Contacts of the strand formed by residues 264 - 270 (chain D) in PDB entry 2Y7Q
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 ILE 264 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232D PRO* 4.4 5.6 - - + -
256D VAL* 3.3 33.7 - - + -
259D TYR* 3.8 35.2 - - + +
262D GLY 3.9 0.2 + - - -
263D THR* 1.3 74.3 - - - +
265D GLN* 1.3 59.1 + - - +
266D ILE* 4.8 7.3 - - + +
279D LEU* 3.3 3.2 - - - +
280D SER* 2.6 58.9 + - - +
293D THR* 4.0 15.7 - - + -
314D VAL* 3.3 25.1 - - + -
315D THR 4.1 5.6 - - - +
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Residues in contact with GLN 265 (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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263D THR 4.3 0.2 + - - -
264D ILE* 1.3 75.1 - - - +
266D ILE* 1.3 62.5 + - - +
267D THR* 3.8 1.7 + - - +
277D VAL* 5.3 5.2 - - + -
278D ASP 3.1 15.5 - - - +
279D LEU* 3.6 17.0 - - + -
313D GLN 3.6 0.5 - - - +
315D THR* 2.9 48.8 + - - +
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Residues in contact with ILE 266 (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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254D CYS* 5.1 0.2 - - - -
256D VAL* 3.6 30.5 - - + -
264D ILE* 4.8 9.6 - - + +
265D GLN* 1.3 76.2 - - - +
267D THR* 1.3 64.1 + - - +
268D TRP* 4.1 11.1 + - + +
276D ASP 3.8 0.9 - - - +
277D VAL* 3.3 6.7 - - - -
278D ASP* 3.0 34.1 + - - +
280D SER* 6.5 0.4 - - - -
293D THR* 4.4 11.2 - - + -
294D GLN 4.7 0.9 - - - +
295D SER* 3.4 38.8 + - - +
312D CYS* 3.7 27.1 - - - -
313D GLN 3.8 4.3 - - - +
314D VAL* 4.7 5.6 - - + -
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Residues in contact with THR 267 (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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265D GLN* 4.3 1.6 + - - +
266D ILE* 1.3 75.7 - - - +
268D TRP* 1.3 66.1 + - - +
269D LEU* 4.0 15.7 - - + -
274D VAL* 5.0 6.1 - - - -
276D ASP 3.7 2.0 - - - +
277D VAL* 3.5 24.4 - - + +
311D THR 3.8 0.7 - - - +
312D CYS* 3.7 1.9 - - - -
313D GLN* 2.7 68.2 + - - +
315D THR* 3.9 9.4 + - - -
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Residues in contact with TRP 268 (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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236D ILE* 4.3 11.4 - - + -
253D LEU* 3.8 42.2 - - + -
254D CYS* 3.7 24.0 - - + -
266D ILE* 4.2 11.5 - - + +
267D THR* 1.3 72.0 - - - +
269D LEU* 1.3 61.5 + - - +
270D GLU 4.0 0.2 - - - -
273D GLN 3.5 0.2 - - - +
274D VAL* 3.4 2.6 - - - -
275D MET* 2.7 33.8 + - - -
276D ASP* 2.9 39.4 + - + +
295D SER* 3.2 35.4 + - - -
296D GLU 4.4 2.1 - - - -
297D LEU* 3.4 39.5 - - + +
310D TYR* 4.2 4.9 - + + -
311D THR 2.9 31.9 - - - -
312D CYS* 4.1 12.6 - - + -
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Residues in contact with LEU 269 (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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267D THR* 4.4 15.9 - - + +
268D TRP* 1.3 75.3 - - - +
270D GLU* 1.3 58.5 + - - +
271D ASP 3.3 2.6 + - - -
272D GLY* 4.3 15.5 - - - +
273D GLN* 3.0 30.7 - - - +
274D VAL* 3.5 9.9 - - - +
309D THR 3.4 0.9 - - - +
310D TYR* 3.2 8.3 - - - -
311D THR* 2.8 61.0 + - + +
313D GLN* 4.4 25.6 - - + +
322D GLU* 4.7 3.1 - - - +
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Residues in contact with GLU 270 (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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268D TRP 3.8 2.4 + - - -
269D LEU* 1.3 69.0 - - - +
271D ASP* 1.3 77.5 + - + +
272D GLY 3.2 0.7 - - - -
273D GLN* 2.6 30.7 + - + +
274D VAL 5.8 0.2 - - - +
275D MET* 4.8 5.8 - - - +
299D LEU* 4.6 0.3 - - - +
303D HIS* 3.0 30.7 - - - -
308D ARG* 3.9 19.4 + - + -
310D TYR* 2.9 39.3 - - + -
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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