Contacts of the helix formed by residues 180 - 191 (chain A) in PDB entry 4EZJ
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 LEU 180 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176A THR* 2.9 43.0 + - + +
177A ARG* 4.4 3.8 - - - +
178A ARG 3.2 0.8 - - - -
179A GLY* 1.4 73.2 - - - +
181A VAL* 1.4 63.3 + - - +
182A THR 3.3 2.0 - - - -
183A PRO* 3.3 5.5 - - + +
184A ARG* 3.2 26.6 + - - +
674A ASP* 4.1 13.5 - - - +
678A ALA* 5.3 5.2 - - + -
679A ARG* 3.8 33.2 - - + +
682A LEU* 3.9 14.8 - - + +
715A VAL* 3.8 19.3 - - + +
716A ILE* 4.7 11.2 - - + -
719A ALA* 3.9 27.5 - - + +
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Residues in contact with VAL 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 ARG 3.4 14.4 - - - +
178A ARG* 3.3 21.9 + - - +
180A LEU* 1.4 77.0 - - - +
182A THR* 1.3 60.1 + - - +
184A ARG* 3.4 31.2 + - - +
185A MET* 3.0 59.1 + - + +
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Residues in contact with THR 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A ARG 4.6 1.8 + - - -
179A GLY 4.2 4.8 + - - -
181A VAL* 1.3 78.4 - - - +
183A PRO* 1.4 65.0 - - + +
185A MET* 3.2 9.0 + - - +
186A ALA* 2.9 32.1 + - + +
679A ARG* 5.7 1.3 - - - +
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Residues in contact with PRO 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A GLY 3.3 13.9 - - - +
180A LEU* 3.3 15.0 - - + +
182A THR* 1.4 91.7 - - + +
184A ARG* 1.4 57.8 + - - +
186A ALA* 3.9 7.2 - - + +
187A GLU* 3.2 24.1 + - - +
679A ARG* 3.1 50.3 - - + +
682A LEU* 4.9 7.6 - - + -
683A LYS* 4.5 18.0 - - + +
686A LEU* 5.2 0.2 - - - -
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Residues in contact with ARG 184 (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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180A LEU 3.2 16.8 + - - +
181A VAL* 3.4 41.4 + - - +
183A PRO* 1.4 76.1 - - - +
185A MET* 1.4 67.9 + - - +
187A GLU* 2.9 7.3 + - - +
188A VAL* 2.8 45.1 + - + +
318A VAL* 5.3 3.4 - - - +
319A ARG 5.4 3.2 + - - -
682A LEU* 4.5 5.7 - - + +
686A LEU* 3.6 22.2 - - + -
719A ALA* 3.1 29.9 + - - +
722A ARG* 3.5 52.1 + - - +
723A GLY* 3.7 1.5 - - - +
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Residues in contact with MET 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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181A VAL* 3.0 46.7 + - + +
182A THR* 3.8 7.2 - - - +
184A ARG* 1.4 90.3 - - - +
186A ALA* 1.3 56.5 + - - +
188A VAL* 3.4 5.7 + - - +
189A ALA* 3.0 32.7 + - - +
320A LYS 6.4 2.0 - - - -
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Residues in contact with ALA 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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182A THR* 2.9 21.0 + - + +
183A PRO* 3.9 8.7 - - + +
185A MET* 1.3 75.1 - - - +
187A GLU* 1.4 51.6 + - - +
189A ALA* 4.0 5.9 - - - +
190A SER* 2.5 33.3 + - - -
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Residues in contact with GLU 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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183A PRO 3.2 18.7 + - - +
184A ARG 2.9 5.4 + - - +
186A ALA* 1.4 75.1 - - - +
188A VAL* 1.4 63.3 + - - +
189A ALA 3.3 0.2 - - - -
190A SER* 3.4 8.9 + - - -
191A ARG* 3.3 25.4 + - - +
683A LYS* 3.4 34.7 - - + +
686A LEU* 3.7 20.4 - - + -
687A ARG* 2.7 57.9 + - - +
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Residues in contact with VAL 188 (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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184A ARG* 2.8 28.4 + - + +
185A MET* 4.0 5.8 - - - +
187A GLU* 1.4 71.5 - - - +
189A ALA* 1.4 61.2 + - - +
190A SER 3.4 0.5 + - - -
191A ARG* 3.5 36.5 + - - +
318A VAL* 3.8 29.6 - - + -
686A LEU* 4.5 3.4 - - + -
723A GLY* 3.5 33.9 - - - +
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Residues in contact with ALA 189 (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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185A MET 3.0 18.9 + - - +
186A ALA* 4.0 7.4 - - - +
188A VAL* 1.4 77.3 - - - +
190A SER* 1.3 58.3 + - - +
191A ARG 3.7 3.3 + - - +
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Residues in contact with SER 190 (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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186A ALA 2.5 24.8 + - - -
187A GLU* 3.5 16.3 + - - -
188A VAL 3.3 0.4 - - - -
189A ALA* 1.3 77.5 - - - +
191A ARG* 1.4 62.2 + - - +
192A ASP 3.8 1.0 + - - -
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Residues in contact with ARG 191 (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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187A GLU* 3.3 16.9 + - - +
188A VAL* 3.5 36.7 + - - +
189A ALA 4.5 3.1 - - - +
190A SER* 1.4 77.8 - - - +
192A ASP* 1.4 61.0 + - - +
193A PRO* 3.2 16.5 - - + +
196A TYR* 3.4 49.6 + - + -
316A ASP* 3.9 7.3 + - - +
318A VAL* 3.3 19.6 - - - +
686A LEU* 3.3 29.6 + - - +
687A ARG* 4.9 9.2 - - + +
723A GLY 2.8 30.1 + - - -
724A CYS 3.5 4.2 + - - -
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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