Contacts of the strand formed by residues 234 - 243 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171A TYR* 6.3 1.1 - - + -
221A GLN* 3.6 35.7 + - + +
222A ARG 3.4 4.9 - - - +
223A LYS* 3.8 33.7 - - + +
232A LEU* 3.4 20.8 - - - +
233A SER* 1.3 81.3 + - - +
235A VAL* 1.3 59.9 + - - +
268A GLN* 3.6 23.8 - - - +
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Residues in contact with VAL 235 (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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221A GLN* 3.1 6.4 - - - +
222A ARG* 2.7 47.9 + - + +
224A LYS* 3.8 38.4 - - + +
232A LEU* 4.1 8.3 - - + +
234A LEU* 1.3 75.1 - - - +
236A THR* 1.3 74.0 + - - +
237A LEU* 4.2 16.2 - - + -
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Residues in contact with THR 236 (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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219A LEU* 3.8 24.1 - - + +
220A ILE 3.9 2.9 - - - +
221A GLN* 3.3 23.1 + - - -
235A VAL* 1.3 79.0 - - - +
237A LEU* 1.3 63.8 + - - +
238A PHE 3.8 19.1 - - - +
239A ARG* 4.4 2.9 - - + +
434A ASP* 3.5 34.3 - - + +
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Residues in contact with LEU 237 (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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203A ILE* 4.0 9.9 - - + -
220A ILE* 2.8 20.0 + - + +
222A ARG* 3.9 25.6 - - + +
235A VAL* 4.2 17.5 - - + -
236A THR* 1.3 72.6 - - - +
238A PHE* 1.4 85.9 + - + +
259A ALA* 3.9 30.7 - - + -
261A LEU* 4.3 2.2 - - + -
267A LEU* 3.8 29.8 - - + -
433A GLY 4.5 1.6 - - - +
434A ASP* 3.5 17.8 - - - +
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Residues in contact with PHE 238 (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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203A ILE* 4.4 13.5 - - + -
218A HIS 4.1 0.2 - - - +
219A LEU* 3.4 2.9 - - - -
220A ILE* 2.8 53.9 + - + +
236A THR* 3.8 3.4 - - - +
237A LEU* 1.4 102.4 - - + +
239A ARG* 1.3 62.9 + - - +
255A SER* 3.8 14.8 - - - +
256A ALA 4.4 0.9 - - - -
257A GLY* 3.4 47.1 - - - -
258A ILE 3.4 18.6 - - - -
259A ALA* 4.7 1.1 - - + -
307A GLN* 4.0 13.0 - - - -
309A ILE* 6.3 1.1 - - + -
433A GLY 5.7 0.9 - - - -
434A ASP 3.4 3.8 - - - +
437A PHE* 3.7 30.5 - + + -
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Residues in contact with ARG 239 (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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218A HIS 3.4 5.2 - - - +
219A LEU* 3.5 29.6 - - + -
236A THR* 4.4 0.9 - - + -
238A PHE* 1.3 78.3 - - - +
240A CYS* 1.3 63.9 + - - +
241A ILE* 5.5 8.9 - - + +
255A SER* 3.9 4.5 + - - -
357A GLN* 2.8 30.0 + - - -
359A LEU* 4.5 11.5 - - - +
430A SER* 5.2 0.4 + - - -
432A ASP* 3.3 25.9 + - - +
434A ASP* 2.8 55.2 + - - +
435A VAL* 3.8 24.0 - - + +
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Residues in contact with CYS 240 (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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217A GLY* 3.0 3.1 - - - -
218A HIS* 2.9 48.5 + - + +
239A ARG* 1.3 78.2 - - - +
241A ILE* 1.3 61.8 + - - +
242A GLN* 5.2 0.9 - - - -
253A CYS* 2.1 47.8 - - - -
254A TYR 3.3 30.7 - - - -
255A SER* 3.9 8.7 - - - -
403A SER* 3.8 7.9 - - - -
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Residues in contact with ILE 241 (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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214A TYR* 5.6 1.1 - - - +
215A ALA* 3.8 25.1 - - + +
216A MET 3.6 10.3 - - - +
217A GLY* 4.7 1.8 - - - +
239A ARG* 5.5 9.4 - - + +
240A CYS* 1.3 74.6 - - - +
242A GLN* 1.4 67.7 + - - +
253A CYS* 3.4 1.0 - - - -
359A LEU* 3.4 38.4 - - + -
401A ASN* 3.6 29.8 - - - +
402A ASN* 3.5 1.4 - - - +
403A SER* 2.8 43.9 + - - +
435A VAL* 4.7 4.9 - - + -
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Residues in contact with GLN 242 (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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90A ARG* 3.9 26.2 + - - +
209A TYR* 5.5 1.3 - - + -
215A ALA* 3.3 1.8 - - - -
216A MET 2.8 37.9 + - - +
240A CYS* 5.2 0.4 - - - -
241A ILE* 1.4 77.6 + - - +
243A ASN* 1.3 67.1 + - - +
244A MET* 3.5 13.1 + - - +
251A ASN* 3.7 21.5 + - + +
252A SER 3.9 12.7 + - - +
253A CYS* 3.5 29.8 - - + +
254A TYR 5.6 0.4 - - - +
393A GLN* 4.6 2.9 + - - +
401A ASN 3.7 3.4 - - - -
402A ASN* 3.3 13.4 + - - +
403A SER* 3.5 23.8 + - - -
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Residues in contact with ASN 243 (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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214A TYR* 3.1 21.1 + - - +
215A ALA* 4.1 1.8 - - - +
242A GLN* 1.3 75.1 - - - +
244A MET* 1.3 60.1 + - - +
245A PRO* 4.4 0.3 - - - +
251A ASN* 3.3 17.8 + - - -
396A PRO* 3.4 29.7 - - + +
398A THR 4.6 0.8 + - - -
399A LEU 3.0 24.5 + - - -
401A ASN 2.7 34.7 + - - +
402A ASN* 3.1 27.7 + - - +
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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