Contacts of the helix formed by residues 203 - 208 (chain A) in PDB entry 1ZEB
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 GLY 203 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150A ARG* 3.8 9.2 - - - -
152A GLN* 2.9 36.1 + - - -
202A GLY* 1.3 74.1 - - - -
204A ARG* 1.3 68.5 + - - +
205A LYS 3.2 3.2 + - - -
206A TYR* 3.6 7.8 + - - -
207A MET* 3.7 3.5 - - - +
268A LEU* 4.2 3.4 - - - -
270A GLU 3.0 2.0 + - - -
271A PRO 3.2 9.6 - - - -
272A GLY 3.0 10.1 + - - -
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Residues in contact with ARG 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 GLY 3.7 0.8 - - - -
203A GLY* 1.3 75.9 - - - +
205A LYS* 1.3 64.4 + - - +
207A MET* 3.1 15.6 + - - +
208A PHE* 3.2 20.4 - - + -
214A ASP* 2.6 46.4 + - - +
215A PRO* 3.8 12.7 - - - +
216A GLU* 2.9 25.5 + - - +
217A TYR* 3.8 0.4 - - - -
246A TYR* 3.3 27.6 - - - +
248A TRP* 3.3 24.3 + - - +
268A LEU* 3.0 41.8 + - + +
269A PHE 3.1 15.8 + - - -
270A GLU* 3.0 15.7 + - - +
271A PRO* 3.1 17.7 + - + +
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Residues in contact with LYS 205 (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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150A ARG* 5.2 0.6 - - - +
203A GLY 3.2 0.2 - - - -
204A ARG* 1.3 78.5 - - - +
206A TYR* 1.3 94.5 + - + +
207A MET 3.1 1.4 + - - -
208A PHE* 3.5 4.7 + - - +
214A ASP* 5.6 0.2 - - - -
222A SER 4.5 15.2 + - - +
223A GLN* 3.8 16.7 + - - +
224A GLY 3.3 21.1 - - - +
225A GLY* 3.2 9.3 - - - -
226A THR* 3.1 40.2 + - + -
271A PRO* 3.2 26.1 + - + +
272A GLY* 4.1 9.4 - - - +
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Residues in contact with TYR 206 (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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150A ARG* 3.1 49.5 + - + -
152A GLN* 3.4 28.7 - - - +
169A TYR* 3.4 38.7 - + + +
170A SER* 3.9 9.2 - - - -
173A ASP* 4.5 3.8 - - - -
187A ALA* 3.7 18.9 - - + +
203A GLY* 3.9 4.0 - - - -
204A ARG 3.2 1.0 + - - -
205A LYS* 1.3 104.4 + - + +
207A MET* 1.3 58.4 + - - +
208A PHE 3.4 0.9 - - - -
226A THR* 3.5 20.9 - - + -
227A ARG* 3.0 32.6 + - - +
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Residues in contact with MET 207 (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* 3.6 18.8 - - - -
187A ALA* 3.8 16.6 - - - +
190A LEU* 4.1 9.2 - - + -
191A ILE* 3.8 21.5 - - + -
203A GLY 3.7 4.7 - - - +
204A ARG 3.1 15.3 + - - +
206A TYR* 1.3 79.1 - - - +
208A PHE* 1.3 61.5 + - + +
227A ARG* 3.8 4.7 - - - -
231A LYS 3.7 0.5 - - - +
232A ASN* 3.5 3.5 - - - +
233A LEU* 2.8 54.4 + - + -
234A VAL* 3.8 14.8 - - + +
266A MET* 3.9 24.0 - - + -
268A LEU* 3.6 20.0 - - + -
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Residues in contact with PHE 208 (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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204A ARG* 3.2 33.7 - - + -
205A LYS* 3.5 2.4 + - - -
206A TYR 3.4 0.6 + - - -
207A MET* 1.3 80.2 - - + +
209A ARG* 1.3 65.6 + - - +
212A THR* 3.8 33.0 - - + +
215A PRO* 5.9 5.4 - - + -
225A GLY* 4.2 6.1 - - - +
226A THR 3.1 9.2 + - - -
227A ARG* 3.1 23.0 + - - +
231A LYS 3.9 2.2 - - - -
232A ASN* 3.3 39.9 - - - +
234A VAL* 3.4 27.4 - - + -
246A TYR* 3.8 27.6 - + - -
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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