Contacts of the strand formed by residues 234 - 243 (chain B) in PDB entry 4ZCH
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 234 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171B TYR* 6.3 2.0 - - + -
221B GLN* 3.4 47.6 - - + +
222B ARG 3.3 18.6 - - - +
223B LYS* 4.0 17.7 - - + +
232B LEU* 3.5 17.5 - - - +
233B SER* 1.3 82.2 + - - +
235B VAL* 1.4 67.2 + - - +
268B GLN* 3.8 18.2 - - + +
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Residues in contact with VAL 235 (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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221B GLN* 3.3 6.5 - - - +
222B ARG* 2.8 61.2 + - + +
224B LYS* 4.3 21.8 - - + +
232B LEU* 4.0 28.0 - - + +
234B LEU* 1.4 79.1 - - - +
236B THR* 1.3 65.1 + - - +
237B LEU* 3.6 8.7 + - + -
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Residues in contact with THR 236 (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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219B LEU* 3.9 24.9 - - + +
220B ILE 3.7 6.5 - - - +
221B GLN* 3.4 20.1 + - - -
235B VAL* 1.3 72.2 - - - +
237B LEU* 1.3 66.3 + - - +
238B PHE 3.6 22.2 - - - +
239B ARG* 4.5 0.7 - - + -
434B ASP* 3.6 30.9 - - - +
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Residues in contact with LEU 237 (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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203B ILE* 4.0 17.9 - - + -
220B ILE* 2.8 19.7 + - + +
222B ARG* 3.8 42.6 - - + +
235B VAL* 3.6 6.9 + - + +
236B THR* 1.3 74.7 - - - +
238B PHE* 1.4 86.1 + - + +
259B ALA* 3.7 21.1 - - + -
261B LEU* 4.5 1.3 - - + -
267B LEU* 3.9 21.1 - - + -
433B GLY 4.5 1.7 - - - +
434B ASP* 3.5 18.0 - - - +
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Residues in contact with PHE 238 (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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203B ILE* 4.4 15.5 - - + -
218B HIS* 5.9 0.2 - - - -
220B ILE* 2.9 50.6 + - + +
236B THR* 3.6 5.8 - - - +
237B LEU* 1.4 104.2 - - + +
239B ARG* 1.3 64.3 + - - +
255B SER* 4.0 18.6 - - - +
256B ALA 4.2 5.2 - - - -
257B GLY* 3.3 45.5 - - - -
258B ILE 3.6 13.5 - - - -
259B ALA* 4.7 1.6 - - + -
307B GLN* 4.1 13.2 - - - -
433B GLY 6.1 0.2 - - - -
434B ASP 3.3 7.2 - - - +
437B PHE* 3.8 25.1 - + + -
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Residues in contact with ARG 239 (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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218B HIS* 3.4 11.9 - - - +
219B LEU* 3.7 23.1 - - + -
236B THR* 4.5 0.7 - - + -
238B PHE* 1.3 76.0 - - - +
240B CYS* 1.3 60.4 + - - +
241B ILE* 3.5 34.2 - - - +
255B SER* 3.8 5.8 + - - -
357B GLN* 2.8 29.1 + - - -
359B LEU* 3.8 17.8 - - - +
401B ASN* 5.0 4.6 - - - +
430B SER* 5.1 0.6 + - - -
432B ASP* 4.7 12.7 + - - -
434B ASP* 2.8 36.4 + - - +
435B VAL* 3.6 22.1 - - + +
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Residues in contact with CYS 240 (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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217B GLY* 3.0 3.1 - - - -
218B HIS* 2.9 52.6 + - + +
239B ARG* 1.3 76.7 + - - +
241B ILE* 1.3 62.6 + - - +
253B CYS* 2.0 46.2 - - - -
254B TYR 3.4 27.4 - - - -
255B SER* 4.0 7.8 - - - -
403B SER* 3.8 11.0 - - - -
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Residues in contact with ILE 241 (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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215B ALA* 3.5 35.7 - - + +
216B MET 3.6 11.7 - - - +
217B GLY* 4.6 0.9 - - - +
239B ARG* 3.5 26.5 - - - +
240B CYS* 1.3 75.5 - - - +
242B GLN* 1.3 70.7 + - - +
253B CYS* 4.1 0.2 - - - -
359B LEU* 3.7 25.4 - - + -
401B ASN* 3.3 28.9 - - + +
402B ASN* 3.5 1.4 - - - +
403B SER* 2.9 40.2 + - - +
435B VAL* 4.1 4.9 - - + -
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Residues in contact with GLN 242 (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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90B ARG* 3.8 15.6 + - - +
209B TYR* 5.0 2.5 - - + -
215B ALA* 3.1 7.3 - - - +
216B MET 2.7 42.7 + - - +
241B ILE* 1.3 73.2 - - - +
243B ASN* 1.3 62.6 + - - +
244B MET* 4.5 10.8 - - - -
251B ASN* 3.3 38.1 - - + +
252B SER 3.7 13.4 + - - +
253B CYS* 3.3 29.9 - - + -
393B GLN* 4.8 2.8 + - - -
401B ASN 3.5 6.3 - - - -
402B ASN* 2.9 25.0 - - - +
403B SER 4.0 9.5 - - - +
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Residues in contact with ASN 243 (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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214B TYR* 3.3 14.3 + - - +
215B ALA* 3.9 6.1 - - - +
242B GLN* 1.3 76.8 + - - +
244B MET* 1.3 66.3 + - - +
245B PRO* 4.7 0.3 - - - +
251B ASN* 4.0 10.7 - - - +
396B PRO* 3.3 35.9 - - + +
399B LEU 2.9 24.5 + - - -
400B PRO* 3.4 0.3 - - - +
401B ASN 2.9 32.3 + - - +
402B ASN* 3.5 23.8 + - - +
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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