Contacts of the strand formed by residues 312 - 320 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170B ARG* 3.4 23.4 - - - +
171B GLY* 3.7 18.7 + - - -
254B VAL* 3.5 11.2 - - - +
258B LYS 3.2 7.7 + - - +
259B ASP* 3.5 16.6 + - - +
260B VAL 3.0 24.5 + - - -
305B ARG 3.9 6.7 - - - -
306B ASN* 3.7 13.2 - - - -
307B VAL 4.5 0.4 - - - +
311B GLY* 1.3 75.2 - - - -
313B LEU* 1.3 61.5 + - - +
314B THR* 4.8 1.9 + - - -
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Residues in contact with LEU 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B PHE* 4.4 12.8 - - + -
171B GLY* 3.3 13.3 - - - -
247B ILE* 4.3 17.9 - - + -
250B ALA* 4.0 14.4 - - + -
251B LYS* 5.2 3.1 - - + -
254B VAL* 4.1 10.3 - - + -
260B VAL* 3.4 32.5 - - + +
262B ILE* 4.0 13.2 - - + -
303B ALA* 3.4 30.1 - - + +
304B ALA* 3.3 21.0 - - - +
305B ARG 3.1 16.9 + - - +
312B SER* 1.3 76.2 - - - +
314B THR* 1.3 61.2 + - - +
315B ILE* 4.3 5.8 - - + -
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Residues in contact with THR 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B LEU* 4.6 3.5 - - + +
168B ILE* 4.7 6.7 - - + -
169B GLY 3.6 10.4 + - - +
170B ARG* 3.8 3.3 - - - -
171B GLY 3.0 22.0 + - - -
172B GLN* 3.3 20.6 - - + +
260B VAL 3.0 12.5 + - - +
261B ILE* 4.3 21.2 - - + +
262B ILE* 2.6 34.5 + - - +
312B SER* 4.8 2.3 + - - -
313B LEU* 1.3 71.0 - - - +
315B ILE* 1.3 59.1 + - - +
316B ILE* 4.0 20.9 - - + -
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Residues in contact with ILE 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B GLN 3.3 6.1 + - - -
173B ARG* 3.5 5.9 - - - -
174B GLY 3.5 21.3 + - - +
247B ILE* 4.4 5.6 - - + -
262B ILE* 3.3 32.5 - - + +
264B LEU* 4.7 16.2 - - + -
300B PHE* 3.6 29.6 - - + +
301B PHE* 4.0 25.4 - - + +
304B ALA* 3.7 31.6 - - + +
313B LEU* 4.3 9.9 - - + -
314B THR* 1.3 78.7 - - - +
316B ILE* 1.3 67.2 + - - +
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Residues in contact with ILE 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B ILE* 4.9 18.6 - - + -
172B GLN* 4.2 16.2 - - + +
174B GLY* 3.5 30.1 - - - +
176B ILE* 3.7 31.4 - - + -
188B LEU* 5.8 4.2 - - + +
191B ILE* 5.6 8.3 - - + -
262B ILE 3.0 6.9 + - - -
263B LEU* 3.6 22.5 - - + +
264B LEU* 2.8 29.2 + - - +
314B THR* 4.0 15.7 - - + -
315B ILE* 1.3 76.5 - - - +
317B ALA* 1.3 59.8 + - - +
318B THR* 4.8 1.4 - - + +
341B MET* 5.0 6.3 - - - -
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Residues in contact with ALA 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B GLY 3.5 5.9 + - - -
175B LEU* 3.2 19.6 - - + -
176B ILE* 2.6 32.6 + - - +
264B LEU* 3.3 20.0 - - + -
267B ILE* 3.7 28.3 - - + -
301B PHE* 4.1 12.6 - - + -
315B ILE* 4.0 1.2 - - + -
316B ILE* 1.3 73.6 - - - +
318B THR* 1.3 55.9 + - - +
319B ALA 4.0 0.2 - - - -
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Residues in contact with THR 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176B ILE* 3.2 32.5 - - + -
184B LYS* 4.9 13.5 - - + +
187B LEU* 6.1 2.0 - - + -
188B LEU* 4.9 12.6 - - + -
264B LEU 3.3 14.8 + - - +
265B ASP* 2.3 45.1 + - - +
267B ILE* 3.2 13.2 - - - +
316B ILE* 4.8 1.3 - - + +
317B ALA* 1.3 74.0 - - - +
319B ALA* 1.3 64.0 + - - +
320B LEU* 3.6 13.0 - - - +
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Residues in contact with ALA 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B LEU* 4.6 12.6 - - + -
176B ILE 2.9 18.5 + - - +
177B VAL* 4.5 10.3 - - + -
178B ALA* 3.4 18.7 + - - +
184B LYS* 5.0 0.9 - - - +
267B ILE* 3.8 14.1 - - + +
268B THR* 4.0 2.5 - - - +
317B ALA 4.0 2.0 + - - -
318B THR* 1.3 73.4 - - - +
320B LEU* 1.3 63.4 + - - +
321B ILE* 5.0 0.2 - - - -
332B TYR* 4.1 29.4 - - + -
335B PHE* 6.5 1.3 - - + -
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Residues in contact with LEU 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B ALA 3.9 8.3 - - - +
180B PRO* 4.9 8.5 - - + -
184B LYS* 3.7 32.1 - - + +
265B ASP* 4.6 10.1 - - - +
266B SER* 5.4 1.6 - - - -
268B THR* 3.2 38.0 + - + +
269B ARG* 5.3 17.7 - - + +
318B THR* 3.6 18.4 - - - +
319B ALA* 1.3 74.4 - - - +
321B ILE* 1.3 64.7 + - - +
323B THR* 3.8 19.3 - - + -
328B ASP* 4.2 21.0 - - - +
332B TYR* 4.3 2.8 - - - +
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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