Contacts of the strand formed by residues 261 - 267 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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338C SER* 3.5 6.0 + - - -
339C VAL* 2.9 52.3 + - + +
252E LEU* 4.5 2.0 - - + -
259E PHE* 3.8 22.4 - + + -
260E GLY* 1.3 79.6 - - - +
262E LEU* 1.3 64.6 + - - +
263E LEU* 4.2 13.5 - - + -
277E LEU* 3.4 32.1 - - + -
279E GLU 3.4 12.6 - - - +
280E VAL* 4.4 11.2 - - + -
281E ASP* 3.8 4.4 + - - -
286E ALA* 3.8 19.1 - - + -
291E MET* 4.9 2.9 - - - -
297E LEU* 5.3 2.7 - - + -
317E ILE* 4.2 14.8 - - + -
326E LEU* 3.8 28.7 - - + -
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Residues in contact with LEU 262 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282A PRO* 3.6 33.2 - - + +
283A GLY* 3.8 7.4 - - - +
336C GLU* 3.5 22.2 - - + +
337C THR 3.7 8.5 - - - +
338C SER* 3.7 25.1 - - - +
261E PHE* 1.3 73.2 - - - +
263E LEU* 1.3 58.2 + - - +
276E PHE 3.5 0.3 - - - +
277E LEU* 3.6 3.5 - - - -
278E TRP* 2.7 50.3 + - + +
279E GLU* 2.9 39.5 + - + +
281E ASP* 6.0 0.2 - - - -
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Residues in contact with LEU 263 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336C GLU* 3.1 4.4 - - - +
337C THR* 2.8 40.0 + - - +
339C VAL* 5.3 1.8 - - + -
261E PHE* 4.0 9.1 + - + -
262E LEU* 1.3 71.7 - - - +
264E ARG* 1.3 59.1 + - - +
275E GLN* 3.7 24.0 - - + +
276E PHE 3.4 19.5 - - - +
277E LEU* 3.9 15.5 - - + -
297E LEU* 4.3 9.2 - - + -
310E HIS* 3.2 20.6 - - + +
313E THR* 4.0 26.7 - - + -
314E VAL* 4.2 10.3 - - + -
317E ILE* 4.0 18.8 - - + -
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Residues in contact with ARG 264 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293C ALA* 3.8 32.6 + - - +
294C GLY* 3.9 7.9 - - - -
331C PRO* 4.0 17.0 - - - +
332C GLU 4.8 6.9 + - - -
333C ALA* 5.1 5.7 - - - +
335C ARG 3.4 10.5 + - - +
336C GLU* 2.8 41.3 + - + +
262E LEU* 3.9 0.6 + - + -
263E LEU* 1.3 76.1 - - - +
265E GLU* 1.3 71.9 + - - +
266E GLU* 3.6 7.1 + - - -
275E GLN* 3.9 4.3 - - - -
276E PHE* 3.0 32.9 + - - +
278E TRP* 3.4 56.2 - - + +
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Residues in contact with GLU 265 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331C PRO* 5.4 4.2 - - - +
332C GLU* 4.7 1.6 - - - +
335C ARG* 2.9 58.6 + - + +
264E ARG* 1.3 82.1 + - - +
266E GLU* 1.3 76.9 + - - +
267E LYS* 4.0 12.3 + - + +
273E PRO* 3.6 18.5 - - + +
274E GLY 3.3 7.2 - - - +
275E GLN* 2.8 36.7 + - - +
309E GLY* 3.6 5.0 - - - -
310E HIS* 3.1 18.6 + - + +
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Residues in contact with GLU 266 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276C PHE* 3.5 34.7 - - + -
278C TRP* 5.6 0.2 - - + -
294C GLY* 2.7 42.8 - - - +
296C ARG* 5.2 2.6 + - - +
331C PRO* 4.7 6.1 - - - +
264E ARG* 3.6 3.4 + - - -
265E GLU* 1.3 80.5 - - - +
267E LYS* 1.3 66.0 + - - +
268E GLY 3.7 0.7 + - - -
274E GLY* 2.7 38.3 + - - +
276E PHE* 3.8 17.6 - - + -
278E TRP* 3.4 29.9 - - + -
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Residues in contact with LYS 267 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276C PHE* 4.0 13.8 - - - -
296C ARG* 3.7 19.0 + - - +
332C GLU* 4.1 18.8 - - - +
335C ARG* 4.3 5.6 - - - +
265E GLU* 4.0 18.4 + - + +
266E GLU* 1.3 76.4 + - - +
268E GLY* 1.3 69.3 + - - +
271E GLY* 3.6 25.7 + - - +
272E ARG 3.5 3.1 - - - -
273E PRO* 4.1 18.0 - - + +
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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