Contacts of the strand formed by residues 286 - 291 (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 PHE 286 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A LEU 5.8 0.7 - - - -
86A PHE* 4.1 12.6 - - + -
105A SER* 3.6 15.9 - - - -
106A ALA 3.1 27.8 - - - -
107A GLY* 4.7 1.8 - - - -
109A PHE* 6.2 1.3 - + - -
156A GLN* 4.6 12.1 - - + +
157A LEU 3.1 16.2 - - - +
158A ILE* 4.1 11.4 - - + -
176A TRP* 3.5 8.8 - - - -
204A TYR* 4.1 24.0 - + - -
205A GLY* 3.5 0.9 - - - -
206A GLN* 2.9 65.6 + - + +
254A TYR* 4.4 3.6 - + - -
269A LEU* 4.2 0.5 - - - +
282A GLY 4.0 11.0 - - - -
283A ASP 4.0 9.6 - - - -
284A VAL 4.0 4.5 - - - -
285A THR* 1.3 76.5 - - - +
287A PHE* 1.3 64.4 + - - +
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Residues in contact with PHE 287 (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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156A GLN* 3.6 1.0 - - - -
157A LEU* 2.7 43.4 + - + +
176A TRP* 3.7 36.1 - + + -
191A ASN 5.6 1.3 - - - -
193A ILE* 3.7 26.5 - - + -
203A ILE* 4.0 21.1 - - + -
204A TYR* 3.4 20.0 - - - -
205A GLY* 4.4 0.2 - - - -
220A ILE* 4.0 16.4 - - + -
267A LEU* 3.7 20.0 - - + -
268A GLN* 3.6 24.5 - - - -
269A LEU* 3.6 28.7 - - + -
286A PHE* 1.3 76.0 - - - +
288A GLY* 1.3 60.8 + - - +
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Residues in contact with GLY 288 (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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155A LEU 3.2 13.0 - - - -
193A ILE* 3.9 10.3 - - - -
203A ILE* 3.5 5.7 - - - +
204A TYR* 2.9 50.3 + - - +
287A PHE* 1.3 79.8 - - - +
289A ALA* 1.3 61.8 + - - +
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Residues in contact with ALA 289 (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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108A VAL* 5.8 0.2 - - - +
154A CYS* 3.3 3.5 - - - +
155A LEU* 2.9 33.1 + - - +
186A LEU* 3.8 21.1 - - + +
193A ILE* 4.4 5.9 - - + +
201A PHE* 4.7 6.5 - - + -
202A PHE 3.3 12.1 - - - +
203A ILE* 4.2 17.5 - - + -
204A TYR* 3.8 5.7 + - - -
267A LEU* 4.6 9.9 - - + -
288A GLY* 1.3 75.4 - - - +
290A LEU* 1.3 60.3 + - - +
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Residues in contact with LEU 290 (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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56A LEU* 4.7 8.5 - - + -
108A VAL* 3.7 27.1 - - + -
142A LEU* 4.5 17.5 - - + -
152A GLN* 3.5 32.1 - - + +
153A ASP 3.3 11.0 - - - +
154A CYS* 3.8 10.5 - - + +
186A LEU* 4.4 0.4 - - - -
201A PHE* 3.3 6.6 - - - -
202A PHE* 2.9 67.3 + - + -
204A TYR* 4.6 2.2 - - + -
289A ALA* 1.3 74.7 - - - +
291A LYS* 1.3 59.8 + - - +
292A LEU* 4.4 7.4 - - + -
441A LEU* 5.8 3.4 - - + -
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Residues in contact with LYS 291 (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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152A GLN* 3.0 27.7 + - - +
153A ASP* 2.8 31.9 + - + +
185A ALA* 3.8 13.0 - - + -
186A LEU* 4.4 0.4 - - - +
197A GLU* 4.0 27.3 + - - +
198A THR 3.3 25.3 + - - -
199A GLY* 4.2 7.4 - - - -
200A TYR 3.6 10.5 - - - +
201A PHE* 3.6 28.3 - - + -
290A LEU* 1.3 71.3 - - - +
292A LEU* 1.3 71.0 + - - +
294A GLY 4.1 17.8 + - - -
333A ARG* 6.1 0.2 - - - +
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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