Contacts of the strand formed by residues 211 - 217 (chain P) in PDB entry 1ZGL
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 PHE 211 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130P VAL* 5.5 1.2 - - - +
146P LEU* 3.9 22.3 - - + +
162P TRP* 5.3 3.9 - - + -
163P TRP 3.8 2.2 - - - -
164P VAL* 3.5 35.7 - - + -
197P LEU* 3.8 14.1 - - + -
199P VAL* 4.0 34.3 - - + -
203P PHE* 4.8 3.6 - - + -
204P TRP* 3.7 44.6 - + + -
209P ASN* 3.6 27.8 - - + -
210P HIS* 1.3 71.9 - - - +
212P ARG* 1.3 59.5 + - - +
213P CYS 4.2 0.2 + - - -
241P GLU* 2.8 6.4 - - - -
242P ALA* 2.5 48.9 + - - +
244P GLY 4.9 0.4 - - - -
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Residues in contact with ARG 212 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162P TRP* 3.6 4.9 - - - -
163P TRP* 2.6 91.1 + - + +
210P HIS* 5.4 1.1 - - + +
211P PHE* 1.3 73.0 - - - +
213P CYS* 1.3 60.2 + - - +
214P GLN* 3.1 32.5 + - - +
237P ILE* 4.8 14.6 - - - +
239P SER* 4.9 8.9 - - - +
240P ALA 3.4 15.5 - - - +
241P GLU* 4.0 11.9 - - + +
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Residues in contact with CYS 213 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128P VAL* 3.9 2.3 - - - +
130P VAL* 3.9 10.3 - - + +
148P CYS* 2.0 52.3 - - + -
160P LEU* 3.6 24.2 - - - -
161P SER 3.7 3.6 - - - -
162P TRP* 3.9 19.0 - - + -
211P PHE 4.2 1.2 + - - -
212P ARG* 1.3 71.4 - - - +
214P GLN* 1.3 63.3 + - - +
239P SER* 3.5 4.3 - - - -
240P ALA 3.0 29.0 + - - -
241P GLU* 4.5 0.4 - - - +
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Residues in contact with GLN 214 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159P GLU 5.3 0.7 - - - +
160P LEU* 3.1 25.2 - - - +
161P SER* 2.9 26.0 + - - +
163P TRP* 4.2 0.9 - - + -
212P ARG* 3.1 35.9 + - - +
213P CYS* 1.3 71.5 - - - +
215P VAL* 1.3 74.5 + - - +
237P ILE* 4.9 6.3 - - + -
238P VAL 4.2 0.2 - - - -
239P SER* 4.3 6.5 - - - -
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Residues in contact with VAL 215 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126P PRO* 3.5 36.3 - - + -
128P VAL* 3.4 36.1 - - + -
150P ALA* 4.8 10.1 - - + -
158P VAL* 4.4 15.0 - - + -
159P GLU 3.4 5.4 - - - -
160P LEU* 3.8 20.0 - - + +
214P GLN* 1.3 89.0 - - - +
216P GLN* 1.3 60.2 + - - +
217P PHE* 3.5 2.9 + - - +
237P ILE* 3.6 5.3 - - - -
238P VAL* 3.4 24.3 + - + +
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Residues in contact with GLN 216 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E THR* 4.9 6.9 + - - -
157P HIS 3.4 1.2 - - - +
158P VAL* 3.1 10.5 - - - -
159P GLU* 2.7 45.1 + - + +
214P GLN* 5.3 0.4 - - - +
215P VAL* 1.3 69.2 - - - +
217P PHE* 1.3 86.2 + - - +
218P TYR* 3.0 36.1 + - + +
235P THR* 4.5 9.2 - - - +
236P GLN 2.8 17.8 + - - +
237P ILE* 3.6 25.7 - - + +
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Residues in contact with PHE 217 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123P VAL* 3.8 8.7 - - + -
124P PHE 2.9 29.8 - - - -
125P PRO* 3.9 9.0 - - + -
126P PRO* 3.7 24.9 - - + -
153P PHE* 4.5 7.0 - + - -
154P TYR 3.7 19.1 - - - -
155P PRO* 4.5 2.7 - - + -
157P HIS* 3.6 9.9 - - + -
158P VAL* 4.1 9.0 - - + -
215P VAL 3.5 1.8 + - - +
216P GLN* 1.3 90.3 + - - +
218P TYR* 1.3 92.7 + - - +
233P PRO 4.0 17.9 - - - -
234P VAL 3.2 24.7 - - - -
235P THR* 3.6 12.8 - - - +
236P GLN* 3.0 21.2 + - + +
238P VAL* 5.5 0.2 - - + -
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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