Contacts of the strand formed by residues 261 - 267 (chain A) 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 PHE 261 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252A LEU* 4.2 0.9 - - + -
259A PHE* 3.9 24.4 - + + +
260A GLY* 1.3 79.8 - - - +
262A LEU* 1.3 60.9 + - - +
263A LEU* 4.0 34.2 + - + -
277A LEU* 3.9 28.0 - - + -
279A GLU 3.3 13.2 - - - +
280A VAL* 4.4 2.2 - - - -
281A ASP* 3.8 4.4 + - - -
286A ALA* 3.8 21.1 - - + -
291A MET* 3.8 15.5 - - + -
297A LEU* 5.5 1.6 - - + -
317A ILE* 4.3 24.9 - - + -
326A LEU* 3.8 18.8 - - + -
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Residues in contact with LEU 262 (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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261A PHE* 1.3 73.4 - - - +
263A LEU* 1.3 67.1 - - - +
264A ARG* 4.4 21.3 - - + +
277A LEU* 3.6 2.9 - - - -
278A TRP* 2.7 44.9 + - + +
279A GLU* 2.9 49.9 + - + +
281A ASP* 5.7 0.4 + - - -
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Residues in contact with LEU 263 (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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261A PHE* 4.0 22.8 + - + -
262A LEU* 1.3 79.1 - - - +
264A ARG* 1.3 61.3 + - - +
275A GLN* 3.9 20.6 - - + +
276A PHE 3.3 20.6 - - - +
277A LEU* 4.3 2.9 - - + +
297A LEU* 4.0 17.7 - - + -
310A HIS* 3.1 32.4 + - + -
313A THR* 3.9 25.4 - - + -
314A VAL* 4.1 17.0 - - + -
317A ILE* 4.1 10.1 - - + -
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Residues in contact with ARG 264 (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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262A LEU* 3.8 19.4 + - + +
263A LEU* 1.3 75.2 - - - +
265A GLU* 1.3 74.7 + - - +
266A GLU* 3.7 5.2 + - - -
275A GLN* 4.0 4.3 - - - -
276A PHE* 2.8 41.0 + - - +
278A TRP* 3.5 60.2 - - + +
310A HIS* 4.3 0.9 - - - -
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Residues in contact with GLU 265 (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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264A ARG* 1.3 88.9 - - - +
266A GLU* 1.3 74.0 + - - +
267A LYS* 3.5 27.3 - - + +
273A PRO* 3.6 19.6 - - + +
274A GLY 3.3 8.7 - - - +
275A GLN* 3.0 30.8 + - - +
309A GLY* 3.8 1.9 - - - -
310A HIS* 3.1 30.4 + - + +
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Residues in contact with GLU 266 (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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264A ARG* 3.7 6.4 + - - -
265A GLU* 1.3 80.2 - - - +
267A LYS* 1.3 70.7 + - - +
268A GLY 4.0 0.2 + - - -
272A ARG 3.9 0.2 - - - +
274A GLY* 2.8 35.2 + - - +
276A PHE* 3.7 19.4 - - + -
278A TRP* 3.1 40.1 - - + -
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Residues in contact with LYS 267 (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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265A GLU* 3.5 26.2 - - + +
266A GLU* 1.3 82.6 + - - +
268A GLY* 1.3 70.7 + - - +
271A GLY* 3.4 29.1 + - - +
272A ARG 3.4 4.0 - - - -
273A PRO* 4.2 10.1 - - + -
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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