Contacts of the strand formed by residues 179 - 184 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168D VAL* 4.6 8.1 - - + -
171D VAL* 4.4 11.4 - - + -
172D SER* 5.0 4.9 - - - -
175D LEU* 4.7 1.8 - - + -
177D GLY 4.6 3.6 - - - +
178D PRO* 1.3 77.9 - - - +
180D ASP* 1.3 65.8 + - - +
181D ILE* 3.9 22.9 - - + -
213D TYR 3.0 12.5 + - - +
214D ALA* 3.1 8.1 - - - +
215D ARG 2.9 21.8 + - - -
262D VAL* 4.4 2.7 - - - -
263D LYS* 4.4 6.5 - - + -
264D GLY 3.3 21.5 - - - +
265D VAL 4.5 0.2 - - - +
266D TYR* 4.1 11.4 - - + +
307D VAL* 4.0 22.7 - - + -
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Residues in contact with ASP 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179D VAL* 1.3 72.5 - - - +
181D ILE* 1.3 62.6 + - - +
215D ARG* 2.9 34.5 + - - +
216D ARG* 2.9 42.2 + - + +
258D LEU* 3.9 17.5 - - + -
259D GLY* 2.9 31.9 + - - +
262D VAL* 4.0 3.4 - - - +
264D GLY 3.0 7.6 + - - +
265D VAL* 3.2 6.9 - - + +
266D TYR 2.9 24.6 + - - -
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Residues in contact with ILE 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168D VAL* 4.1 20.9 - - + -
179D VAL* 3.9 11.9 - - + -
180D ASP* 1.3 80.7 - - - +
182D LEU* 1.3 69.5 + - - +
183D HIS* 4.2 4.0 - - + +
205D PHE* 4.4 8.7 - - + -
208D ILE* 4.0 22.9 - - + -
214D ALA* 3.8 24.0 - - + -
216D ARG 2.8 14.3 + - - +
217D LEU* 3.4 19.0 + - + -
218D LEU* 2.8 35.2 + - - +
258D LEU* 4.6 4.7 - - - -
266D TYR* 3.2 21.8 - - + +
268D SER* 4.7 1.6 - - - +
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Residues in contact with LEU 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181D ILE* 1.3 74.2 - - - +
183D HIS* 1.3 57.2 + - - +
184D LEU* 4.4 11.7 - - + -
218D LEU* 3.6 7.6 - - + +
220D VAL* 3.8 30.7 - - + -
256D LEU* 4.2 17.7 - - + -
258D LEU* 4.1 13.4 - - + +
265D VAL* 4.8 1.1 - - + +
266D TYR 3.1 5.7 + - - +
267D ILE* 3.3 26.6 - - + +
268D SER 2.8 32.2 + - - +
298D ILE* 4.2 21.1 - - + -
299D LEU* 4.4 6.5 - - + -
302D LEU* 4.2 22.2 - - + -
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Residues in contact with HIS 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161D HIS* 3.4 8.2 - + - -
181D ILE* 4.3 0.9 - - + -
182D LEU* 1.3 72.2 - - - +
184D LEU* 1.3 59.0 + - - +
185D ASP* 2.8 28.7 + - + +
187D HIS 3.6 13.2 - - - -
188D PRO 3.4 7.4 - - - -
189D ASP* 4.4 0.7 - - + -
205D PHE* 3.3 45.6 - + + -
217D LEU* 3.6 20.2 - - + -
218D LEU 2.8 10.2 + - - +
219D GLN* 2.8 38.6 + - + +
220D VAL* 2.7 32.4 + - - +
268D SER* 3.4 7.0 - - - -
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Residues in contact with LEU 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182D LEU* 4.4 19.5 - - + -
183D HIS* 1.3 72.4 - - - +
185D ASP* 1.3 63.1 + - - +
220D VAL* 3.4 31.9 - - + +
267D ILE* 4.7 0.7 - - + -
268D SER 2.8 12.5 + - - +
269D ILE* 3.7 31.0 - - + -
270D ASP* 2.9 30.8 + - - +
273D CYS* 3.6 16.4 - - + -
290D LEU* 4.0 16.6 - - + -
295D VAL* 4.2 15.5 - - + -
298D ILE* 4.5 11.7 - - + -
299D LEU* 4.3 13.9 - - + -
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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