Contacts of the strand formed by residues 312 - 320 (chain A) in PDB entry 6XAV
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 SER 312 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170A ARG* 3.4 21.2 + - - +
171A GLY 3.8 14.2 + - - -
254A VAL* 3.5 10.7 - - - +
258A LYS 3.4 6.1 + - - +
259A ASP* 3.3 20.1 + - - +
260A VAL 3.2 23.5 + - - -
305A ARG 3.7 7.9 - - - -
306A ASN* 3.6 17.0 - - - -
307A VAL 4.4 1.1 - - - +
311A GLY* 1.3 75.9 - - - -
313A LEU* 1.3 61.0 + - - +
314A THR* 4.3 1.7 + - - -
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Residues in contact with LEU 313 (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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133A PHE* 4.5 11.9 - - + -
171A GLY* 3.3 8.6 - - - -
247A ILE* 4.2 20.0 - - + -
250A ALA* 4.1 13.2 - - + -
251A LYS* 5.1 2.9 - - + -
254A VAL* 4.0 9.9 - - + -
260A VAL* 3.5 35.7 - - + +
262A ILE* 4.3 10.1 - - + -
303A ALA* 3.4 29.4 - - + +
304A ALA* 3.3 10.9 - - - +
305A ARG 3.0 31.4 + - - +
312A SER* 1.3 75.1 - - - +
314A THR* 1.3 61.4 + - - +
315A ILE* 4.3 8.5 - - + -
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Residues in contact with THR 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A LEU* 4.8 1.9 - - + +
168A ILE* 4.6 5.4 - - + -
169A GLY 3.5 8.1 + - - +
170A ARG* 3.6 2.6 - - - -
171A GLY 2.7 27.4 + - - -
172A GLN* 3.4 27.7 + - + +
260A VAL 3.0 10.8 + - - +
261A ILE* 3.3 21.3 - - + +
262A ILE 2.8 31.4 + - - +
312A SER* 4.3 1.8 + - - -
313A LEU* 1.3 71.5 + - - +
315A ILE* 1.3 58.4 + - - +
316A ILE* 4.0 21.3 - - + -
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Residues in contact with ILE 315 (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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172A GLN 3.3 8.0 + - - +
173A ARG* 4.1 0.3 - - - -
174A GLY 3.7 22.7 + - - +
247A ILE* 4.6 9.0 - - + -
262A ILE* 3.3 22.2 - - + +
264A LEU* 5.0 4.5 - - + -
300A PHE* 3.5 44.9 - - + +
301A PHE* 3.8 21.4 - - + +
304A ALA* 3.7 27.2 - - + +
313A LEU* 4.3 16.2 - - + -
314A THR* 1.3 76.4 - - - +
316A ILE* 1.3 67.9 + - - +
317A ALA* 4.7 5.8 - - + +
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Residues in contact with ILE 316 (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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168A ILE* 4.5 27.6 - - + -
172A GLN* 4.7 5.8 - - + +
174A GLY* 4.2 18.6 - - - +
176A ILE* 3.7 30.7 - - + -
188A LEU* 5.6 3.3 - - + +
191A ILE* 5.2 13.2 - - + -
261A ILE* 5.3 1.6 - - + -
262A ILE 2.9 10.8 + - - +
263A LEU* 3.4 24.4 - - + +
264A LEU 3.2 21.3 + - - +
265A ASP* 4.5 2.6 - - - +
314A THR* 4.0 21.5 - - + -
315A ILE* 1.3 78.8 - - - +
317A ALA* 1.3 60.6 + - - +
318A THR* 5.1 1.4 - - + +
341A MET* 4.9 3.8 - - - -
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Residues in contact with ALA 317 (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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174A GLY 3.6 7.2 + - - +
175A LEU* 3.4 17.0 - - + -
176A ILE* 2.6 35.7 + - - +
264A LEU* 3.2 16.6 - - + +
267A ILE* 3.7 27.8 - - + -
301A PHE* 4.7 7.2 - - + -
315A ILE* 3.9 7.8 + - + -
316A ILE* 1.3 73.7 - - - +
318A THR* 1.3 56.3 + - - +
319A ALA 4.1 0.4 - - - -
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Residues in contact with THR 318 (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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176A ILE* 3.3 31.2 - - + -
184A LYS* 4.8 22.3 - - + +
187A LEU* 6.0 1.3 - - + -
188A LEU* 4.6 9.4 - - + -
264A LEU 3.6 3.2 + - - -
265A ASP* 3.3 43.2 + - - +
266A SER 4.7 0.5 + - - -
267A ILE* 3.3 17.1 + - - +
316A ILE 5.1 1.1 - - - +
317A ALA* 1.3 76.0 - - - +
319A ALA* 1.3 61.3 + - - +
320A LEU* 3.7 14.1 - - - +
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Residues in contact with ALA 319 (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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175A LEU* 4.8 13.7 - - + -
176A ILE 2.9 11.0 + - - +
177A VAL* 4.5 17.7 - - + -
178A ALA* 3.3 27.8 + - - +
184A LYS* 4.9 0.9 - - - +
267A ILE* 4.1 8.9 - - + +
268A THR* 3.6 7.0 - - - +
317A ALA 4.1 1.6 + - - -
318A THR* 1.3 73.2 - - - +
320A LEU* 1.3 63.7 + - - +
321A ILE* 4.1 0.4 - - - -
332A TYR* 4.6 18.4 - - + -
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Residues in contact with LEU 320 (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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178A ALA 3.8 10.8 - - - +
180A PRO* 4.7 14.1 - - + -
184A LYS* 3.7 31.9 - - + +
265A ASP 5.5 4.3 - - - +
266A SER* 6.1 0.2 - - - -
268A THR* 3.0 38.7 + - + +
269A ARG* 4.4 28.0 - - + +
272A ARG* 5.3 0.4 - - - +
318A THR* 3.7 14.8 - - - +
319A ALA* 1.3 77.4 - - - +
321A ILE* 1.3 65.6 + - - +
323A THR* 3.8 14.8 - - + -
328A ASP* 3.8 23.4 - - - +
332A TYR* 4.8 1.7 - - - +
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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