Contacts of the strand formed by residues 265 - 270 (chain A) 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 265 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180A ASP 3.2 10.3 - - - +
182A LEU 5.0 0.9 - - - +
258A LEU* 3.4 48.9 - - + +
259A GLY* 3.4 4.3 - - - +
264A GLY* 1.3 76.6 - - - +
266A TYR* 1.3 65.3 + - - +
267A ILE* 4.3 14.1 - - + -
302A LEU* 4.5 6.1 - - + -
304A ALA* 3.4 26.5 - - + -
305A ASP 2.9 14.8 + - - +
306A VAL* 3.2 10.0 - - + +
307A VAL* 2.9 30.0 + - - +
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Residues in contact with TYR 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A PRO 5.2 0.2 - - - -
164A SER* 4.8 0.2 - - - -
167A VAL* 3.1 34.3 - - + +
168A VAL* 3.6 26.2 - - + -
171A VAL* 4.6 15.0 - - + -
179A VAL* 4.3 19.6 - - + +
180A ASP 2.9 6.3 + - - +
181A ILE* 3.2 19.3 - - + +
182A LEU 3.0 23.6 + - - -
205A PHE* 6.3 0.2 - + - -
264A GLY 4.3 0.4 + - - -
265A VAL* 1.3 74.3 - - - +
267A ILE* 1.3 73.0 + - - +
268A SER* 3.9 5.8 - - - -
307A VAL* 5.3 1.8 - - + -
308A GLY* 3.3 19.7 - - - +
309A ALA 3.3 21.1 - - - -
310A ASP* 2.6 40.4 + - - +
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Residues in contact with ILE 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A LEU* 3.3 19.3 - - + +
184A LEU* 4.7 0.9 - - + -
265A VAL* 4.3 4.9 - - + -
266A TYR* 1.3 79.6 - - - +
268A SER* 1.4 60.0 - - - +
269A ILE* 3.8 27.6 - - + -
299A LEU* 4.2 16.2 - - + -
302A LEU* 3.7 30.1 - - + -
306A VAL* 3.8 29.6 - - + -
308A GLY 3.3 5.7 + - - -
309A ALA* 2.9 32.6 - - + +
310A ASP 3.0 5.2 + - - +
336A LEU* 4.1 15.0 - - + -
339A LYS* 4.7 4.3 - - + -
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Residues in contact with SER 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A HIS* 2.8 29.1 + - - -
164A SER* 3.5 0.4 + - - -
181A ILE* 4.8 1.3 - - - +
182A LEU 3.0 9.9 + - - +
183A HIS* 3.6 3.5 - - - -
184A LEU* 2.9 26.7 + - - +
205A PHE* 3.9 20.9 - - - -
266A TYR* 3.9 9.4 + - - -
267A ILE* 1.4 71.1 - - - +
269A ILE* 1.3 60.9 + - - +
270A ASP 4.1 0.2 - - - -
310A ASP* 2.9 25.6 + - - -
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Residues in contact with ILE 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A LEU* 3.7 20.9 - - + -
267A ILE* 3.8 17.7 - - + -
268A SER* 1.3 77.6 + - - +
270A ASP* 1.3 66.4 + - - +
271A VAL 3.6 1.1 + - - +
273A CYS* 4.1 15.5 - - - -
295A VAL* 5.3 0.4 - - + -
299A LEU* 4.2 18.2 - - + -
310A ASP* 3.0 15.3 + - - +
311A VAL* 3.4 7.0 - - + +
312A VAL* 2.9 34.2 + - - +
332A LEU* 4.0 30.3 - - + -
336A LEU* 3.8 24.2 - - + -
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Residues in contact with ASP 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A HIS* 3.6 13.0 + - + +
184A LEU 2.8 8.4 + - - +
185A ASP* 2.8 39.9 - - - +
187A HIS* 4.4 1.4 + - - -
189A ASP* 4.3 1.6 - - - +
268A SER 4.1 0.8 - - - -
269A ILE* 1.3 70.5 - - - +
271A VAL* 1.3 55.7 + - - +
272A ASP* 2.8 47.1 + - - +
273A CYS* 2.7 37.6 + - - +
312A VAL* 3.7 7.1 - - - +
313A GLU* 3.3 26.8 - - - +
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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