Contacts of the strand formed by residues 318 - 322 (chain B) in PDB entry 1EQB
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 LEU 318 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B ALA* 3.8 15.9 - - + -
174B PHE* 5.5 1.1 - - + -
175B SER 3.6 24.7 - - - +
176B ALA* 4.2 7.0 - - - +
177B TYR 3.6 34.3 - - - +
178B SER* 3.3 3.3 - - - +
203B HIS* 3.6 24.0 - - + -
314B THR* 2.6 26.8 + - - -
316B ASN* 2.9 12.3 + - - +
317B HIS* 1.3 89.5 - - + +
319B PHE* 1.3 76.2 + - - +
320B LEU* 5.8 0.4 - - + -
363B ARG* 4.3 7.2 - - + -
364B VAL 3.1 14.1 - - - +
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Residues in contact with PHE 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B SER* 4.2 7.6 - - - -
295B ALA* 3.9 12.3 - - + -
298B MET* 3.8 31.4 - - + -
299B VAL* 3.4 30.3 - - + -
302B PHE* 4.2 18.6 - + - -
309B VAL* 4.3 12.6 - - + -
310B VAL 5.6 0.2 - - - +
313B GLY 4.7 0.2 - - - +
314B THR* 4.2 6.5 - - + -
317B HIS 5.6 0.2 - - - -
318B LEU* 1.3 89.9 - - - +
320B LEU* 1.3 64.2 + - - +
321B VAL* 3.7 28.3 - - + -
362B ILE 4.1 0.2 - - - +
363B ARG* 3.7 2.6 - - - +
364B VAL* 3.0 65.4 + - + -
366B THR* 5.4 1.3 - - + -
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Residues in contact with LEU 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ALA 5.3 2.2 - - - +
123B HIS 6.1 1.1 - - - -
124B GLY* 6.0 0.9 - - - -
176B ALA* 3.7 28.0 - - + +
178B SER* 5.5 0.8 - - - -
309B VAL* 3.3 11.9 - - - +
310B VAL* 3.1 55.3 + - + +
318B LEU* 5.8 0.4 - - + -
319B PHE* 1.3 74.9 - - - +
321B VAL* 1.3 62.7 + - - +
322B ASP 4.0 0.4 - - - -
347B ASN* 3.8 20.0 - - + +
348B SER 4.0 15.9 - - - +
349B VAL* 4.3 9.2 - - + -
350B PRO* 4.4 8.7 - - + -
362B ILE 3.6 3.6 - - - +
363B ARG* 3.7 34.3 - - + -
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Residues in contact with VAL 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B PHE* 3.7 27.4 - - + -
307B TYR* 4.2 17.0 - - + -
308B LYS 3.4 7.9 - - - +
309B VAL* 4.6 4.7 - - + -
319B PHE* 3.7 26.9 - - + -
320B LEU* 1.3 76.2 - - - +
322B ASP* 1.3 60.5 + - - +
323B LEU* 3.4 25.2 + - + +
349B VAL* 4.8 2.0 - - - -
361B GLY* 3.1 25.3 - - - -
362B ILE* 3.0 29.2 + - + +
364B VAL* 4.8 0.9 - - + -
390B LEU* 5.1 0.4 - - + -
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Residues in contact with ASP 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B TYR* 5.5 0.5 - - - -
308B LYS* 2.8 60.4 + - + +
310B VAL* 4.4 13.7 - - + +
320B LEU 4.0 1.6 - - - -
321B VAL* 1.3 70.9 - - - +
323B LEU* 1.3 62.8 + - - +
324B VAL* 3.0 32.6 + - - +
325B ASP* 3.5 14.6 + - - +
326B LYS* 5.2 1.0 - - - +
349B VAL* 3.6 26.0 - - - +
350B PRO* 4.7 5.9 - - - +
360B SER 3.9 2.5 - - - -
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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
------------------------------------------------------------
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