Contacts of the strand formed by residues 302 - 311 (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 VAL 302 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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258B ARG* 3.4 17.5 - - + +
260B VAL* 3.8 26.9 - - + -
290B ALA 5.0 0.5 - - - +
293B TYR* 3.6 41.8 + - + +
294B LYS* 4.3 9.7 - - - +
298B ILE* 4.9 2.9 - - + -
300B ASN* 3.7 25.2 + - + +
301B SER* 1.3 78.8 + - - +
303B SER* 1.3 63.5 + - - +
304B LEU* 4.0 11.7 + - + -
407B PHE* 4.3 7.2 - - + -
451B ILE* 4.6 14.6 - - + -
455B LEU* 4.7 2.9 - - + -
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Residues in contact with SER 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B HIS* 5.8 2.4 + - - +
258B ARG 2.7 15.2 + - - -
259B TYR* 3.3 24.5 - - - -
260B VAL 2.8 25.9 + - - -
294B LYS* 3.6 24.6 + - - +
301B SER* 5.4 2.4 + - - -
302B VAL* 1.3 71.4 + - - +
304B LEU* 1.3 66.2 + - - +
305B VAL* 3.4 11.1 + - - +
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Residues in contact with LEU 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B VAL* 3.4 35.0 - - + -
286B PHE* 3.7 21.8 - - + -
289B ALA* 4.0 7.0 - - + -
290B ALA* 4.0 34.6 - - + +
293B TYR* 3.9 28.9 - - + -
294B LYS* 5.8 0.2 - - - +
302B VAL* 4.0 11.7 + - + -
303B SER* 1.3 70.7 - - - +
305B VAL* 1.3 65.9 + - - +
403B LEU* 3.7 30.5 - - + -
407B PHE* 5.0 2.7 - - + -
473B LEU* 3.8 15.8 - - - +
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Residues in contact with VAL 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B TYR* 4.6 6.5 - - + -
260B VAL 2.8 19.5 + - - +
261B GLU* 4.0 13.2 - - + -
262B THR* 2.8 29.1 + - - -
286B PHE* 3.8 2.7 - - - -
303B SER* 3.8 20.2 - - - +
304B LEU* 1.3 82.0 - - - +
306B VAL* 1.3 62.9 + - - +
307B VAL* 4.7 1.8 - - + -
467B PRO* 3.7 38.6 - - + -
470B PRO* 4.4 10.5 - - + -
473B LEU* 4.7 5.4 - - + -
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Residues in contact with VAL 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B THR 3.4 4.5 - - - +
264B LEU* 3.9 13.9 - - + -
283B LEU* 3.9 17.7 - - + -
286B PHE* 3.3 33.9 - - + -
305B VAL* 1.3 71.9 - - - +
307B VAL* 1.3 62.1 + - - +
308B LYS 3.5 20.6 - - - +
309B ILE* 3.9 10.5 - - + -
470B PRO* 3.4 4.3 - - - +
471B ILE* 2.6 65.4 + - + +
473B LEU* 3.9 4.2 - - + +
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Residues in contact with VAL 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B GLU* 3.9 31.0 - - + +
262B THR 2.9 9.1 + - - +
305B VAL* 4.7 1.1 - - + -
306B VAL* 1.3 76.0 - - - +
308B LYS* 1.3 64.0 + - + +
347B ALA 3.8 17.1 - - - +
348B GLU* 3.8 27.2 - - - +
349B HIS 3.7 19.1 - - - +
350B TYR* 3.8 21.8 - - + -
467B PRO* 4.1 17.3 - - + -
468B GLN 5.4 1.8 - - - +
469B ASN 5.3 2.3 - - - +
470B PRO* 4.8 4.7 - - + -
471B ILE* 4.6 8.5 - - - +
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Residues in contact with LYS 308 (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 3.5 0.6 + - - -
263B MET* 3.3 35.6 - - + -
264B LEU 3.0 21.8 + - - -
306B VAL* 3.5 7.1 - - - +
307B VAL* 1.3 89.9 - - + +
309B ILE* 1.3 77.3 + - - +
310B LEU* 4.2 22.0 - - - -
339B HIS* 2.8 31.5 + - - +
341B PRO* 4.8 1.4 - - - +
348B GLU* 3.9 35.8 + - + +
350B TYR* 4.1 7.6 - - + -
471B ILE* 4.4 4.0 - - - -
1566B MG 4.1 9.8 - - - -
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Residues in contact with ILE 309 (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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264B LEU* 3.2 20.4 - - + +
279B LYS* 4.3 29.6 - - + +
282B LEU* 4.3 20.2 - - + -
283B LEU* 4.0 28.9 - - + -
306B VAL* 3.9 7.0 - - + -
308B LYS* 1.3 84.1 - - - +
310B LEU* 1.3 82.0 + - - +
311B VAL* 4.4 5.6 - - + -
471B ILE* 3.5 26.0 - - + +
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Residues in contact with LEU 310 (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* 4.0 17.9 - - - -
264B LEU 2.9 8.3 + - - +
265B VAL* 3.3 13.8 - - + +
266B ALA* 2.9 27.4 + - - +
308B LYS* 4.2 14.8 - - - -
309B ILE* 1.3 84.1 - - - +
311B VAL* 1.3 65.6 + - - +
312B ILE* 4.2 1.8 - - + -
335B TRP* 3.7 26.0 - - + -
339B HIS* 3.9 27.1 - - + +
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Residues in contact with VAL 311 (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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494A GLU* 5.3 1.3 - - - +
266B ALA* 3.6 8.7 - - + +
271B ALA* 3.9 13.0 - - + -
278B LEU* 3.8 35.0 - - + -
279B LYS* 4.7 16.6 - - + -
282B LEU* 5.3 0.2 - - + -
309B ILE* 4.4 13.9 - - + -
310B LEU* 1.3 78.3 - - - +
312B ILE* 1.3 63.1 + - - +
313B HIS* 3.3 42.2 + - + +
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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