Contacts of the strand formed by residues 191 - 199 (chain C) in PDB entry 3V9G
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 191 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187C SER* 3.9 1.7 - - - -
188C VAL 2.9 35.1 + - - +
189C PRO* 3.3 2.4 - - - +
190C PRO* 1.3 88.5 + - - +
192C THR* 1.3 70.9 + - - +
193C ASN* 4.9 10.3 - - - -
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Residues in contact with THR 192 (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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31A LYS* 5.6 9.2 - - + -
23C ARG 5.4 9.6 - - - +
187C SER* 3.3 11.7 - - - +
191C SER* 1.3 80.5 - - - +
193C ASN* 1.3 67.4 + - - +
194C SER 4.3 0.2 + - - -
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Residues in contact with ASN 193 (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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184C GLN* 4.3 2.3 - - - +
185C PRO* 3.8 25.4 - - + +
186C ILE 2.8 27.9 + - - +
187C SER* 2.7 22.2 + - - +
188C VAL 4.4 5.1 - - - +
191C SER* 4.8 9.8 + - - -
192C THR* 1.3 80.6 - - - +
194C SER* 1.3 63.9 + - - +
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Residues in contact with SER 194 (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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184C GLN* 3.2 11.4 - - - -
185C PRO* 3.8 4.3 - - - +
193C ASN* 1.3 78.9 - - - +
195C THR* 1.3 63.8 + - - +
196C VAL* 4.1 12.5 + - - +
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Residues in contact with THR 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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181C GLU* 4.9 3.1 - - - +
183C GLN 4.2 2.1 + - - -
184C GLN* 2.7 37.0 + - - -
185C PRO* 3.3 22.2 - - - +
194C SER* 1.3 74.0 + - - +
196C VAL* 1.3 67.1 + - - +
197C TYR* 3.5 40.9 + - + +
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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
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181C GLU* 5.8 0.7 - - - -
194C SER* 4.1 14.7 + - - +
195C THR* 1.3 80.4 - - - +
197C TYR* 1.3 63.2 + - - +
198C ARG* 3.0 30.6 + - + +
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Residues in contact with TYR 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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117C ASP* 4.5 2.8 - - - +
124C ARG* 4.7 7.8 + - - -
180C LEU* 3.3 55.0 + - + +
181C GLU* 3.8 31.9 + - - +
183C GLN* 2.8 32.1 + - - +
184C GLN* 4.1 5.6 - - - -
195C THR* 3.5 30.5 - - + +
196C VAL* 1.3 71.8 - - - +
198C ARG* 1.3 65.8 + - - +
199C GLY 3.8 0.5 + - - -
226C MET* 4.5 16.6 - - + +
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Residues in contact with ARG 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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117C ASP* 3.8 14.6 - - - +
196C VAL* 3.0 24.6 + - + +
197C TYR* 1.3 73.9 - - - +
199C GLY* 1.3 71.1 + - - +
200C LEU* 5.0 4.2 - - - +
226C MET* 4.3 2.3 - - - +
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Residues in contact with GLY 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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113C ARG* 4.6 5.9 + - - -
117C ASP* 3.1 18.6 + - - +
198C ARG* 1.3 86.8 + - - +
200C LEU* 1.3 68.3 + - - -
201C GLU* 3.6 2.4 + - - +
226C MET* 3.5 20.2 + - - -
227C GLY 4.2 8.1 - - - -
228C ASN* 4.0 7.4 - - - -
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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