -
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Residues in contact with LEU 195 (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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130C CYS* 3.7 21.8 - - + -
131C THR 3.4 7.4 - - - +
132C VAL* 3.9 19.5 - - + -
154C VAL* 4.0 17.0 - - + -
156C LEU* 4.4 10.5 - - + -
175C LEU* 4.2 17.0 - - + -
177C ALA* 4.6 0.7 - - + -
194C PRO* 1.3 76.8 - - - +
196C VAL* 1.3 56.2 + - - +
197C CYS* 4.4 3.8 - - - -
201C LEU* 3.6 1.3 - - - +
202C GLN* 2.7 34.0 + - + -
203C GLY* 2.9 36.5 + - - +
221C TYR* 3.5 30.5 - - + -
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Residues in contact with VAL 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C HIS* 6.2 4.5 - - + +
29C TRP* 4.3 29.2 - - + +
117C VAL* 5.4 2.2 - - + -
130C CYS* 3.3 1.2 - - - +
131C THR* 2.9 40.2 + - - +
194C PRO* 4.0 22.2 - - + -
195C LEU* 1.3 76.9 - - - +
197C CYS* 1.3 62.7 + - - +
198C ARG 4.5 0.6 + - - +
199C GLY 4.8 5.4 - - - +
200C THR 3.2 23.8 - - - +
201C LEU* 4.3 9.6 - - + -
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Residues in contact with CYS 197 (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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124C GLU* 3.9 10.3 - - + +
128C THR* 3.7 14.4 - - - +
129C THR 3.8 4.3 - - - +
130C CYS* 2.1 44.9 - - - -
156C LEU* 3.9 8.7 - - - -
195C LEU* 4.4 3.1 - - - -
196C VAL* 1.3 74.8 - - - +
198C ARG* 1.3 73.8 + - - +
199C GLY 2.8 3.9 + - - -
200C THR* 2.9 23.7 + - - +
202C GLN* 3.5 26.9 - - + -
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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