Contacts of the strand formed by residues 257 - 265 (chain B) in PDB entry 2J2M
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 GLU 257 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191B ARG 5.6 0.9 - - - +
219B PRO* 3.7 1.6 - - - +
220B LYS* 3.0 60.3 + - + +
221B GLU* 4.7 3.1 + - - +
255B PHE* 3.3 12.3 + - - +
256B PRO* 1.3 77.9 - - - +
258B TRP* 1.3 72.1 + - - +
259B ASP* 6.2 0.2 - - - +
296B THR* 4.6 9.3 + - - +
297B MET 3.1 4.5 - - - +
298B THR* 3.2 35.7 + - + +
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Residues in contact with TRP 258 (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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94B PHE* 3.6 23.6 - + - -
113B PHE* 3.5 25.0 - + - -
190B TYR 3.2 22.7 - - - -
191B ARG* 3.6 14.1 - - + -
193B MET 2.8 23.4 + - - -
217B TRP* 3.5 26.6 - - + -
218B VAL 3.3 7.0 - - - +
219B PRO* 3.5 26.3 - - + +
220B LYS 4.6 0.2 - - - +
246B THR* 5.8 0.4 - - + -
256B PRO* 3.4 35.2 - - + -
257B GLU* 1.3 80.8 - - - +
259B ASP* 1.3 63.5 + - - +
260B LEU 3.9 0.3 + - - -
296B THR* 3.1 4.1 - - - -
297B MET* 2.7 52.4 + - + +
299B LEU* 3.7 17.9 - - + -
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Residues in contact with ASP 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B ARG 3.4 1.4 - - - +
217B TRP* 3.4 6.3 - - - -
218B VAL* 2.9 39.3 + - + +
220B LYS* 5.2 9.0 + - - +
257B GLU* 6.2 0.2 - - - +
258B TRP* 1.3 75.2 - - - +
260B LEU* 1.3 60.1 - - - +
261B PHE* 3.7 24.6 - - + -
293B HIS* 3.0 15.5 + - - +
295B GLY 3.3 2.7 - - - -
296B THR* 3.0 28.9 - - - +
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Residues in contact with LEU 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B PHE* 3.7 38.6 - - + -
80B PHE* 6.2 0.2 - - + -
81B LEU* 5.7 2.2 - - + -
117B PHE* 5.3 0.9 - - + -
124B TRP* 4.9 14.8 - - + -
126B PHE* 5.5 0.2 - - + -
203B TRP* 6.1 1.6 - - + -
215B LEU* 3.9 31.2 - - + -
216B ARG 3.3 14.8 - - - +
217B TRP* 3.6 34.7 - - + +
258B TRP 3.9 1.6 + - - -
259B ASP* 1.3 71.4 - - - +
261B PHE* 1.3 60.6 + - - +
293B HIS* 3.7 2.3 - - - -
294B VAL* 2.7 48.8 + - + -
295B GLY 2.8 11.8 + - - +
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Residues in contact with PHE 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B LEU* 3.5 8.4 - - - +
216B ARG* 2.7 48.1 + - + +
218B VAL* 3.7 31.6 - - + -
259B ASP* 3.7 24.0 - - + -
260B LEU* 1.3 77.5 - - - +
262B VAL* 1.3 59.9 + - - +
291B PHE* 3.7 31.0 - + + -
292B GLN 3.4 7.6 - - - -
293B HIS* 3.3 45.8 - + + -
294B VAL* 4.2 2.9 - - - -
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Residues in contact with VAL 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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72B MET* 4.1 14.8 - - - -
75B TYR* 5.2 0.7 - - + -
203B TRP* 3.8 13.5 - - + -
213B ILE* 3.7 26.0 - - + -
214B LYS 3.3 12.6 - - - +
215B LEU* 3.8 12.3 - - + -
216B ARG* 5.5 0.2 - - - -
261B PHE* 1.3 74.4 - - - +
263B GLN* 1.3 66.6 + - - +
264B VAL* 4.4 10.3 - - + -
290B PRO 3.8 0.9 - - - +
291B PHE* 3.6 0.4 - - - -
292B GLN* 2.7 56.2 + - + +
294B VAL* 3.8 15.9 - - + -
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Residues in contact with GLN 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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212B TYR 3.7 0.2 - - - +
213B ILE* 3.0 11.1 - - - +
214B LYS* 2.9 38.8 + - - +
216B ARG* 2.7 31.6 + - - -
262B VAL* 1.3 73.2 - - - +
264B VAL* 1.3 63.3 + - - +
284B TRP* 2.9 42.2 + - + +
285B PHE 3.8 1.6 + - - -
289B ILE* 2.8 30.4 + - + +
290B PRO 3.5 17.5 - - - +
291B PHE* 3.4 26.7 - - + -
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Residues in contact with VAL 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B TYR* 3.5 52.3 - - + +
211B VAL* 3.6 26.9 - - + -
212B TYR 3.5 2.2 - - - -
213B ILE* 4.3 9.6 - - + -
262B VAL* 4.4 7.9 - - + -
263B GLN* 1.3 80.1 - - - +
265B LEU* 1.3 63.9 + - - +
266B ASP 4.4 0.6 + - - +
289B ILE* 3.6 18.6 - - - +
290B PRO* 4.7 0.8 + - - +
292B GLN* 3.8 15.2 - - - +
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Residues in contact with LEU 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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211B VAL 3.9 0.5 - - - -
212B TYR* 2.9 38.0 + - + +
263B GLN 4.3 0.2 - - - -
264B VAL* 1.3 78.3 - - - +
266B ASP* 1.3 69.7 + - - +
267B PRO 3.5 0.2 - - - -
269B ASP* 3.9 19.5 - - + +
270B VAL* 4.2 11.0 - - + -
273B PHE* 3.6 31.9 - - + -
277B PRO* 3.7 34.8 - - + -
278B LEU* 6.3 0.2 - - + -
284B TRP* 3.8 30.3 - - + -
289B ILE* 4.0 11.2 - - + -
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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