Contacts of the strand formed by residues 312 - 320 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170D ARG* 3.4 21.1 - - - +
171D GLY 3.9 15.2 + - - -
254D VAL* 3.8 8.5 - - - +
258D LYS 3.2 6.6 + - - +
259D ASP* 3.1 20.2 + - - +
260D VAL 2.9 25.3 + - - -
305D ARG 3.8 6.5 - - - -
306D ASN* 3.5 18.8 - - - -
307D VAL 4.4 0.7 - - - +
311D GLY* 1.3 75.2 - - - -
313D LEU* 1.3 60.4 + - - +
314D THR* 4.2 1.3 + - - -
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Residues in contact with LEU 313 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D PHE* 5.0 6.5 - - + -
171D GLY* 3.3 9.6 - - - -
247D ILE* 4.6 8.7 - - + -
250D ALA* 4.3 7.9 - - + -
251D LYS* 5.4 4.5 - - + -
254D VAL* 3.8 16.6 - - + -
260D VAL* 3.4 35.0 - - + +
262D ILE* 4.0 16.4 - - + -
303D ALA* 3.4 35.9 - - + +
304D ALA* 3.3 9.6 - - - +
305D ARG 3.0 33.2 + - - +
312D SER* 1.3 75.0 - - - +
314D THR* 1.3 62.1 + - - +
315D ILE* 4.3 9.6 - - + -
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Residues in contact with THR 314 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145D LEU* 4.6 2.0 - - + +
168D ILE* 4.5 6.5 - - + -
169D GLY 3.5 13.6 + - - +
170D ARG* 3.7 3.6 - - - -
171D GLY 2.8 26.0 + - - -
172D GLN 3.3 17.0 - - - +
260D VAL 2.8 9.6 + - - +
261D ILE* 3.3 28.7 - - + +
262D ILE* 2.7 33.3 + - - +
312D SER* 4.9 1.2 + - - -
313D LEU* 1.3 71.3 + - - +
315D ILE* 1.3 58.6 + - - +
316D ILE* 4.0 21.3 - - + -
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Residues in contact with ILE 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172D GLN 3.3 6.7 + - - -
173D ARG* 3.6 5.5 - - - -
174D GLY 3.4 21.7 + - - +
247D ILE* 4.9 3.6 - - + -
262D ILE* 3.3 29.2 - - + +
264D LEU* 4.8 13.5 - - + -
300D PHE* 3.4 30.1 - - + +
301D PHE* 4.0 28.4 - - + +
303D ALA* 4.7 0.9 - - + -
304D ALA* 3.7 28.0 - - + +
313D LEU* 4.3 16.8 - - + -
314D THR* 1.3 77.6 - - - +
316D ILE* 1.3 62.7 + - - +
317D ALA 4.5 4.0 - - - +
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Residues in contact with ILE 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168D ILE* 4.3 32.5 - - + -
172D GLN* 4.1 5.8 - - + +
174D GLY* 3.4 32.8 - - - +
176D ILE* 3.8 31.9 - - + +
188D LEU* 5.3 0.9 - - - +
191D ILE* 5.6 3.1 - - + -
261D ILE* 5.6 0.7 - - + -
262D ILE 3.1 8.1 + - - -
263D LEU* 4.0 23.3 - - + +
264D LEU 3.4 18.5 + - - +
314D THR* 4.0 22.7 - - + -
315D ILE* 1.3 72.8 - - - +
317D ALA* 1.3 61.7 + - - +
318D THR* 4.5 3.5 - - - +
341D MET* 5.0 2.9 - - - -
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Residues in contact with ALA 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174D GLY 3.3 6.3 + - - -
175D LEU* 3.3 14.0 - - + -
176D ILE* 2.7 32.4 + - - +
264D LEU* 3.3 17.5 - - + +
267D ILE* 4.0 20.4 - - + -
301D PHE* 3.6 28.0 - - + -
315D ILE* 3.8 2.9 + - + +
316D ILE* 1.3 77.3 - - - +
318D THR* 1.3 54.7 + - - +
319D ALA 4.1 0.2 - - - -
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Residues in contact with THR 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175D LEU* 5.3 0.2 - - - -
176D ILE* 3.2 37.5 - - + -
184D LYS* 4.7 19.1 - - + +
188D LEU* 4.9 4.9 - - + -
264D LEU 3.1 12.2 + - - +
265D ASP* 3.2 39.4 + - - +
267D ILE* 3.2 19.3 + - - +
316D ILE 4.5 1.8 - - - +
317D ALA* 1.3 78.0 - - - +
319D ALA* 1.3 62.0 + - - +
320D LEU* 3.5 10.9 - - - +
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Residues in contact with ALA 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175D LEU* 5.0 13.0 - - + +
176D ILE 2.6 18.0 + - - +
177D VAL* 3.9 27.1 - - + -
178D ALA* 3.2 16.8 + - - +
184D LYS* 4.4 4.7 - - - +
267D ILE* 4.6 6.3 - - + -
268D THR* 4.7 1.1 - - - -
317D ALA 4.1 1.0 - - - -
318D THR* 1.3 75.1 - - - +
320D LEU* 1.3 63.6 + - - +
332D TYR* 4.0 20.4 - - + -
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Residues in contact with LEU 320 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178D ALA 3.6 4.9 - - - +
180D PRO* 5.4 7.2 - - + -
184D LYS* 4.7 20.2 - - - +
265D ASP 4.9 8.7 - - - +
266D SER* 5.9 0.4 - - - -
268D THR* 3.5 36.8 + - + +
269D ARG* 4.8 23.1 - - + +
318D THR* 3.5 16.8 - - - +
319D ALA* 1.3 80.9 - - - +
321D ILE* 1.3 67.1 + - - +
323D THR* 4.0 20.2 - - + -
328D ASP* 4.2 24.0 - - + +
332D TYR* 4.4 2.4 - - - +
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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