Contacts of the strand formed by residues 273 - 280 (chain D) in PDB entry 2V90
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 PRO 273 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265D GLU* 3.8 28.7 - - - +
266D GLU 4.1 0.7 - - - +
267D LYS* 4.0 15.9 - - + -
271D GLY 3.6 6.3 - - - +
272D ARG* 1.3 87.3 - - + +
274D GLY* 1.3 59.0 + - - +
275D GLN* 4.0 0.8 - - - +
307D GLY* 3.6 42.5 + - - +
308D LEU 3.7 18.2 - - - +
309D GLY* 4.3 4.0 - - - +
269F LEU* 3.7 6.0 - - - +
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Residues in contact with GLY 274 (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 GLU* 3.3 5.5 - - - +
266D GLU 2.9 39.4 + - - -
272D ARG 3.5 2.0 + - - -
273D PRO* 1.3 74.7 - - - +
275D GLN* 1.3 63.9 + - - -
276D PHE* 3.7 15.8 - - - -
296D ARG* 5.0 7.6 - - - -
307D GLY 5.7 0.2 - - - -
269F LEU* 5.2 5.6 - - - -
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Residues in contact with GLN 275 (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 LEU* 3.9 18.4 - - + +
264D ARG 4.0 0.8 - - - -
265D GLU* 2.8 40.3 + - - +
273D PRO* 4.0 3.4 - - - +
274D GLY* 1.3 74.9 + - - -
276D PHE* 1.3 61.5 + - - +
296D ARG* 3.7 7.5 - - - +
297D LEU* 2.9 36.6 + - + +
305D VAL* 5.5 4.5 - - + +
308D LEU 3.2 21.5 + - - +
309D GLY* 3.8 0.2 - - - -
310D HIS* 2.8 39.1 + - - +
313D THR* 3.6 25.8 - - + +
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Residues in contact with PHE 276 (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 LEU* 3.3 7.3 - - - +
264D ARG 2.9 39.0 + - - +
266D GLU* 3.8 29.6 - - + -
274D GLY* 3.7 25.8 - - - -
275D GLN* 1.3 74.2 - - - +
277D LEU* 1.3 60.6 + - - +
278D TRP* 3.2 19.7 + + + -
295D ASP 3.5 4.9 - - - +
296D ARG* 3.8 33.9 - - + -
266F GLU* 3.4 46.9 - - + -
267F LYS 4.0 16.8 - - - -
268F GLY* 5.3 3.6 - - - -
276F PHE* 5.7 1.3 - + - -
278F TRP* 4.4 5.2 - - + -
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Residues in contact with LEU 277 (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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261D PHE* 3.3 38.6 - - + -
262D LEU 3.5 4.3 - - - +
263D LEU* 3.6 15.5 - - + -
276D PHE* 1.3 68.3 - - - +
278D TRP* 1.3 59.3 + - - +
279D GLU 3.5 2.5 - - - -
280D VAL* 4.6 6.5 - - + -
291D MET* 3.2 28.7 - - + -
292D GLN 4.1 5.6 - - - +
293D ALA* 3.3 2.6 - - - -
294D GLY* 2.7 33.6 + - - -
295D ASP* 2.7 43.6 + - + +
297D LEU* 4.7 11.2 - - + +
328D VAL* 3.3 20.4 - - + -
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Residues in contact with TRP 278 (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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262D LEU* 2.8 27.3 + - + +
264D ARG* 3.6 42.4 - - + +
266D GLU* 3.4 39.5 - - + -
276D PHE* 3.2 14.9 + + + -
277D LEU* 1.3 74.8 - - - +
279D GLU* 1.3 80.2 + - + +
293D ALA* 3.6 7.8 - - - +
266F GLU* 5.7 0.2 - - + -
276F PHE* 4.1 6.5 - - + -
277F LEU 4.0 1.6 - - - -
278F TRP* 2.9 109.9 + + - -
293F ALA* 5.0 2.2 - - + +
294F GLY* 4.0 12.4 - - - +
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Residues in contact with GLU 279 (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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261D PHE* 3.4 4.7 - - - +
262D LEU* 3.0 57.6 + - + +
278D TRP* 1.3 93.6 + - + +
280D VAL* 1.3 66.7 + - - +
281D ASP* 4.1 13.1 - - - +
293D ALA* 4.2 4.0 - - - -
278F TRP* 5.6 1.4 - - + +
279F GLU* 6.1 1.4 - - - +
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Residues in contact with VAL 280 (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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260D GLY 3.7 7.4 - - - +
261D PHE* 4.4 7.9 - - + -
277D LEU* 4.6 7.2 - - + -
279D GLU* 1.3 79.6 - - - +
281D ASP* 1.3 68.0 + - - +
282D PRO* 3.5 5.5 - - - +
286D ALA* 3.9 4.5 - - + -
287D LYS* 3.3 53.4 + - + +
291D MET* 3.9 17.3 - - + +
292D GLN 3.7 7.9 - - - +
293D ALA* 3.6 31.1 - - + +
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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