Contacts of the strand formed by residues 258 - 266 (chain B) 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 ARG 258 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256B SER* 3.3 29.5 + - - +
257B HIS* 1.3 75.0 - - - +
259B TYR* 1.3 56.8 + - - +
260B VAL* 4.1 0.7 - - + -
300B ASN* 5.9 0.4 - - + -
301B SER 2.8 22.4 + - - +
302B VAL* 3.4 19.3 - - + -
303B SER* 2.7 34.2 + - - -
455B LEU* 4.0 46.1 + - + +
460B GLY 3.2 24.1 + - - -
461B GLU* 3.1 26.1 + - - -
463B LEU* 3.4 18.6 - - + -
464B MET* 3.6 13.5 - - - +
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Residues in contact with TYR 259 (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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257B HIS* 3.5 41.6 + - + +
258B ARG* 1.3 70.5 - - - +
260B VAL* 1.3 61.3 + - - +
261B GLU* 3.3 9.1 + - + +
303B SER* 3.3 29.4 - - - +
305B VAL* 4.6 8.1 - - + -
351B ASP* 3.5 10.2 - - - +
463B LEU* 2.7 27.9 + - - +
464B MET 4.1 7.2 - - - -
465B ASP 3.8 22.0 - - - +
466B LYS* 3.5 43.5 + - + -
467B PRO* 3.9 22.9 - - + -
1558B NI 4.1 1.0 - - - +
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Residues in contact with VAL 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B ARG 5.4 0.2 - - - -
259B TYR* 1.3 69.2 - - - +
261B GLU* 1.3 57.9 + - - +
262B THR* 3.2 6.5 + - - +
302B VAL* 3.8 11.2 - - + -
303B SER 2.8 8.5 + - - -
304B LEU* 3.4 31.6 - - + -
305B VAL* 2.8 32.5 + - - +
351B ASP* 5.0 1.1 - - + -
352B THR* 3.7 32.3 - - + -
378B VAL* 4.6 6.5 - - + -
403B LEU* 5.2 3.1 - - + -
407B PHE* 3.6 27.4 - - + -
463B LEU* 3.9 16.6 - - + -
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Residues in contact with GLU 261 (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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259B TYR 3.3 5.2 + - - +
260B VAL* 1.3 70.3 - - - +
262B THR* 1.3 59.8 + - - +
305B VAL* 3.6 15.7 - - + -
307B VAL* 3.9 20.1 - - + +
344B ASP* 3.0 3.2 - - - +
347B ALA 5.1 1.6 - - - +
349B HIS 4.1 4.7 - - - +
350B TYR* 3.3 7.0 - - - +
351B ASP* 2.6 41.2 + - - +
352B THR 3.1 7.6 + - - -
465B ASP* 4.0 6.3 - - - +
466B LYS 3.6 0.3 - - - +
467B PRO* 3.2 26.0 - - + +
468B GLN* 5.3 0.3 - - - +
1557B CD 2.6 24.9 - - - -
1558B NI 2.2 40.1 - - + +
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Residues in contact with THR 262 (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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260B VAL* 3.2 17.3 + - - +
261B GLU* 1.3 73.5 - - - +
263B MET* 1.3 74.9 + - - +
264B LEU* 3.6 21.8 - - + -
286B PHE* 3.3 17.8 - - + -
305B VAL 2.8 13.9 + - - -
306B VAL* 3.4 5.5 - - - +
307B VAL* 2.9 26.2 + - - +
308B LYS 3.5 4.0 + - - +
350B TYR* 3.9 3.8 - - - +
352B THR* 3.3 21.1 - - + +
354B ILE* 3.7 18.2 - - + -
403B LEU* 5.9 0.3 - - - +
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Residues in contact with MET 263 (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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262B THR* 1.3 75.9 - - - +
264B LEU* 1.3 65.2 + - - +
265B VAL* 3.7 28.9 - - + -
308B LYS* 3.3 37.7 - - + +
310B LEU* 4.0 16.4 - - - -
335B TRP* 4.7 3.1 - - + -
336B GLN* 4.1 16.4 - - + -
339B HIS* 4.3 7.4 - - + -
350B TYR* 3.0 56.4 - - + +
352B THR 3.1 6.8 + - - +
353B ALA* 3.2 6.2 - - + -
354B ILE 2.9 25.5 + - - +
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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
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262B THR* 3.6 22.7 - - + -
263B MET* 1.3 73.9 - - - +
265B VAL* 1.3 61.1 + - - +
282B LEU* 4.0 38.6 - - + +
283B LEU* 4.8 3.6 - - + -
286B PHE* 3.7 21.1 - - + -
306B VAL* 3.9 28.9 - - + -
308B LYS 3.0 8.1 + - - +
309B ILE* 3.2 14.3 - - + +
310B LEU 2.9 24.1 + - - +
354B ILE* 3.6 9.9 - - + -
356B PHE* 3.9 25.1 - - + -
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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
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263B MET* 3.7 29.6 - - + -
264B LEU* 1.3 76.5 - - - +
266B ALA* 1.3 64.2 + - - +
310B LEU* 3.3 12.6 - - + +
312B ILE* 3.8 19.7 - - + -
332B PHE* 3.6 28.5 - - + -
335B TRP* 4.1 18.4 - - + -
354B ILE 2.7 11.8 + - - +
355B LEU* 3.5 16.1 - - + -
356B PHE* 2.9 30.7 + - - -
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Residues in contact with ALA 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 76.2 - - - +
267B ASP* 1.3 62.3 + - - +
270B MET* 3.9 19.7 - - + -
278B LEU* 4.0 13.5 - - + -
282B LEU* 4.0 26.5 - - + -
310B LEU 2.9 10.4 + - - +
311B VAL* 3.6 3.0 - - + +
312B ILE* 2.9 33.0 + - - +
356B PHE* 3.7 4.5 - - + -
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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
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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