Contacts of the strand formed by residues 179 - 184 (chain C) in PDB entry 6VSU
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 VAL 179 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168C VAL* 4.5 7.9 - - + +
171C VAL* 4.6 7.2 - - + -
172C SER* 5.0 4.5 - - - -
175C LEU* 4.4 6.3 - - + -
177C GLY 4.4 3.1 - - - +
178C PRO* 1.3 77.8 - - - +
180C ASP* 1.4 69.4 + - - +
181C ILE* 4.0 9.4 - - + -
213C TYR 2.6 18.4 + - - +
214C ALA* 2.7 27.7 - - - +
215C ARG 3.0 2.8 + - - -
262C VAL* 4.3 3.1 - - - -
263C LYS* 4.3 7.0 - - + -
264C GLY* 3.1 34.8 - - - +
265C VAL 4.4 0.2 - - - +
266C TYR* 3.9 20.0 - - + +
307C VAL* 4.2 13.0 - - + -
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Residues in contact with ASP 180 (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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179C VAL* 1.4 70.5 - - - +
181C ILE* 1.3 65.4 + - - +
215C ARG* 2.9 37.0 + - - +
216C ARG* 2.8 54.3 + - + +
258C LEU* 4.0 9.4 - - + +
259C GLY 3.2 20.4 + - - +
262C VAL* 3.6 7.5 - - - +
264C GLY 2.9 7.9 + - - +
265C VAL* 3.0 10.3 - - + -
266C TYR 2.8 24.9 + - - -
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Residues in contact with ILE 181 (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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168C VAL* 4.1 32.3 - - + -
179C VAL* 4.0 11.2 - - + -
180C ASP* 1.3 80.3 - - - +
182C LEU* 1.3 67.0 - - - +
183C HIS* 3.8 1.8 - - + -
205C PHE* 3.9 20.4 - - + -
208C ILE* 4.2 7.4 - - + -
214C ALA* 3.7 25.6 - - + -
216C ARG 2.7 7.2 + - - +
217C LEU* 3.5 22.7 - - + -
218C LEU* 3.0 32.2 + - - +
258C LEU* 4.5 4.7 - - - +
266C TYR* 2.9 22.4 - - + +
268C SER 4.7 0.7 - - - +
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Residues in contact with LEU 182 (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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180C ASP 4.2 0.2 - - - -
181C ILE* 1.3 71.1 - - - +
183C HIS* 1.3 56.5 + - - +
184C LEU* 4.0 19.7 + - + -
218C LEU* 3.6 17.0 - - + +
220C VAL* 3.7 25.6 - - + -
256C LEU* 4.4 12.3 - - + -
258C LEU* 4.3 12.9 - - + +
265C VAL* 4.4 2.3 - - + +
266C TYR 2.8 10.0 + - - +
267C ILE* 3.1 15.7 - - + +
268C SER 2.8 30.3 + - - +
298C ILE* 4.1 22.0 - - + -
299C LEU* 4.6 6.3 - - + -
302C LEU* 3.6 27.6 - - + -
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Residues in contact with HIS 183 (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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161C HIS* 3.4 24.2 - + - -
181C ILE* 4.1 0.9 - - + -
182C LEU* 1.3 71.3 - - - +
184C LEU* 1.3 56.0 + - - +
185C ASP* 3.4 15.8 + - + +
187C HIS 4.1 8.5 - - - -
188C PRO* 3.6 15.5 - - + -
189C ASP* 4.2 0.9 - - - -
205C PHE* 3.4 34.7 - + + -
217C LEU* 4.0 15.9 - - + -
218C LEU 2.9 13.1 + - - +
219C GLN* 2.9 38.5 + - + +
220C VAL 2.9 29.7 + - - -
222C ILE* 5.6 0.6 - - + +
268C SER 3.4 14.8 - - - +
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Residues in contact with LEU 184 (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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182C LEU* 4.0 17.5 - - + -
183C HIS* 1.3 69.6 - - - +
185C ASP* 1.3 60.7 - - - +
220C VAL* 3.3 36.1 - - + +
267C ILE* 4.8 0.7 - - + -
268C SER 3.0 7.4 + - - +
269C ILE* 3.9 34.3 - - + -
270C ASP 2.9 28.8 + - - +
273C CYS* 3.4 15.5 - - - -
290C LEU* 4.2 14.1 - - + -
295C VAL* 4.4 13.0 - - + -
298C ILE* 4.4 12.8 - - + -
299C LEU* 4.3 15.7 - - + -
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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