Contacts of the strand formed by residues 202 - 209 (chain D) in PDB entry 1ZVM
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 ASP 202 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120D ASN* 3.7 23.6 + - + +
201D CYS* 1.3 82.3 - - - +
203D VAL* 1.3 62.1 + - + +
234D LYS 2.8 19.5 + - - +
235D VAL* 3.4 4.5 - - - +
236D GLN* 2.7 61.1 + - - +
237D THR 3.1 8.5 + - - +
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Residues in contact with VAL 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D ASN* 3.9 15.3 - - - +
122D ILE 4.8 1.4 + - - +
201D CYS 3.9 4.0 - - - +
202D ASP* 1.3 82.8 - - + +
204D VAL* 1.3 64.4 + - - +
205D HIS* 3.6 37.7 + - + +
236D GLN* 4.0 16.2 - - - +
237D THR* 3.3 27.1 - - + +
239D GLU* 4.7 7.0 - - + +
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Residues in contact with VAL 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D CYS 5.2 1.3 - - - +
122D ILE* 4.2 12.6 - - + +
124D LEU* 4.2 24.7 - - + -
200D ALA* 3.6 27.8 - - + -
201D CYS 3.9 10.1 - - - +
203D VAL* 1.3 76.5 - - - +
205D HIS* 1.3 73.0 + - - +
230D LEU* 4.3 8.1 - - + -
235D VAL* 3.9 23.6 - - + -
237D THR 2.8 10.6 + - - +
238D LEU* 3.1 14.6 - - + +
239D GLU* 2.8 25.6 + - - +
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Residues in contact with HIS 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D ASN 5.5 3.8 + - - -
122D ILE 3.4 9.5 + - - +
123D LEU* 3.6 9.6 - - + -
124D LEU* 2.7 32.8 + - - +
142D MET* 3.7 23.1 - - + +
203D VAL* 3.6 34.6 + - + +
204D VAL* 1.3 77.9 - - - +
206D VAL* 1.3 55.4 + - - +
238D LEU* 4.3 1.1 - - - -
239D GLU* 3.1 39.3 + - + +
241D TRP* 3.5 32.7 - + + -
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Residues in contact with VAL 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D LEU* 4.5 1.3 - - - -
124D LEU* 3.0 17.7 - - + +
125D TRP* 4.0 3.1 - - - +
205D HIS* 1.3 76.0 - - - +
207D MET* 1.3 63.8 + - - +
208D LEU* 3.9 15.0 - - + -
222D PHE* 3.5 47.3 - - + -
238D LEU* 3.9 18.2 - - + -
239D GLU 3.0 5.9 + - - -
240D ALA* 3.6 24.6 - - + +
241D TRP* 2.8 28.4 + - - +
262D LEU* 4.9 1.1 - - + -
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Residues in contact with MET 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D LEU* 4.0 8.5 - - + +
124D LEU 2.9 8.4 + - - +
125D TRP* 4.1 8.5 - - + -
126D SER 3.1 25.8 + - - -
128D ILE* 3.4 14.9 - - + +
131D LEU* 3.8 42.8 - - + +
132D ALA* 3.8 20.0 - - - -
135D PHE* 4.3 13.0 - - + -
206D VAL* 1.3 72.4 - - - +
208D LEU* 1.3 63.5 + - - +
241D TRP* 3.5 28.7 - - + +
243D ILE* 3.5 31.0 - - + -
284D PHE* 4.5 6.5 - - + -
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Residues in contact with LEU 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D SER* 3.8 23.8 - - - -
128D ILE* 4.2 7.4 - - - -
206D VAL* 3.9 17.5 - - + +
207D MET* 1.3 84.4 - - - +
209D ASP* 1.3 60.8 + - - +
210D GLY 3.3 0.9 + - - -
215D ILE* 3.7 26.9 - - + +
216D PHE* 4.6 5.8 - - + -
222D PHE* 4.3 9.0 - - + -
240D ALA* 4.3 16.8 - - + -
241D TRP 2.9 10.2 + - - +
242D VAL* 3.7 3.1 - - + -
243D ILE* 2.8 33.1 + - - +
259D ILE* 3.8 28.5 - - + -
262D LEU* 4.3 11.7 - - + -
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Residues in contact with ASP 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D SER 4.1 6.6 + - - +
127D ARG* 3.8 22.7 - - + +
128D ILE* 4.1 15.3 - - + +
208D LEU* 1.3 71.0 - - - +
210D GLY* 1.3 58.0 + - - +
211D SER* 2.5 34.2 + - - -
212D ARG* 3.4 33.9 + - + +
215D ILE* 3.7 20.0 + - - -
243D ILE 4.2 3.2 - - - +
245D GLY* 5.7 0.7 + - - -
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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