Contacts of the strand formed by residues 312 - 316 (chain A) in PDB entry 2JFF
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 VAL 312 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308A GLU* 3.3 3.4 - - - +
309A HIS 3.0 33.3 + - - +
310A ASN* 3.9 9.0 - - + +
311A GLY* 1.3 81.6 - - - +
313A ARG* 1.3 68.4 + - - +
314A TRP* 3.3 30.9 - - + +
401A VAL* 3.4 27.8 - - + -
402A GLN 3.4 30.5 - - - +
403A PRO* 5.3 0.2 - - + -
405A ASP 3.5 11.2 - - - +
407A VAL* 4.2 6.5 - - + -
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Residues in contact with ARG 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A VAL* 4.9 11.0 - - + -
307A LEU 3.5 4.7 - - - +
308A GLU* 3.5 38.7 + - + +
311A GLY 4.3 1.3 - - - +
312A VAL* 1.3 72.8 - - - +
314A TRP* 1.3 61.1 + - - +
315A ILE* 4.0 15.9 - - + +
334A HIS* 3.6 18.4 + - - -
335A VAL* 4.7 4.0 - - - +
336A ASP* 4.4 20.0 + - - +
404A GLY 5.4 3.5 + - - -
405A ASP 3.4 9.8 + - - +
406A MET* 3.4 36.6 - - + +
407A VAL 2.9 26.3 + - - +
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Residues in contact with TRP 314 (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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305A VAL* 3.7 3.0 - - - +
306A VAL* 2.9 31.6 + - + +
307A LEU* 2.7 40.1 + - + +
309A HIS 5.0 1.2 + - - -
312A VAL* 3.3 30.2 + - + +
313A ARG* 1.3 75.7 - - - +
315A ILE* 1.3 59.8 + - - +
394A MET* 3.7 22.2 - - + -
397A LEU* 4.2 11.9 - - + -
398A ALA* 4.5 8.5 - - + -
401A VAL* 4.4 9.0 - - + -
407A VAL* 3.4 42.6 - - + -
429A PHE* 4.4 2.9 - + + -
433A ALA* 3.7 33.7 - - + -
436A LEU* 4.2 20.2 - - + -
437A GLY* 3.7 24.7 + - - -
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Residues in contact with ILE 315 (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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303A PHE* 3.6 56.3 - - + -
304A GLU 3.4 3.1 - - - +
305A VAL* 4.0 18.8 - - + -
313A ARG* 4.5 7.6 - - + +
314A TRP* 1.3 80.0 - - - +
316A ASN* 1.3 61.5 + - - +
317A ASP 3.5 2.3 + - - -
406A MET* 3.6 38.8 - - + -
407A VAL 2.8 11.8 + - - +
408A LEU* 3.7 20.8 - - + -
409A LEU 3.1 26.7 + - - +
429A PHE* 3.5 7.1 - - - -
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Residues in contact with ASN 316 (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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301A HIS* 3.0 43.2 + - - +
304A GLU* 2.7 41.4 + - + +
306A VAL* 3.6 22.8 - - + +
314A TRP 4.1 0.4 + - - -
315A ILE* 1.3 67.4 - - - +
317A ASP* 1.3 57.5 + - - +
318A SER* 3.0 27.9 + - - -
409A LEU* 4.0 3.3 - - - +
426A GLY* 3.4 19.3 + - - -
429A PHE* 3.6 15.7 - - + -
430A ALA* 5.1 1.2 - - - +
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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