Contacts of the strand formed by residues 177 - 185 (chain A) in PDB entry 1ZOY
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 TYR 177 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A VAL* 3.7 14.5 - - + +
49A THR 2.7 8.0 + - - -
50A LYS* 3.1 20.7 + - - -
174A PHE* 3.5 51.7 - + + +
175A VAL 3.1 26.0 - - - -
176A GLU* 1.3 76.7 - - - +
178A PHE* 1.3 60.2 + - - +
194A ALA* 4.6 12.8 - - + -
195A LEU 3.6 3.4 - - - -
196A CYS* 3.6 46.4 - - + +
197A ILE* 3.7 0.7 - - - -
198A GLU* 6.1 0.7 - - + -
203A HIS* 3.9 27.3 - + + -
205A ILE* 5.4 1.1 - - + -
700A FAD 3.2 9.7 - - - -
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Residues in contact with PHE 178 (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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50A LYS* 3.6 26.2 - - + -
177A TYR* 1.3 71.6 - - - +
179A ALA* 1.3 77.5 + - - +
180A LEU* 3.3 17.8 + - + +
194A ALA* 3.1 3.8 - - - -
195A LEU* 2.7 46.5 + - + +
197A ILE* 3.2 16.9 - - + +
233A ASP* 2.9 32.3 - - - -
521A VAL* 4.4 18.6 - - + -
524A LEU* 4.2 23.6 - - + -
525A GLU* 3.7 25.4 - - + -
528A ASN* 4.2 9.4 - - - -
700A FAD 3.8 3.4 - - - -
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Residues in contact with ALA 179 (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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25A VAL* 3.7 24.7 - - + -
48A VAL* 4.5 5.4 - - + +
177A TYR 3.8 0.4 + - - -
178A PHE* 1.3 83.3 - - - +
180A LEU* 1.3 61.6 + - - +
192A VAL* 5.0 4.0 - - + -
193A ILE 3.8 6.1 - - - +
194A ALA* 3.8 5.4 - - + -
233A ASP* 5.1 1.2 - - - +
237A MET* 4.0 24.4 - - + +
240A ARG* 5.5 1.0 + - - -
528A ASN* 5.6 0.3 + - - -
700A FAD 2.9 30.1 + - + +
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Residues in contact with LEU 180 (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 PHE* 3.8 23.3 - - + +
179A ALA* 1.3 73.8 - - - +
181A ASP* 1.3 71.9 + - - +
193A ILE* 2.8 21.1 + - + +
194A ALA 4.3 4.7 - - - +
195A LEU* 4.1 17.7 - - + +
202A ILE* 5.0 9.6 - - + -
237A MET* 3.6 3.3 - - - +
240A ARG* 3.4 19.6 + - - -
450A SER* 4.1 29.6 - - - +
451A VAL 5.0 0.2 - - - +
454A LEU* 3.9 22.4 - - + -
524A LEU* 3.9 34.5 - - + -
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Residues in contact with ASP 181 (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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179A ALA 3.8 0.8 - - - -
180A LEU* 1.3 88.1 - - - +
182A LEU* 1.3 67.3 + - - +
192A VAL* 3.5 2.8 - - - -
193A ILE* 3.0 31.2 + - + +
237A MET* 3.3 19.1 - - - +
240A ARG* 2.7 45.2 + - - +
450A SER* 2.8 32.3 + - - +
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Residues in contact with LEU 182 (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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181A ASP* 1.3 84.1 + - - +
183A LEU* 1.3 61.5 + - - +
184A MET* 3.3 38.7 + - + +
189A CYS* 3.8 11.9 - - - -
191A GLY 3.5 2.7 - - - -
192A VAL* 4.0 10.5 - - + -
193A ILE* 5.2 0.3 - - - +
210A THR* 4.7 2.2 - - + -
212A VAL* 4.2 18.2 - - + -
237A MET* 3.3 35.5 + - + +
238A VAL* 4.6 23.8 - - + +
241A ALA* 4.8 5.6 - - + -
243A LEU* 5.0 0.2 - - + -
393A LEU* 3.8 22.7 - - + -
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Residues in contact with LEU 183 (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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182A LEU* 1.3 71.6 - - - +
184A MET* 1.3 59.4 + - - +
189A CYS* 3.6 1.7 - - - -
190A ARG* 2.6 38.4 + - - +
191A GLY* 2.6 20.7 + - - +
192A VAL 3.6 32.1 - - - +
193A ILE* 4.2 15.5 - - + -
204A ARG* 4.2 18.2 - - + -
205A ILE 4.1 6.1 - - - +
206A ARG* 4.5 5.2 - - + -
442A ILE* 4.1 22.7 - - + -
446A ALA* 3.8 37.9 - - + +
447A GLY* 4.1 4.7 - - - +
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Residues in contact with MET 184 (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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182A LEU* 3.3 51.8 + - + +
183A LEU* 1.3 74.9 - - - +
185A GLU* 1.3 68.2 + - - +
187A GLY* 4.6 10.3 - - - +
188A GLU* 3.5 28.5 - - - +
189A CYS* 3.8 10.3 - - + -
241A ALA* 3.9 25.6 - - + +
243A LEU* 4.8 3.4 - - + -
390A VAL* 4.9 9.4 - - - -
393A LEU* 4.7 3.1 - - + -
442A ILE* 5.7 1.2 - - - +
446A ALA* 6.0 1.7 - - - +
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Residues in contact with GLU 185 (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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184A MET* 1.3 78.1 - - - +
186A ASN* 1.3 87.8 + - - +
187A GLY 3.3 0.2 - - - -
188A GLU* 2.9 25.9 + - - +
190A ARG* 3.3 42.0 + - + +
441A SER* 3.6 14.7 + - - +
442A ILE* 4.0 12.6 - - + +
443A LYS* 3.4 50.1 + - - +
446A ALA* 5.0 2.4 - - - +
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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