Contacts of the strand formed by residues 257 - 266 (chain A) in PDB entry 2JIH
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 HIS 257 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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256A SER* 1.3 85.2 - - - +
258A ARG* 1.3 68.9 + - - +
259A TYR* 3.6 41.5 + - + +
301A SER* 3.0 25.1 + - - +
303A SER* 5.8 2.6 + - - -
463A LEU 3.7 6.2 - - - +
464A MET* 4.0 12.8 - - - +
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Residues in contact with ARG 258 (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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256A SER* 4.1 19.5 + - - -
257A HIS* 1.3 73.8 - - - +
259A TYR* 1.3 57.4 + - - +
260A VAL* 4.0 0.4 - - + -
300A ASN* 4.7 7.0 + - + +
301A SER* 2.9 19.2 + - - +
302A VAL* 3.4 14.1 - - + -
303A SER* 2.6 35.9 + - - -
455A LEU* 3.4 68.4 + - + +
458A GLY* 6.0 0.2 - - - -
460A GLY 3.9 9.5 + - - -
463A LEU* 3.3 21.1 - - + +
464A MET* 3.2 35.4 - - - -
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Residues in contact with TYR 259 (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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257A HIS* 3.6 44.8 + - + +
258A ARG* 1.3 71.8 - - - +
260A VAL* 1.3 61.0 + - - +
261A GLU* 3.4 7.5 + - + +
303A SER* 3.3 30.1 - - - +
305A VAL* 4.6 7.2 - - + -
351A ASP* 3.6 3.6 - - - +
463A LEU* 2.9 26.0 + - - +
464A MET 4.0 8.1 - - - -
465A ASP 3.7 24.2 - - - +
466A LYS* 3.7 36.3 + - + +
467A PRO* 3.8 24.9 - - + -
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Residues in contact with VAL 260 (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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258A ARG 5.1 0.4 - - - -
259A TYR* 1.3 71.4 - - - +
261A GLU* 1.3 58.3 + - - +
262A THR* 3.1 9.7 + - - +
302A VAL* 3.9 9.9 - - + -
303A SER 2.7 9.1 + - - +
304A LEU* 3.9 26.0 - - + -
305A VAL* 3.1 25.1 + - - +
351A ASP* 4.8 0.9 - - + -
352A THR* 3.6 31.2 - - + -
378A VAL* 4.6 6.5 - - + -
403A LEU* 5.5 3.4 - - + -
407A PHE* 3.5 31.6 - - + -
463A LEU* 4.1 19.7 - - + -
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Residues in contact with GLU 261 (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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259A TYR 4.5 4.0 - - - +
260A VAL* 1.3 70.1 - - - +
262A THR* 1.3 58.2 + - - +
305A VAL* 3.8 13.7 - - + -
307A VAL* 3.9 16.8 - - + +
344A ASP* 2.8 4.5 - - - +
347A ALA* 4.8 3.3 - - - +
349A HIS 3.8 17.5 - - - +
350A TYR* 3.4 2.8 - - - +
351A ASP* 2.7 39.1 + - - +
352A THR* 3.1 8.1 + - - +
465A ASP* 3.2 7.3 - - - +
466A LYS 3.9 0.7 - - - +
467A PRO* 3.4 25.2 - - + +
468A GLN* 4.6 1.6 + - - +
1554A CD 2.5 27.3 - - - -
1558A CD 2.2 31.1 - - - -
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Residues in contact with THR 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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260A VAL* 3.1 15.8 + - - +
261A GLU* 1.3 73.8 - - - +
263A MET* 1.3 76.7 + - - +
264A LEU* 3.8 11.2 - - + -
286A PHE* 3.5 16.6 - - + -
304A LEU* 5.4 0.3 - - - +
305A VAL 2.8 17.8 + - - -
306A VAL* 3.5 4.5 - - - +
307A VAL* 2.9 26.2 + - - +
308A LYS 3.4 3.6 + - - -
350A TYR* 4.0 4.0 - - - -
352A THR* 3.4 19.8 - - + +
354A ILE* 3.6 25.6 - - + -
403A LEU* 5.7 0.5 - - - +
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Residues in contact with MET 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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262A THR* 1.3 77.8 - - - +
264A LEU* 1.3 62.5 + - - +
265A VAL* 3.6 28.5 - - + -
308A LYS* 3.1 31.6 - - + +
310A LEU* 4.1 13.5 - - - +
335A TRP* 4.5 2.9 - - + -
336A GLN* 3.8 19.3 - - + -
339A HIS* 4.4 5.4 - - + -
350A TYR* 3.2 62.5 - - + +
352A THR 2.9 10.1 + - - +
353A ALA* 3.4 5.8 - - + -
354A ILE 3.1 25.8 + - - +
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Residues in contact with LEU 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 THR* 3.8 14.6 - - + -
263A MET* 1.3 71.7 - - - +
265A VAL* 1.3 60.7 + - - +
282A LEU* 3.9 40.6 - - + +
283A LEU* 4.3 8.3 - - + -
286A PHE* 3.6 29.4 - - + -
306A VAL* 3.8 28.0 - - + -
308A LYS 2.9 7.7 + - - +
309A ILE* 3.1 15.5 - - + +
310A LEU 2.9 23.9 + - - -
354A ILE* 3.7 7.2 - - + -
356A PHE* 4.0 22.0 - - + -
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Residues in contact with VAL 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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263A MET* 3.6 37.7 - - + +
264A LEU* 1.3 78.5 - - - +
266A ALA* 1.3 63.5 + - - +
282A LEU* 5.1 0.9 - - - -
310A LEU* 3.2 13.0 - - + +
312A ILE* 3.5 28.5 - - + -
332A PHE* 3.9 20.2 - - + -
335A TRP* 4.0 16.8 - - + -
354A ILE 3.0 12.2 + - - +
355A LEU* 4.0 8.7 - - + -
356A PHE* 3.0 29.0 + - - -
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Residues in contact with ALA 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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265A VAL* 1.3 74.7 - - - +
267A ASP* 1.3 60.7 + - - +
270A MET* 3.7 22.7 - - + -
278A LEU* 4.0 19.5 - - + -
282A LEU* 4.0 21.1 - - + +
310A LEU 3.0 9.1 + - - +
311A VAL* 3.5 2.8 - - + +
312A ILE* 2.9 30.6 + - - +
356A PHE* 3.6 6.3 - - + +
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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