Contacts of the strand formed by residues 182 - 187 (chain A) in PDB entry 2ZB8
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 ARG 182 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A LYS 3.2 3.3 + - - +
157A THR* 3.3 30.7 + - + +
158A MET 2.9 26.1 + - - -
180A CYS* 4.1 0.3 - - - +
181A SER* 1.3 92.0 + - - +
183A VAL* 1.3 66.4 + - - +
184A VAL* 4.2 9.9 - - + -
203A ASP* 3.1 15.2 - - + +
220A SER* 2.9 26.7 + - - +
222A PRO* 3.9 31.3 - - - +
223A ALA* 5.6 4.8 - - - +
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Residues in contact with VAL 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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158A MET* 3.4 10.5 - - + +
160A VAL* 4.2 9.0 - - + -
172A GLY* 3.6 41.7 - - - +
175A GLY* 4.2 2.2 - - - -
176A HIS* 3.6 37.0 - - + +
180A CYS* 4.0 9.9 - - + -
182A ARG* 1.3 77.9 - - - +
184A VAL* 1.3 63.8 + - - +
202A PHE* 3.7 21.0 - - + -
203A ASP* 2.8 41.7 + - - +
204A ALA 3.5 0.3 + - - -
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Residues in contact with VAL 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A THR* 4.8 0.2 - - + -
158A MET 3.0 9.1 + - - +
159A VAL* 3.2 7.3 - - + +
160A VAL* 2.9 24.3 + - - +
182A ARG* 4.2 11.9 - - + -
183A VAL* 1.3 80.0 - - - +
185A GLY* 1.3 69.5 + - - +
186A ILE* 5.3 0.9 - - + -
202A PHE* 4.0 2.9 - - - -
203A ASP* 5.1 0.4 - - + -
204A ALA* 3.3 19.5 - - + +
206A ILE* 4.2 13.9 - - + -
217A LEU* 4.4 4.9 - - + -
220A SER* 3.6 33.7 - - - +
221A CYS* 3.6 29.2 - - - -
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Residues in contact with GLY 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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160A VAL 3.4 7.6 - - - -
163A ALA* 3.5 16.2 - - - -
184A VAL* 1.3 73.8 - - - +
186A ILE* 1.3 65.9 + - - +
187A CYS 4.1 0.4 - - - -
196A LEU* 4.6 2.5 - - - -
202A PHE* 3.5 13.0 - - - -
204A ALA 2.9 11.9 + - - -
205A ALA* 3.3 3.9 - - - -
206A ILE* 2.8 27.9 + - - +
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Residues in contact with ILE 186 (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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159A VAL* 3.8 16.6 - - + -
160A VAL 2.8 10.0 + - - +
161A SER* 4.4 6.3 - - - -
162A GLY 3.2 10.6 + - - -
163A ALA* 3.1 20.9 + - - +
184A VAL* 5.0 0.9 - - + +
185A GLY* 1.3 78.1 - - - +
187A CYS* 1.3 63.8 + - - +
206A ILE* 3.3 23.8 - - + +
208A TYR* 3.9 30.0 - - + +
213A VAL* 4.2 8.5 - - + -
217A LEU* 4.0 16.6 - - + -
236A ILE* 4.2 18.8 - - + -
240A VAL* 3.6 31.0 - - + -
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Residues in contact with CYS 187 (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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163A ALA* 4.6 0.7 - - + -
164A ALA* 4.2 17.3 - - + +
186A ILE* 1.3 77.0 - - - +
188A GLY* 1.3 60.3 + - - +
189A THR 3.7 1.8 - - - -
192A LYS* 3.5 33.0 - - + -
193A CYS* 3.5 32.3 - - - -
196A LEU* 4.1 8.7 - - - -
205A ALA* 5.0 0.7 - - - -
206A ILE 2.9 6.8 + - - -
207A ASN* 3.1 6.8 - - - -
208A TYR* 2.9 32.9 + - - -
700A NAP 3.4 11.7 - - - +
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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