Contacts of the strand formed by residues 270 - 276 (chain A) in PDB entry 6S6A
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 THR 270 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A LEU* 3.7 20.2 - - + -
205A LEU* 4.3 10.3 - - + +
206A PHE 3.1 14.4 - - - +
208A ARG* 3.7 6.2 - - - +
214A ILE* 3.8 13.7 - - + -
265A ILE* 3.8 4.3 - - - +
266A PHE* 2.9 33.8 + - - +
267A THR* 2.9 35.6 + - + +
268A SER 3.6 0.6 - - - -
269A ASN* 1.3 84.6 - - - +
271A TYR* 1.3 66.5 + - - +
301A GLU* 4.7 3.1 - - - +
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Residues in contact with TYR 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A LEU* 3.6 9.4 - - - +
206A PHE* 2.8 36.8 + - + +
208A ARG* 3.7 43.0 + - + +
211A PHE* 3.7 32.3 - + + -
239A LYS* 3.9 14.2 - - - -
249A PHE* 3.2 35.4 + + - -
250A GLN* 3.2 24.0 + - - +
263A ILE* 4.1 7.4 - - + -
264A ASP* 3.2 26.7 - - - -
265A ILE* 3.3 23.7 - - + +
266A PHE* 4.2 1.8 - - - -
270A THR* 1.3 75.1 - - - +
272A VAL* 1.3 59.7 + - - +
321C ASN* 5.4 0.2 + - - -
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Residues in contact with VAL 272 (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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191A LEU* 5.1 0.4 - - + -
194A PHE* 4.4 11.0 - - + -
203A VAL* 3.7 22.7 - - + -
204A LEU 3.3 14.1 - - - +
205A LEU* 4.2 9.6 - - + -
206A PHE* 4.4 4.0 - - - -
262A PHE 5.2 1.1 - - - +
263A ILE* 3.3 5.6 - - - +
264A ASP* 2.9 48.0 + - + +
266A PHE* 4.0 29.1 - - + +
271A TYR* 1.3 76.2 - - - +
273A MET* 1.3 65.5 + - - +
274A VAL* 4.4 10.3 - - + +
290A ILE* 4.7 9.9 - - + -
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Residues in contact with MET 273 (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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202A GLU 3.8 0.5 - - - +
203A VAL* 3.3 6.2 - - - -
204A LEU* 3.0 53.1 + - + +
206A PHE* 3.8 16.1 - - + -
231A ILE* 3.9 15.3 - - + -
254A VAL* 6.0 0.2 - - + -
261A ALA* 3.8 23.3 - - + -
262A PHE 3.2 6.7 - - - +
263A ILE* 3.5 32.3 - - + -
272A VAL* 1.3 74.5 - - - +
274A VAL* 1.3 62.2 + - - +
275A VAL* 4.1 11.2 - - + +
295C VAL* 4.0 21.5 - - + -
299C TYR* 4.3 13.9 - - + -
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Residues in contact with VAL 274 (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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194A PHE* 4.2 23.8 - - + -
198A ILE* 4.2 12.1 - - + -
200A ALA* 3.9 12.6 - - + -
202A GLU 3.7 2.9 - - - -
203A VAL* 4.3 5.6 - - + -
260A ALA 4.0 0.2 - - - +
261A ALA* 3.3 5.0 - - - +
262A PHE* 2.9 37.7 + - + +
272A VAL* 4.4 8.1 - - + -
273A MET* 1.3 74.9 - - - +
275A VAL* 1.3 63.7 + - - +
276A MET* 3.6 29.6 - - + -
286A THR* 4.6 4.5 - - + -
290A ILE* 4.0 25.6 - - + -
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Residues in contact with VAL 275 (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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200A ALA* 3.4 5.5 - - - +
201A ASP* 3.0 35.4 + - + +
202A GLU* 2.8 26.0 + - + +
204A LEU* 5.9 0.4 - - + -
259A PHE* 4.4 6.7 - - + -
260A ALA 3.5 8.7 - - - +
261A ALA* 4.3 6.7 - - + -
273A MET* 4.1 14.1 - - + -
274A VAL* 1.3 76.1 - - - +
276A MET* 1.3 64.7 + - - +
299C TYR* 4.0 56.8 - - + -
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Residues in contact with MET 276 (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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198A ILE* 3.8 12.3 - - - +
199A GLU* 2.8 35.7 - - + +
200A ALA* 3.7 6.1 - - - -
201A ASP* 4.3 2.9 - - - -
259A PHE* 3.4 5.1 - - - +
260A ALA* 2.9 36.5 + - + +
262A PHE* 4.3 20.4 - - + -
274A VAL* 3.6 26.7 - - + -
275A VAL* 1.3 74.1 - - - +
277A SER* 1.3 58.1 + - - +
278A ASP* 3.6 14.9 + - - +
279A PRO* 4.9 5.6 - - + -
281A ILE* 4.4 28.3 - - + -
286A THR* 4.4 11.2 - - - +
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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