Contacts of the strand formed by residues 196 - 204 (chain B) in PDB entry 1HZW
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 HIS 196 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B GLU* 5.0 5.1 + - - -
91B PHE* 4.0 18.1 - + - -
109B TRP* 6.0 0.7 - + - -
135B TYR* 3.2 58.3 - + - -
139B TRP* 5.6 0.2 + - - -
181B ALA* 3.6 7.3 - - - +
195B CYS* 1.3 81.0 - - + +
197B ALA* 1.3 62.0 + - - +
198B LEU* 3.4 3.1 + - - -
212B LEU* 3.2 28.9 - - + +
213B TYR 3.9 6.5 - - - -
214B GLN* 4.3 4.9 - - + +
226B ASN* 4.3 22.6 + - - -
229B SER* 5.5 2.2 + - - -
230B TYR* 2.7 35.4 + + + +
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Residues in contact with ALA 197 (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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178A ILE* 4.6 6.7 - - + -
198A LEU* 4.1 17.0 - - + -
180B CYS* 3.6 2.1 - - - -
181B ALA* 2.7 28.7 + - - -
182B TRP* 3.1 38.0 + - + +
194B PRO* 4.7 4.0 - - - +
195B CYS 3.1 8.9 + - - +
196B HIS* 1.3 72.7 - - - +
198B LEU* 1.3 59.0 + - - +
213B TYR* 3.1 17.7 + - + +
215B ARG* 5.1 1.1 - - + -
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Residues in contact with LEU 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A TRP* 4.6 2.9 - - + -
197A ALA* 3.8 27.8 - - + -
198A LEU* 3.9 22.7 - - + -
213A TYR* 3.9 28.0 - - + -
178B ILE* 4.1 15.0 - - + -
179B MET 3.3 13.9 - - - +
180B CYS* 3.7 14.6 - - + -
181B ALA 4.5 0.4 - - - +
196B HIS 3.4 2.3 - - - -
197B ALA* 1.3 84.5 - - - +
199B CYS* 1.3 72.7 + - - +
200B GLN* 4.3 0.7 - - + +
212B LEU* 3.4 5.6 - - - +
213B TYR* 2.7 40.2 + - + -
230B TYR* 6.0 0.2 - - - -
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Residues in contact with CYS 199 (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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139B TRP* 6.0 0.2 - - - -
177B ILE 4.1 0.2 - - - +
178B ILE* 3.4 5.0 - - - +
179B MET* 3.0 58.6 + - - +
198B LEU* 1.3 80.6 - - - +
200B GLN* 1.3 61.0 + - - +
201B PHE* 3.7 26.4 - - - -
210B CYS* 4.0 10.5 - - - -
211B GLN 3.0 12.8 - - - +
212B LEU* 4.2 2.2 - - - -
230B TYR* 3.9 27.4 - - + -
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Residues in contact with GLN 200 (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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59A PHE* 3.5 17.2 - - + -
213A TYR* 2.6 49.5 + - + +
215A ARG* 3.0 35.8 + - - +
253A GLY* 3.6 4.6 - - - -
254A ASP* 4.3 1.6 + - - +
175B ARG* 3.3 19.4 - - - +
177B ILE 3.3 12.1 - - - +
178B ILE* 3.9 10.8 - - + -
199B CYS* 1.3 76.3 - - - +
201B PHE* 1.3 76.3 + - - +
202B TYR* 5.6 0.3 - - - +
210B CYS* 3.2 3.5 - - - -
211B GLN 2.7 30.6 + - - -
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Residues in contact with PHE 201 (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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164B VAL* 3.6 31.2 - - + -
168B ILE* 4.2 1.6 - - + -
174B ASP 4.7 2.3 - - - +
177B ILE* 2.8 41.0 + - + +
179B MET* 4.8 3.1 - - + -
199B CYS* 3.7 21.8 - - - -
200B GLN* 1.3 89.7 - - - +
202B TYR* 1.3 64.3 + - - +
208B LEU* 3.9 23.6 - - + -
209B SER 3.1 14.6 - - - +
210B CYS* 3.5 27.8 - - + -
233B LEU* 3.9 18.2 - - + -
234B THR* 3.9 15.3 - - - -
237B ILE* 3.5 24.5 - - + -
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Residues in contact with TYR 202 (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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45A VAL* 4.4 1.7 - - - +
47A LYS* 3.3 23.7 - - + +
57A SER* 2.6 46.3 + - - -
58A VAL* 4.3 0.2 - - - -
59A PHE* 3.4 57.3 + + + -
254A ASP* 3.3 20.2 - - + -
174B ASP 5.3 3.1 - - - -
175B ARG* 6.0 0.4 - - + -
177B ILE* 4.9 2.9 - - - -
200B GLN* 5.6 0.7 - - - +
201B PHE* 1.3 77.7 - - - +
203B VAL* 1.3 64.9 + - - +
204B VAL* 3.7 28.5 - - + +
207B GLU 3.4 2.5 - - - +
208B LEU* 3.5 2.1 - - - -
209B SER* 2.8 41.9 + - - -
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Residues in contact with VAL 203 (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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47A LYS* 3.2 23.6 - - - +
168B ILE* 3.9 17.5 - - + -
172B PRO* 3.3 44.6 + - + +
173B ASP* 4.6 3.3 - - - +
177B ILE* 4.7 1.6 - - + -
202B TYR* 1.3 83.0 - - - +
204B VAL* 1.3 66.1 + - - +
206B SER 4.8 2.2 - - - +
207B GLU 3.3 8.1 - - - +
208B LEU* 3.8 19.3 - - + -
243B LEU* 3.8 34.1 - - + -
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Residues in contact with VAL 204 (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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45A VAL* 3.8 26.2 - - + -
46A ARG 3.6 24.2 - - - +
47A LYS* 4.0 15.3 - - + -
173B ASP* 5.8 1.6 - - - +
202B TYR* 3.7 23.8 - - + -
203B VAL* 1.3 80.0 - - - +
205B ASN* 1.3 80.7 + - - +
206B SER 3.1 2.0 - - - -
207B GLU* 2.8 24.5 + - + +
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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