Contacts of the strand formed by residues 306 - 312 (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 306 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153A ARG* 3.0 17.5 + - - -
265A VAL* 3.2 9.6 - - + +
267A ILE* 3.8 31.0 - - + -
304A ALA* 3.4 22.3 + - + +
305A ASP* 1.3 71.8 + - - +
307A VAL* 1.3 59.1 + - - +
308A GLY 3.5 22.4 - - - +
309A ALA* 4.8 0.7 - - + -
339A LYS* 4.1 24.1 + - + +
340A ILE* 3.6 41.0 - - + +
342A LYS* 4.5 3.3 + - - +
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Residues in contact with VAL 307 (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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147A MET* 5.0 3.3 - - + +
153A ARG* 3.5 35.5 - - - +
154A PRO* 3.6 19.6 - - - +
171A VAL* 3.6 28.5 - - + +
175A LEU* 3.7 19.7 - - + -
179A VAL* 4.2 13.9 - - + -
263A LYS 4.0 20.0 - - - +
264A GLY* 4.0 1.3 - - - -
265A VAL 2.9 15.8 + - - +
266A TYR* 4.7 1.8 - - - +
305A ASP* 4.0 13.9 - - - +
306A VAL* 1.3 72.3 - - - +
308A GLY* 1.3 58.8 + - - +
340A ILE* 5.4 0.4 - - - -
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Residues in contact with GLY 308 (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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153A ARG* 5.5 0.4 - - - -
154A PRO* 3.4 16.8 - - - -
171A VAL* 5.0 1.3 - - - -
266A TYR* 3.3 23.5 - - - -
267A ILE 3.3 16.1 + - - -
306A VAL* 3.5 10.4 - - - +
307A VAL* 1.3 84.2 - - - +
309A ALA* 1.3 64.8 + - - +
340A ILE* 4.6 4.4 - - - +
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Residues in contact with ALA 309 (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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154A PRO 3.2 6.8 + - - +
155A LEU* 3.2 9.3 - - + -
156A VAL* 3.1 21.2 + - - +
266A TYR* 3.3 11.9 + - - -
267A ILE* 2.9 18.2 - - + +
306A VAL* 4.8 0.4 - - + -
308A GLY* 1.3 76.2 - - - +
310A ASP* 1.3 61.2 + - - +
336A LEU* 4.0 25.4 - - + -
340A ILE* 3.9 20.9 - - + -
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Residues in contact with ASP 310 (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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155A LEU* 4.7 0.9 - - - -
156A VAL* 3.1 24.5 - - + +
163A ILE* 5.3 0.7 - - + -
164A SER* 2.5 27.1 + - - -
167A VAL* 5.4 0.4 - - + -
266A TYR* 2.6 30.7 + - - +
267A ILE 3.0 8.1 + - - +
268A SER* 2.9 22.1 + - - -
269A ILE* 3.0 20.6 + - - +
309A ALA* 1.3 71.2 - - - +
311A VAL* 1.3 68.9 + - - +
312A VAL* 3.3 18.8 - - + +
336A LEU* 4.3 1.7 - - - +
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Residues in contact with VAL 311 (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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89A ILE* 4.6 6.5 - - + +
155A LEU* 4.6 2.0 - - + -
156A VAL 3.0 7.2 + - - +
157A LEU* 3.7 5.5 - - + -
158A GLY* 3.0 21.5 + - - +
269A ILE* 3.4 9.4 - - + +
271A VAL* 4.0 22.0 - - + -
310A ASP* 1.3 79.0 - - - +
312A VAL* 1.3 61.8 + - - +
314A PHE* 5.9 0.8 - - + +
329A ALA* 4.1 21.3 - - + +
332A LEU* 4.2 19.5 - - + -
333A VAL* 4.0 22.7 - - + -
336A LEU* 3.6 24.7 - - + -
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Residues in contact with VAL 312 (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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158A GLY* 4.3 2.9 - - - +
159A GLY 3.5 10.1 - - - +
160A ASP 4.3 4.0 - - - +
161A HIS* 3.6 38.6 - - + +
163A ILE* 4.0 26.0 - - + -
164A SER* 4.4 2.7 - - - +
269A ILE 2.9 14.9 + - - +
270A ASP* 4.0 1.6 - - - -
271A VAL* 3.2 22.5 + - - +
310A ASP* 3.3 30.1 - - + +
311A VAL* 1.3 77.0 - - - +
313A GLU* 1.3 70.4 - - + +
314A PHE* 3.2 7.5 + - - -
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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