Contacts of the strand formed by residues 254 - 262 (chain A) in PDB entry 1JZ3
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 LEU 254 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220A THR* 4.0 9.0 - - + -
246A MET* 3.6 22.2 - - + -
249A GLU 3.2 25.6 - - - +
250A LEU* 4.0 3.1 - - + -
251A ARG 3.0 21.5 + - - +
252A ASP 3.9 1.2 - - - +
253A TYR* 1.3 104.9 - - + +
255A ARG* 1.3 80.9 + - - +
273A PRO* 3.6 9.0 - - - +
274A PHE* 3.8 22.1 + - + -
315A LEU* 4.6 4.3 - - + -
316A HIS 3.7 4.9 - - - +
323A ILE* 3.5 29.4 - - + -
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Residues in contact with ARG 255 (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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252A ASP 2.8 28.7 + - - -
253A TYR* 3.6 5.7 - - - +
254A LEU* 1.3 85.2 + - - +
256A VAL* 1.3 63.9 + - - +
271A THR* 4.1 12.0 - - + +
272A ALA 3.4 9.0 - - - +
273A PRO* 3.6 31.5 - - - +
274A PHE* 4.4 3.8 - - - -
315A LEU* 3.6 8.8 - - - +
316A HIS* 2.8 52.7 + - + +
318A ALA* 3.5 40.1 - - + +
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Residues in contact with VAL 256 (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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244A VAL* 4.1 12.8 - - + -
255A ARG* 1.3 75.2 - - - +
257A THR* 1.3 74.1 + - - +
258A VAL* 4.0 9.4 - - + -
270A GLY 3.8 1.0 - - - +
271A THR* 3.3 2.8 - - - +
272A ALA 3.0 30.8 + - - -
274A PHE* 3.4 33.9 - - + -
289A VAL* 3.7 20.4 - - + -
291A LEU* 4.0 16.2 - - + +
313A VAL* 4.0 14.1 - - + -
314A GLU 3.2 10.1 - - - +
315A LEU* 4.3 7.6 - - + -
316A HIS* 3.9 0.9 - - - -
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Residues in contact with THR 257 (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 VAL* 1.3 72.1 - - - +
258A VAL* 1.3 66.6 + - - +
259A SER* 4.6 3.8 - - - +
269A SER* 3.9 16.2 - - - +
270A GLY 3.2 8.7 - - - +
271A THR* 2.8 23.3 + - - +
312A VAL 3.3 3.1 - - - +
313A VAL 3.8 0.2 - - - -
314A GLU* 2.9 53.7 + - - +
316A HIS* 2.6 27.4 + - - -
8406A DMS 4.3 3.3 + - - +
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Residues in contact with VAL 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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227A VAL* 6.5 0.2 - - + -
240A LEU* 4.7 7.4 - - + -
242A ALA* 4.0 25.8 - - + -
244A VAL* 4.6 1.1 - - + -
256A VAL* 4.0 11.9 - - + -
257A THR* 1.3 77.9 - - - +
259A SER* 1.3 67.6 + - - +
260A LEU* 5.9 0.4 - - + -
269A SER* 3.3 2.9 + - - -
270A GLY 2.8 32.2 + - - -
291A LEU* 3.8 27.6 - - + -
293A LEU* 3.6 16.0 - - + +
311A ALA* 4.7 11.9 - - + -
312A VAL 3.3 8.1 - - - +
313A VAL* 4.5 15.0 - - + -
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Residues in contact with SER 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 THR* 4.0 4.7 + - - -
258A VAL* 1.3 78.1 - - - +
260A LEU* 1.3 61.2 + - - +
261A TRP* 3.0 24.5 + - - -
266A GLN* 3.7 18.8 + - - -
268A ALA 3.5 4.5 - - - -
269A SER* 3.8 10.3 - - - -
293A LEU* 4.6 0.2 - - - -
310A ARG 3.5 1.6 - - - +
311A ALA* 3.3 5.0 - - - +
312A VAL* 2.9 41.9 + - - +
314A GLU* 4.8 6.7 + - - -
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Residues in contact with LEU 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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240A LEU* 4.0 22.2 - - + -
258A VAL* 6.0 0.4 - - + -
259A SER* 1.3 72.7 - - - +
261A TRP* 1.3 58.7 + - - +
266A GLN* 3.5 4.0 - - - -
267A VAL* 2.8 47.0 + - + +
268A ALA* 2.9 18.0 + - + +
293A LEU* 4.1 11.2 - - + -
295A VAL* 3.7 30.1 - - + -
309A TYR* 3.6 24.0 - - + -
310A ARG 3.4 16.4 - - - +
311A ALA* 4.3 7.0 - - + -
330A VAL* 4.6 2.9 - - + -
332A PHE* 3.8 18.2 - - + -
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Residues in contact with TRP 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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40A GLU* 5.6 1.6 - - - -
43A ARG* 3.5 31.4 - - + -
259A SER* 3.0 28.1 + - - -
260A LEU* 1.3 79.5 - - - +
262A GLN* 1.3 59.9 - - - +
263A GLY 3.7 10.2 + - - +
264A GLU* 3.5 22.0 - - - -
265A THR 3.2 7.0 - - - -
266A GLN* 3.5 47.1 - - + -
309A TYR* 3.2 12.0 - - - +
310A ARG* 2.8 49.2 + - + +
312A VAL* 4.1 16.1 - - + +
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Residues in contact with GLN 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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261A TRP* 1.3 69.6 - - - +
263A GLY* 1.3 67.2 + - - +
264A GLU 3.2 0.3 + - - -
265A THR* 2.8 28.0 + - - -
267A VAL* 3.6 22.7 - - + +
299A LYS* 3.1 37.7 - - - +
308A LEU 5.1 6.1 - - - +
309A TYR* 3.7 25.8 + - + +
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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