Contacts of the helix formed by residues 175 - 182 (chain A) in PDB entry 4ZGA
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 175 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173A GLY 3.4 2.6 + - - +
174A PHE* 1.3 76.8 - - - +
176A ALA* 1.3 57.3 + - - +
177A SER* 3.1 25.6 + - - +
178A TYR* 2.7 57.0 + - + +
320A PRO* 3.2 32.3 - - - +
321A PHE* 6.1 0.2 - - - +
361A GLY* 3.8 8.3 - - - -
362A MET 2.9 29.1 + - - +
363A GLU* 4.4 3.8 + - - +
482A ASN* 4.8 4.8 + - - +
483A SER* 3.8 37.1 - - - +
485A GLN 3.5 7.9 - - - +
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Residues in contact with ALA 176 (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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174A PHE 3.8 1.2 + - - -
175A ARG* 1.3 71.6 - - - +
177A SER* 1.3 57.4 + - - +
178A TYR 3.3 0.2 - - - -
179A MET* 3.5 21.7 + - - +
200A PRO 3.8 12.7 - - - +
201A TYR* 3.2 34.8 - - + -
485A GLN* 3.2 13.7 + - + -
486A THR* 3.3 19.2 - - - +
487A VAL* 4.2 7.6 - - + -
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Residues in contact with SER 177 (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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175A ARG* 2.8 30.4 + - - +
176A ALA* 1.3 74.8 - - - +
178A TYR* 1.3 70.6 + - - +
179A MET 2.9 2.0 - - - -
180A LYS* 2.8 26.9 + - - +
181A LYS 4.2 0.2 + - - -
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Residues in contact with TYR 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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173A GLY 3.9 9.7 + - - -
174A PHE* 3.9 17.0 - + + -
175A ARG* 2.7 50.0 + - + +
177A SER* 1.3 82.5 + - - +
179A MET* 1.3 55.2 + - - +
181A LYS* 2.9 31.4 + - - +
186A MET* 4.1 5.7 - - - +
311A PRO* 4.0 15.7 - - + +
315A GLY* 4.8 2.1 - - - -
320A PRO* 3.5 41.7 + - + +
325A MET* 3.9 20.9 - - + -
329A LEU* 4.1 30.7 - - + +
362A MET* 4.4 9.7 - - - +
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Residues in contact with MET 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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174A PHE* 3.7 22.2 - - + -
176A ALA 3.6 11.6 - - - +
177A SER 2.9 1.2 - - - -
178A TYR* 1.3 74.0 - - - +
180A LYS* 1.3 66.5 + - - +
181A LYS 3.2 0.4 - - - -
182A GLY* 3.7 6.9 + - - -
186A MET* 4.0 17.0 - - - -
189A ILE* 4.2 18.8 - - + +
190A GLU* 3.8 19.1 - - - +
193A ARG* 3.2 51.3 + - + +
200A PRO 6.0 0.9 - - - +
356A PHE* 4.9 1.3 - - + -
487A VAL* 3.7 25.1 - - + -
489A VAL* 4.5 11.0 - - + -
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Residues in contact with LYS 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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177A SER* 2.8 20.3 + - - +
179A MET* 1.3 78.9 - - - +
181A LYS* 1.3 53.1 + - - +
182A GLY* 2.8 16.8 + - - -
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Residues in contact with LYS 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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177A SER 4.2 0.2 + - - -
178A TYR* 2.9 18.3 + - - +
180A LYS* 1.3 75.6 - - - +
182A GLY* 1.3 61.5 + - - +
184A LYS* 5.1 2.6 + - - +
185A VAL* 4.2 21.7 + - + +
186A MET* 5.1 5.2 - - + -
329A LEU* 4.9 13.0 - - + -
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Residues in contact with GLY 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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178A TYR 4.7 0.2 + - - -
179A MET 3.7 5.3 + - - -
180A LYS 2.8 12.6 + - - -
181A LYS* 1.3 75.3 - - - +
183A SER* 1.3 60.9 + - - -
184A LYS 3.2 3.8 - - - -
185A VAL* 2.9 20.8 + - - +
186A MET* 3.0 13.9 + - - +
190A GLU* 3.9 15.8 + - - -
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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