Contacts of the strand formed by residues 262 - 268 (chain B) in PDB entry 3H8E
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 262 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260B LYS 4.5 4.5 - - - -
261B PRO* 1.3 74.4 - - - +
263B VAL* 1.3 63.4 + - - +
264B LEU* 5.8 2.2 - - + -
311B VAL* 4.0 29.2 - - + -
312B ASN 2.9 17.5 + - - +
313B LEU* 3.4 10.6 - - + +
314B VAL 2.9 23.4 + - - -
369B GLN* 2.2 39.7 - - + -
370B ALA* 3.6 12.8 - - + +
372B ILE* 6.4 0.4 - - + -
490B TYR* 3.3 33.9 - + + -
491B LEU* 3.9 20.2 - - + -
494B ARG* 3.6 30.7 - - + -
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Residues in contact with VAL 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B PRO* 4.7 2.5 - - + -
262B PHE* 1.3 76.6 - - - +
264B LEU* 1.3 68.3 + - - +
265B VAL* 4.0 13.0 - - + -
314B VAL* 3.1 23.3 - - + +
316B LEU* 3.8 30.1 - - + -
363B ALA* 4.1 8.1 - - + +
366B PHE* 4.3 15.0 - - + -
368B PRO* 3.7 24.7 - - + -
370B ALA 2.9 11.9 + - - +
371B VAL* 3.4 8.8 - - + -
372B ILE* 2.9 26.2 + - - +
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Residues in contact with LEU 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B PHE* 4.1 1.8 + - + -
263B VAL* 1.3 80.6 - - - +
265B VAL* 1.3 56.1 + - - +
266B GLY 4.1 0.2 - - - -
297B VAL* 3.9 31.2 - - + +
300B THR* 3.9 32.3 - - + -
313B LEU* 3.9 26.9 - - + -
314B VAL 2.8 8.2 + - - +
315B CYS* 3.3 3.4 - - - -
316B LEU 2.8 31.2 + - - +
372B ILE* 3.4 33.2 - - + +
374B ILE* 4.3 2.0 - - + -
487B LEU* 4.2 17.3 - - + -
490B TYR* 5.8 2.7 - - + -
491B LEU* 4.5 5.8 - - + -
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Residues in contact with VAL 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B VAL* 4.0 19.1 - - + -
264B LEU* 1.3 73.8 - - - +
266B GLY* 1.3 63.4 + - - +
267B LYS 4.2 0.2 + - - -
297B VAL* 4.3 1.8 - - - -
316B LEU* 3.3 15.9 - - + +
318B ALA* 5.3 0.4 - - + -
356B LEU* 3.6 25.1 - - + +
359B THR* 3.7 26.7 - - + -
360B LEU* 4.3 10.5 - - + -
363B ALA* 4.9 1.8 - - + -
371B VAL* 4.0 17.7 - - + -
372B ILE 2.8 7.9 + - - +
373B ASP* 3.1 12.4 - - + +
374B ILE* 2.8 27.4 + - - +
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Residues in contact with GLY 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265B VAL* 1.3 75.0 - - - +
267B LYS* 1.3 65.2 + - - -
268B GLY 3.3 0.2 + - - -
293B GLY 3.8 5.4 - - - -
294B ALA* 3.7 18.5 - - - +
297B VAL* 4.0 7.6 - - - +
316B LEU 2.9 10.5 + - - -
317B LEU* 3.7 3.0 - - - +
318B ALA* 3.0 27.5 + - - +
356B LEU* 4.3 3.8 - - - -
374B ILE 3.5 5.6 - - - -
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Residues in contact with LYS 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266B GLY* 1.3 69.2 - - - -
268B GLY* 1.3 59.3 + - - +
269B ILE* 3.5 36.8 - - + +
291B MET* 3.5 12.0 - - - +
293B GLY 3.6 3.1 + - - -
294B ALA 3.0 16.2 + - - +
318B ALA* 4.2 2.7 - - - -
351B GLU* 4.2 9.9 + - - -
352B GLY* 3.5 28.9 - - - +
355B VAL* 4.8 3.6 - - + -
356B LEU* 4.0 14.3 - - + +
374B ILE 3.0 9.0 + - - +
375B ALA* 3.6 32.8 - - + -
376B THR* 3.2 35.8 + - - +
377B LEU* 4.3 10.0 + - - +
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Residues in contact with GLY 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199B PRO* 5.0 2.3 - - - +
202B LEU* 4.8 2.1 - - - +
266B GLY 3.3 1.6 + - - -
267B LYS* 1.3 75.0 - - - +
269B ILE* 1.4 61.4 + - - +
291B MET* 3.8 10.2 - - - +
294B ALA* 3.6 17.5 - - - -
318B ALA 2.8 23.4 + - - -
319B CYS* 3.1 27.2 - - - +
320B ALA 3.1 4.9 + - - +
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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