Contacts of the strand formed by residues 196 - 204 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A GLU* 6.2 0.2 - - - -
91A PHE* 5.7 5.2 - + - -
135A TYR* 3.1 39.8 + + + +
181A ALA* 3.5 6.4 - - - +
194A PRO* 4.0 2.2 - - - +
195A CYS* 1.3 81.2 - - + +
197A ALA* 1.3 65.7 + - - +
198A LEU* 3.3 3.2 + - - -
212A LEU* 3.5 15.7 - - + +
213A TYR 3.8 6.5 - - - -
214A GLN* 3.5 23.3 + - + +
226A ASN* 3.3 44.9 + - + +
229A SER* 5.9 1.8 - - - -
230A TYR* 3.4 35.6 + + - +
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Residues in contact with ALA 197 (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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180A CYS* 3.6 1.2 - - - -
181A ALA* 2.7 31.4 + - - -
182A TRP* 3.0 34.6 + - + +
194A PRO* 4.7 1.1 - - - +
195A CYS 3.4 4.9 + - - +
196A HIS* 1.3 72.7 - - - +
198A LEU* 1.3 57.9 + - - +
213A TYR* 3.2 21.3 + - + +
215A ARG* 5.2 0.7 - - + -
178B ILE* 4.5 6.5 - - + -
198B LEU* 3.8 25.6 - - + -
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Residues in contact with LEU 198 (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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178A ILE* 4.3 12.8 - - + -
179A MET 3.3 15.5 - - - +
180A CYS* 3.7 15.7 - - + -
181A ALA* 4.4 0.4 - - - +
196A HIS 3.3 2.1 - - - -
197A ALA* 1.3 82.5 - - - +
199A CYS* 1.3 71.7 + - - +
200A GLN* 5.1 0.2 - - + -
212A LEU* 3.5 6.3 - - - +
213A TYR* 2.8 37.6 + - + +
230A TYR* 5.8 0.7 - - - -
182B TRP* 4.8 2.9 - - + -
197B ALA* 4.1 24.2 - - + -
198B LEU* 3.9 26.7 - - + -
213B TYR* 3.9 29.2 - - + -
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Residues in contact with CYS 199 (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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139A TRP* 5.5 0.4 - - - -
177A ILE 4.1 0.2 - - - +
178A ILE* 3.4 5.5 - - - +
179A MET* 3.0 54.5 + - - -
198A LEU* 1.3 79.9 - - - +
200A GLN* 1.3 60.3 + - - +
201A PHE* 3.8 25.3 - - - -
210A CYS* 4.0 10.1 - - - -
211A GLN 3.0 13.5 - - - +
212A LEU* 4.3 2.2 - - - -
230A TYR* 3.8 31.9 - - + -
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Residues in contact with GLN 200 (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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175A ARG* 3.3 20.7 - - - +
177A ILE 3.3 11.9 - - - +
178A ILE* 3.9 12.1 - - + -
199A CYS* 1.3 74.9 - - - +
201A PHE* 1.3 76.1 + - - +
202A TYR* 5.8 0.3 - - - +
210A CYS* 3.2 3.9 - - - -
211A GLN 2.8 31.3 + - - -
59B PHE* 3.3 16.7 - - + -
213B TYR* 2.6 40.2 + - + +
215B ARG* 3.0 45.2 + - - +
253B GLY* 3.5 5.5 - - - -
254B ASP* 4.3 1.7 + - - +
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Residues in contact with PHE 201 (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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164A VAL* 4.2 17.9 - - + -
168A ILE* 4.2 5.4 - - + -
174A ASP 4.6 3.1 - - - +
175A ARG* 5.8 0.2 - - - -
177A ILE* 2.7 51.1 + - + +
179A MET* 4.6 5.2 - - + -
199A CYS* 3.8 18.8 - - - -
200A GLN* 1.3 88.7 - - - +
202A TYR* 1.3 64.2 + - - +
208A LEU* 4.0 22.4 - - + -
209A SER 3.3 14.6 - - - +
210A CYS* 3.5 31.0 - - + -
233A LEU* 3.9 16.6 - - + -
234A THR* 4.0 12.3 - - - -
237A ILE* 3.6 29.6 - - + -
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Residues in contact with TYR 202 (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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174A ASP 5.4 3.4 - - - -
177A ILE* 5.0 2.7 - - - -
200A GLN* 5.9 0.4 - - - -
201A PHE* 1.3 77.9 - - - +
203A VAL* 1.3 66.2 + - - +
204A VAL* 3.6 30.0 - - + +
207A GLU 3.5 1.2 - - - +
208A LEU* 3.4 3.8 - - - +
209A SER* 2.7 42.0 + - - +
45B VAL* 4.4 1.6 - - - +
47B LYS* 3.3 29.5 - - + +
57B SER* 2.6 45.2 + - - -
59B PHE* 3.3 59.5 + + + -
254B ASP* 3.4 14.8 - - + -
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Residues in contact with VAL 203 (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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168A ILE* 3.8 15.7 - - + -
172A PRO* 3.4 42.8 + - + +
173A ASP* 4.7 2.4 - - - +
177A ILE* 4.9 1.6 - - + -
202A TYR* 1.3 83.9 - - - +
204A VAL* 1.3 67.7 + - - +
206A SER 4.7 2.5 - - - +
207A GLU 3.2 10.8 - - - +
208A LEU* 3.7 11.7 - - + -
243A LEU* 3.6 39.0 - - + -
47B LYS* 3.2 23.4 - - - +
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Residues in contact with VAL 204 (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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202A TYR* 3.6 24.2 - - + +
203A VAL* 1.3 79.5 - - - +
205A ASN* 1.3 80.9 + - + +
206A SER 3.2 1.8 - - - -
207A GLU* 2.9 25.5 + - + +
209A SER* 6.2 0.2 - - - +
45B VAL* 3.4 33.9 - - + -
46B ARG 3.6 16.4 - - - +
47B LYS* 4.2 13.9 - - + -
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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