Contacts of the strand formed by residues 322 - 330 (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 322 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A ARG* 3.6 38.9 - - - +
38A ASN* 3.9 3.1 - - - +
39A SER* 3.6 19.3 - - - +
314A GLU* 3.6 34.5 - - + +
315A LEU 3.6 3.6 - - - +
316A HIS* 3.8 6.3 - - + -
320A GLY 3.5 4.8 + - - -
321A THR* 1.3 79.3 - - - +
323A ILE* 1.3 62.0 + - - +
324A GLU 3.4 30.7 - - - +
325A ALA* 4.3 2.7 - - + -
8406A DMS 3.8 7.1 - - + +
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Residues in contact with ILE 323 (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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37A ARG* 3.4 17.5 + - - +
218A PRO* 3.8 17.3 - - + +
220A THR* 3.4 33.7 - - + +
253A TYR* 5.3 1.1 - - + -
254A LEU* 3.5 31.4 - - + -
315A LEU* 2.8 27.2 + - + +
316A HIS* 4.2 8.7 - - - -
317A THR* 4.5 9.9 - - + +
321A THR* 4.0 12.1 - - + +
322A LEU* 1.3 78.4 - - - +
324A GLU* 1.3 65.4 + - - +
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Residues in contact with GLU 324 (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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35A SER* 2.6 41.3 + - - +
36A TRP 3.3 13.5 - - - +
37A ARG* 3.9 3.6 - - - +
217A LYS* 2.7 29.7 + - - +
218A PRO* 3.7 17.3 - - + -
221A GLN* 3.5 3.1 - - - +
222A ILE* 2.9 31.0 + - + +
313A VAL 4.1 0.2 - - - +
315A LEU* 2.9 31.9 + - + +
322A LEU* 3.4 10.1 - - - +
323A ILE* 1.3 83.1 - - - +
325A ALA* 1.3 60.6 + - - +
326A GLU* 4.2 3.8 - - - -
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Residues in contact with ALA 325 (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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35A SER 3.9 0.3 - - - -
36A TRP* 2.8 42.2 + - + +
39A SER* 4.3 11.4 - - - +
42A ALA* 4.1 20.0 - - + -
222A ILE* 4.5 0.4 - - - -
312A VAL* 4.6 1.8 - - + -
313A VAL 3.2 10.1 - - - +
314A GLU* 4.4 4.7 - - + -
322A LEU* 4.3 14.8 - - + -
324A GLU* 1.3 77.2 - - - +
326A GLU* 1.3 67.5 + - - +
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Residues in contact with GLU 326 (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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32A PRO 4.3 1.1 - - - +
33A PHE* 3.2 23.5 - - + +
34A ALA* 2.7 26.0 + - - +
35A SER* 2.9 24.0 + - - -
36A TRP* 4.3 6.5 - - - -
217A LYS* 2.9 29.7 + - - +
222A ILE* 3.9 21.9 - - + +
225A PHE* 3.8 20.6 - - + -
312A VAL* 3.7 3.5 - - - +
313A VAL* 2.7 32.8 + - + +
324A GLU* 4.5 1.6 - - - +
325A ALA* 1.3 75.8 - - - +
327A ALA* 1.3 63.7 + - - +
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Residues in contact with ALA 327 (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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32A PRO 4.6 3.4 + - - +
36A TRP* 4.1 8.2 - - + -
42A ALA* 3.8 14.8 - - + +
225A PHE* 3.9 13.3 - - - -
310A ARG* 3.6 23.8 - - - +
311A ALA 3.1 16.4 - - - +
312A VAL* 4.2 5.8 - - + -
313A VAL* 4.4 2.0 - - - +
326A GLU* 1.3 80.5 + - - +
328A CYS* 1.3 64.7 + - - +
8404A DMS 3.2 19.7 - - - +
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Residues in contact with CYS 328 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225A PHE* 4.0 23.3 - - + -
227A VAL* 4.1 13.9 - - - -
310A ARG* 3.6 14.7 - - - +
311A ALA* 2.9 33.4 + - - +
327A ALA* 1.3 77.7 - - - +
329A ASP* 1.3 73.3 + - - +
330A VAL* 3.9 14.6 - - - -
449A ASN* 4.3 17.5 - - + +
8404A DMS 4.7 4.3 - - + -
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Residues in contact with ASP 329 (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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308A LEU* 4.1 26.2 - - + +
309A TYR 3.5 6.4 - - - +
310A ARG* 2.9 28.6 + - - +
328A CYS* 1.3 84.0 - - - +
330A VAL* 1.4 60.6 + - - +
400A THR* 4.7 4.0 - - - +
403A ASP* 4.5 13.9 - - - +
404A ARG* 2.9 39.3 + - - +
449A ASN 3.8 3.8 - - - +
451A PRO* 3.8 14.0 - - - +
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Residues in contact with VAL 330 (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* 4.0 13.5 - - + -
229A THR* 4.2 9.9 - - + -
240A LEU* 4.0 14.6 - - + -
260A LEU* 4.6 0.9 - - + -
308A LEU* 3.3 8.5 - - - -
309A TYR* 2.8 43.4 + - + +
311A ALA* 3.6 32.8 - - + +
328A CYS* 3.9 11.2 - - - +
329A ASP* 1.4 79.9 - - - +
331A GLY* 1.3 60.1 + - - +
332A PHE* 3.9 27.7 + - + -
8401A DMS 3.5 9.9 - - - +
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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