Contacts of the helix formed by residues 186 - 196 (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 MET 186 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174A PHE* 4.0 14.8 - - + -
178A TYR 4.1 15.9 - - - +
179A MET* 4.0 28.3 - - - -
181A LYS* 5.1 2.5 - - + -
182A GLY 3.0 11.8 + - - +
183A SER* 4.0 3.1 - - - -
185A VAL* 1.3 81.7 - - + +
187A PRO* 1.3 60.3 - - - +
189A ILE* 3.7 20.6 - - + -
190A GLU* 2.9 39.3 + - - +
329A LEU* 3.4 48.5 - - + +
333A ASP* 3.2 11.7 - - - +
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Residues in contact with PRO 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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145A VAL* 4.1 17.6 - - + +
183A SER* 3.2 29.6 - - - +
184A LYS 4.6 2.0 - - - +
185A VAL* 3.1 9.9 - - - +
186A MET* 1.3 85.8 - - - +
188A ASN* 1.3 61.3 + - + +
190A GLU* 3.0 2.3 + - - +
191A LYS* 2.8 30.0 + - - +
333A ASP* 3.0 14.8 - - - +
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Residues in contact with ASN 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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144A TRP* 3.4 26.4 - - + -
145A VAL* 3.0 35.9 - - - +
187A PRO* 1.3 79.6 - - - +
189A ILE* 1.3 61.2 + - - +
191A LYS* 3.0 15.2 + - - +
192A LEU* 3.4 14.3 + - - +
333A ASP* 2.8 29.0 + - - +
334A LYS* 4.8 1.6 + - - +
336A VAL* 4.1 5.6 - - + -
337A GLY* 2.9 38.0 - - - +
340A MET* 4.7 0.2 - - - +
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Residues in contact with ILE 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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174A PHE* 5.0 1.3 - - + -
179A MET* 4.2 20.4 - - + -
186A MET* 3.7 25.8 - - + +
188A ASN* 1.3 73.0 - - - +
190A GLU* 1.3 61.0 + - - +
192A LEU* 3.5 13.5 + - + +
193A ARG* 3.3 19.4 + - - +
329A LEU 4.4 1.1 - - - +
332A ILE* 4.4 7.4 - - + -
333A ASP* 2.5 45.6 + - + +
336A VAL* 3.8 20.2 - - + -
356A PHE* 3.8 42.8 - - + -
489A VAL* 5.4 1.5 - - + +
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Residues in contact with GLU 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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179A MET* 3.8 22.8 - - - +
182A GLY* 3.9 15.4 + - - -
183A SER* 4.1 24.2 - - - +
186A MET* 2.9 32.2 + - - +
187A PRO 3.0 5.8 + - - +
189A ILE* 1.3 76.5 - - - +
191A LYS* 1.3 63.9 + - - +
193A ARG* 3.1 42.8 + - - +
194A SER* 3.1 30.0 + - - -
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Residues in contact with LYS 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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144A TRP* 3.4 30.5 - - + +
145A VAL* 5.2 10.3 - - + +
149A CYS* 5.5 5.6 - - - -
187A PRO 2.8 11.5 + - - +
188A ASN* 3.0 2.6 + - - +
190A GLU* 1.3 75.8 - - - +
192A LEU* 1.3 54.3 - - - +
194A SER* 3.8 3.0 - - - -
195A CYS* 2.5 44.4 + - + +
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Residues in contact with LEU 192 (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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144A TRP* 3.8 11.9 - - + -
188A ASN 3.4 9.9 + - - +
189A ILE* 3.7 10.5 - - - +
190A GLU 3.3 0.4 - - - -
191A LYS* 1.3 76.9 - - - +
193A ARG* 1.3 54.3 + - - +
196A GLY* 2.6 33.6 + - - -
336A VAL* 3.7 31.0 - - + -
340A MET* 4.1 16.2 - - + -
354A VAL* 4.6 16.2 - - + -
356A PHE* 5.3 11.4 - - + -
489A VAL* 3.8 19.2 - - + +
491A TYR* 3.3 49.6 - - + -
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Residues in contact with ARG 193 (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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179A MET* 3.2 39.6 - - + +
189A ILE 3.3 7.9 + - - +
190A GLU* 3.1 30.5 + - - +
191A LYS 3.3 0.4 - - - -
192A LEU* 1.3 76.9 - - - +
194A SER* 1.3 86.5 + - - +
195A CYS 3.2 1.0 + - - -
196A GLY 3.6 6.6 - - - +
198A HIS* 3.3 65.8 + - + +
199A SER 6.0 0.7 - - - -
489A VAL* 4.0 14.3 - - + +
500A LYS* 6.3 0.2 - - - +
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Residues in contact with SER 194 (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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149A CYS* 5.6 2.3 - - - -
190A GLU* 3.1 19.9 + - - -
191A LYS* 3.9 3.6 - - - -
193A ARG* 1.3 97.2 - - - +
195A CYS* 1.3 59.8 + - - +
198A HIS* 5.2 4.7 - - - -
498A LYS* 3.4 28.7 + - - +
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Residues in contact with CYS 195 (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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144A TRP* 5.9 1.1 - - - -
149A CYS* 2.0 54.7 - - - -
150A GLU 4.9 1.3 - - - -
191A LYS* 2.5 21.6 + - + +
194A SER* 1.3 78.4 - - - +
196A GLY* 1.3 60.9 + - - +
491A TYR* 3.9 24.0 - - + -
497A TYR* 3.6 15.4 - - - -
498A LYS* 2.9 25.8 + - - +
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Residues in contact with GLY 196 (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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192A LEU 2.6 21.4 + - - -
193A ARG 3.6 6.8 - - - +
195A CYS* 1.3 76.3 - - - +
197A THR* 1.3 60.4 + - - -
490A GLY 3.4 7.9 - - - -
491A TYR* 3.8 13.8 - - - -
496A LYS 3.6 11.7 - - - -
498A LYS* 3.1 18.5 + - - -
499A THR 3.2 7.6 + - - +
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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