Contacts of the strand formed by residues 323 - 328 (chain A) in PDB entry 1ZJK
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 SER 323 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A PRO* 3.6 14.6 - - - +
315A GLN* 4.4 4.4 + - - +
318A TYR* 3.9 11.2 - - - -
321A LYS 4.6 2.5 - - - -
322A ASP* 1.3 81.3 + - - +
324A PHE* 1.3 67.3 + - - +
345A THR* 3.4 20.4 - - - +
346A ALA 3.3 14.7 + - - -
347A VAL* 4.2 5.9 - - - +
354A TRP* 4.7 1.3 - - - -
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Residues in contact with PHE 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A PRO* 3.6 19.1 - - + -
311A VAL* 3.6 26.2 - - + -
313A PRO* 4.0 9.2 - - + -
318A TYR* 4.1 9.0 - - + -
323A SER* 1.3 78.6 - - - +
325A SER* 1.3 72.0 + - - +
326A ILE* 3.6 26.5 - - + -
344A PHE* 4.2 4.9 - + - -
345A THR* 3.3 2.7 - - - -
346A ALA* 2.9 47.8 + - + -
354A TRP* 3.3 45.8 - + - -
356A ARG 5.9 0.9 - - - -
358A MET* 3.6 25.8 - - + -
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Residues in contact with SER 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A VAL* 3.4 7.1 - - - -
312A SER* 3.1 39.4 + - - -
324A PHE* 1.3 78.2 - - - +
326A ILE* 1.3 63.6 + - - +
327A PHE* 3.6 22.4 - - - -
344A PHE* 3.1 17.5 - - - -
345A THR* 2.7 22.5 + - - +
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Residues in contact with ILE 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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305A ALA* 5.1 0.7 - - - -
306A PRO* 3.9 20.6 - - + -
310A HIS 3.3 11.7 - - - +
311A VAL* 4.6 5.8 - - + -
324A PHE* 3.6 16.6 - - + -
325A SER* 1.3 79.1 - - - +
327A PHE* 1.3 71.6 + - - +
334A LEU* 3.6 38.3 - - + +
344A PHE* 3.3 21.0 + - + +
358A MET* 3.5 32.1 - - - -
359A PRO* 3.7 18.6 - - + -
361A CYS* 4.1 16.4 - - - -
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Residues in contact with PHE 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A GLY* 4.3 1.1 - - - -
310A HIS* 3.1 57.2 + + + +
312A SER* 3.6 22.9 - - - -
325A SER* 3.6 30.5 - - - -
326A ILE* 1.3 82.3 - - - +
328A CYS* 1.3 64.3 + - - +
334A LEU* 5.1 4.7 - - + -
343A SER* 5.2 13.9 - - - -
344A PHE 5.5 0.4 - - - -
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Residues in contact with CYS 328 (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 ASN 3.4 7.4 - - - +
310A HIS* 5.1 4.5 + - - -
327A PHE* 1.3 77.6 - - - +
329A GLU* 1.3 65.5 + - - +
332A TYR* 3.6 23.8 - - + +
333A GLU* 3.8 0.9 - - - -
334A LEU* 3.7 35.5 - - - +
361A CYS* 2.0 49.1 - - - -
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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