Contacts of the strand formed by residues 192 - 200 (chain C) in PDB entry 1VF5
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 ASN 192 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188C ASP* 2.8 33.5 - - - +
189C GLU 3.2 6.7 + - - +
190C TYR 2.5 10.6 + - - +
191C GLY* 1.3 77.2 + - - +
193C VAL* 1.3 88.8 + - - +
194C LYS* 3.3 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 193 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187C GLU* 3.4 31.4 - - + +
188C ASP* 3.1 12.3 - - + +
189C GLU* 4.3 4.5 - - - +
190C TYR 4.6 6.1 - - - +
192C ASN* 1.3 92.8 + - - +
194C LYS* 1.3 60.2 + - - +
195C TYR* 3.2 34.6 - - + +
213C ALA* 3.3 15.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 194 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186C GLU* 2.6 30.9 - - - +
187C GLU 2.8 11.7 + - - +
188C ASP* 3.8 6.5 - - - +
192C ASN* 3.3 26.5 + - - +
193C VAL* 1.3 74.7 + - - +
195C TYR* 1.3 56.9 + - - +
196C GLN* 3.3 27.6 - - + +
210C THR* 4.0 6.5 - - - +
211C ILE 3.5 6.3 - - - +
212C PRO* 3.3 41.1 - - + +
213C ALA* 3.9 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 195 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184C ALA 3.6 1.6 - - - -
185C LYS* 3.1 58.3 - - + +
186C GLU 3.8 11.4 - - - -
187C GLU* 5.1 2.2 - - - +
193C VAL* 3.2 37.1 - - + +
194C LYS* 1.3 78.5 - - - +
196C GLN* 1.3 71.2 + - - +
197C VAL* 4.0 0.2 - - - +
211C ILE* 3.1 32.2 + - + +
212C PRO 4.2 2.0 - - - +
213C ALA* 3.8 21.5 - - + -
214C GLY 5.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 196 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184C ALA* 2.7 35.6 + - + +
185C LYS* 3.6 3.6 + - - +
186C GLU* 3.6 21.6 + - - +
194C LYS* 3.3 29.5 - - - +
195C TYR* 1.3 86.1 - - - +
197C VAL* 1.3 67.6 + - - +
209C ASP 3.6 5.2 - - - +
210C THR* 2.7 39.6 + - - -
211C ILE 4.2 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 197 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C ILE* 3.7 24.9 - - + -
182C LYS 4.4 1.1 - - - +
183C ILE* 5.5 1.6 - - - -
184C ALA* 3.4 8.9 - - - +
195C TYR 4.0 0.2 - - - +
196C GLN* 1.3 85.3 - - - +
198C SER* 1.3 76.4 + - - +
199C ILE* 3.7 17.7 - - + -
208C VAL* 3.4 12.7 - - - +
209C ASP* 3.0 28.4 + - + +
210C THR 4.5 1.3 - - - -
211C ILE* 3.8 34.8 - - + +
217C LEU* 5.9 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 198 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C ILE* 3.6 6.8 - - - +
182C LYS* 3.2 38.4 + - - +
184C ALA* 2.8 28.6 - - - +
197C VAL* 1.3 75.8 + - - +
199C ILE* 1.3 55.9 + - - +
200C GLN* 2.4 29.6 - - - +
208C VAL* 3.6 10.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 199 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C ALA* 3.9 26.7 - - + -
175C SER 4.0 2.2 - - - +
176C ALA* 4.9 9.2 - - + +
178C GLY 5.0 3.6 - - - +
180C ILE* 3.6 22.9 - - + +
197C VAL* 3.7 19.0 - - + +
198C SER* 1.3 75.4 - - - +
200C GLN* 1.3 71.6 + - - +
201C THR* 3.6 18.8 - - - +
206C THR* 4.8 0.9 + - - -
207C VAL* 2.7 25.4 - - + +
208C VAL* 2.8 24.4 - - - +
209C ASP* 3.1 34.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 200 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179C THR* 3.2 13.2 - - + +
180C ILE* 3.9 3.0 - - - +
181C THR* 2.6 49.0 + - + +
182C LYS* 3.9 9.9 - - - +
198C SER* 2.4 30.0 + - - +
199C ILE* 1.3 81.6 + - - +
201C THR* 1.3 75.9 + - - +
202C ASP* 2.8 14.3 + - + +
206C THR* 3.2 11.6 + - - +
207C VAL 3.0 23.3 + - - +
208C VAL* 4.9 2.8 - - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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