Contacts of the strand formed by residues 193 - 198 (chain C) in PDB entry 2VHW
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 193 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C PRO* 4.1 10.5 + - - +
169C ALA 2.9 14.1 + - - -
170C ASP* 3.7 13.5 - - - +
171C VAL* 2.8 26.9 + - - +
191C GLY 3.9 0.6 + - - -
192C ALA* 1.3 70.1 - - - +
194C VAL* 1.3 60.2 + - - +
195C THR* 5.2 3.4 + - - +
214C ARG 6.0 0.4 - - - +
216C HIS* 3.9 27.4 - - + +
193E THR* 6.1 0.4 - - + -
216E HIS* 3.1 32.0 + - + +
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Residues in contact with VAL 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C VAL* 3.3 11.9 - - + +
173C VAL* 4.1 12.6 - - + -
184C ALA* 3.9 31.2 - - + +
187C ALA* 3.8 13.0 - - + -
188C ASN* 3.5 32.2 + - + +
192C ALA 3.5 11.5 + - - +
193C THR* 1.3 76.8 - - - +
195C THR* 1.3 62.9 + - - +
196C VAL* 4.1 2.5 - - + -
214C ARG 4.4 3.7 + - - +
215C ILE* 3.8 17.3 - - + -
216C HIS* 2.9 32.1 + - - +
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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
----------------------------------------------------------
170C ASP* 5.0 5.2 + - - -
171C VAL 2.9 10.4 + - - -
172C VAL* 3.3 13.5 - - - +
173C VAL 2.8 26.0 + - - +
193C THR* 5.2 3.1 + - - +
194C VAL* 1.3 75.4 + - - +
196C VAL* 1.3 65.1 + - - +
197C LEU* 4.3 13.2 - - + -
216C HIS* 3.3 20.8 + - + +
218C ARG* 3.6 34.7 + - + +
228C ALA* 5.0 6.3 - - + -
231C ARG* 5.5 5.0 + - - -
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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
----------------------------------------------------------
173C VAL* 3.3 13.9 - - + +
175C GLY 4.0 10.1 - - - +
176C ALA* 3.7 20.0 - - + -
180C GLY 5.4 1.3 - - - +
184C ALA* 3.7 22.9 - - + -
194C VAL* 4.1 1.8 - - + -
195C THR* 1.3 77.2 - - - +
197C LEU* 1.3 65.9 + - - +
204C LEU* 3.6 5.2 - - + +
207C LEU* 3.6 26.5 - - + -
215C ILE* 3.5 26.0 - - + -
216C HIS 2.8 11.2 + - - +
217C THR* 3.3 4.6 - - + -
218C ARG 3.0 22.9 + - - -
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Residues in contact with LEU 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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172C VAL* 3.6 30.7 - - + -
173C VAL 2.9 9.8 + - - +
174C ILE* 3.7 10.9 - - + -
175C GLY* 2.7 33.8 + - - -
195C THR* 4.3 7.2 - - + -
196C VAL* 1.3 76.1 - - - +
198C ASP* 1.3 59.7 + - - +
204C LEU* 4.2 0.9 - - - -
218C ARG* 3.3 18.6 - - + +
220C SER* 3.8 27.6 - - - +
224C GLU* 3.9 12.1 - - + +
225C LEU* 3.7 34.8 - - + +
228C ALA* 4.1 13.2 - - + -
1372C NAI 3.7 2.4 - - - -
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Residues in contact with ASP 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C ALA* 2.6 33.0 + - + +
197C LEU* 1.3 74.5 - - - +
199C ILE* 1.3 73.9 + - - +
200C ASN* 2.9 19.9 + - - +
203C LYS* 4.3 0.8 - - - +
204C LEU* 3.7 31.3 - - + +
218C ARG 3.6 2.2 + - - -
219C TYR* 3.7 2.1 - - - -
220C SER* 3.1 22.2 + - - -
1372C NAI 2.7 51.6 + - - -
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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
------------------------------------------------------------
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