Contacts of the strand formed by residues 195 - 200 (chain C) in PDB entry 2Q41
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 TYR 195 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123C LYS* 3.4 48.4 + - + -
124C VAL 3.6 17.3 - - - -
125C LEU* 3.4 38.9 - - + +
148C ASP* 3.2 21.2 + - - -
186C PHE* 3.8 19.8 - + - -
190C ALA* 4.7 8.5 - - + -
193C GLY 3.5 0.4 - - - -
194C SER* 1.3 92.4 - - - +
196C ASP* 1.3 63.1 + - - +
197C ALA 4.1 4.0 - - - +
198C VAL* 4.7 1.8 - - + -
224C ALA* 2.9 21.4 + - + +
225C LEU* 3.2 17.6 - - + -
226C ARG* 2.8 33.1 + - - +
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Residues in contact with ASP 196 (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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118C ILE* 3.7 8.5 - - + +
120C ASN 5.4 0.4 - - - -
121C PRO* 4.2 19.1 - - + -
122C LYS* 2.8 30.8 + - - +
123C LYS* 2.7 26.1 + - - +
124C VAL* 5.4 0.4 - - - -
195C TYR* 1.3 74.5 - - - +
197C ALA* 1.3 61.5 + - - +
225C LEU* 3.7 2.2 - - - -
226C ARG* 3.0 42.6 + - - +
229C GLY* 3.6 5.0 - - - -
230C VAL 3.3 18.0 + - - -
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Residues in contact with ALA 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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114C PRO* 5.3 2.5 - - + -
115C LEU* 3.9 16.8 - - + -
118C ILE* 4.3 2.0 - - + -
123C LYS 3.9 2.2 + - - -
124C VAL* 3.3 19.6 - - + +
125C LEU 3.0 24.9 + - - -
195C TYR* 3.4 4.1 - - - +
196C ASP* 1.3 83.5 - - + +
198C VAL* 1.3 69.5 + - - +
199C ILE* 5.3 1.8 - - + -
225C LEU* 3.5 1.8 - - - -
230C VAL* 3.2 24.7 - - + -
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Residues in contact with VAL 198 (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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114C PRO* 5.8 0.5 - - - +
125C LEU* 3.3 12.3 - - + +
127C ILE* 4.6 14.6 - - + -
187C LEU* 4.5 15.7 - - + -
195C TYR* 4.7 6.1 - - + -
197C ALA* 1.3 80.5 - - - +
199C ILE* 1.3 66.4 + - - +
200C VAL* 4.1 20.0 - - + -
221C VAL* 3.6 39.7 - - + +
224C ALA* 5.3 1.3 - - + -
225C LEU* 3.7 13.0 - - + -
230C VAL 3.0 7.1 + - - +
231C VAL* 3.4 4.8 - - + +
232C CYS* 3.0 24.8 + - - +
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Residues in contact with ILE 199 (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 ILE* 3.9 34.5 - - + +
111C THR* 4.0 29.8 - - + +
114C PRO* 4.5 10.1 - - + -
115C LEU* 4.8 3.6 - - + -
124C VAL* 4.7 11.2 - - + -
125C LEU 2.9 10.4 + - - +
126C VAL* 3.4 21.7 - - + +
127C ILE* 2.9 26.0 + - - +
134C VAL* 4.4 7.6 - - + -
138C VAL* 4.3 21.1 - - + -
197C ALA* 5.3 1.3 - - + -
198C VAL* 1.3 79.6 - - - +
200C VAL* 1.3 63.8 + - - +
201C ASP* 3.4 4.2 + - + +
232C CYS* 3.5 4.7 - - + +
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Residues in contact with VAL 200 (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 ILE* 4.2 3.7 - - - +
127C ILE* 3.9 11.0 - - + +
198C VAL* 4.1 15.0 - - + -
199C ILE* 1.3 73.0 - - - +
201C ASP* 1.3 56.1 + - - +
202C SER* 2.8 32.0 + - - +
212C LEU* 4.1 17.3 - - + +
217C PHE* 3.9 30.1 - - + -
221C VAL* 5.5 0.2 - - + -
231C VAL* 4.6 1.8 - - + -
232C CYS 2.9 8.6 + - - +
233C THR* 3.3 32.1 - - + -
234C GLN* 3.4 19.9 + - - +
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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