Contacts of the helix formed by residues 191 - 200 (chain A) in PDB entry 4WMJ
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 191 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189A ASN* 3.0 24.8 + - + +
190A ILE* 1.3 80.2 - - - +
192A GLY* 1.3 62.2 + - - +
193A THR* 3.1 23.3 + - - -
194A HIS* 3.0 25.5 + - - +
195A LEU 4.2 1.0 + - - -
224A ASN* 5.1 0.2 + - - -
345B ASP* 3.4 12.1 - - - +
346B GLN* 2.8 30.8 + - + +
415B THR* 4.2 8.8 + - - -
424B HIS* 4.8 1.3 - - - -
425B HIS* 5.0 1.8 + - - -
428B LEU* 3.7 29.8 - - + +
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Residues in contact with GLY 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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190A ILE 3.0 7.4 + - - -
191A ASP* 1.3 72.9 + - - +
193A THR* 1.3 65.2 - - - +
194A HIS 3.1 0.4 + - - -
195A LEU* 3.5 2.6 + - - -
196A ALA* 2.9 25.6 + - - +
415B THR* 5.4 0.6 + - - -
417B ASN* 4.1 11.8 + - - -
419B ILE* 3.7 25.1 - - - +
424B HIS* 3.7 15.6 - - - +
425B HIS* 5.4 1.2 + - - +
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Residues in contact with THR 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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191A ASP* 3.1 22.5 + - - -
192A GLY* 1.3 76.8 - - - +
194A HIS* 1.3 63.1 + - - +
197A GLU* 3.0 26.3 + - + +
345B ASP* 5.3 1.4 + - - -
346B GLN* 4.0 16.4 - - + -
347B TYR* 3.5 48.2 - - + +
415B THR* 4.2 4.9 + - - -
416B HIS* 5.4 0.2 - - - +
417B ASN* 3.0 28.7 + - - +
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Residues in contact with HIS 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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165A ASP* 5.5 0.7 - - - -
186A PHE 3.5 19.7 + - - -
187A VAL* 3.8 4.5 - - + -
188A SER* 3.0 42.8 + - - -
189A ASN* 3.1 21.6 + - + +
191A ASP 3.0 13.0 + - - +
193A THR* 1.3 79.4 - - - +
195A LEU* 1.3 64.5 + - - +
197A GLU* 3.6 2.6 + - + +
198A VAL* 3.5 23.2 + - + +
346B GLN* 3.5 40.5 + - + +
389B ASN* 4.8 1.8 - - - -
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Residues in contact with LEU 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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159A ILE* 4.6 5.4 - - + -
187A VAL* 4.0 26.2 - - + +
191A ASP 4.2 0.8 + - - -
192A GLY 3.5 6.3 + - - +
194A HIS* 1.3 79.6 - - - +
196A ALA* 1.4 63.5 + - - +
198A VAL* 3.0 6.3 + - + +
199A LEU* 2.9 49.8 + - + +
209A PHE* 5.1 2.5 - - + -
224A ASN* 3.6 42.2 - - - +
227A SER* 3.6 23.8 - - - -
228A ALA* 3.9 14.4 - - + +
419B ILE* 4.1 10.8 - - + -
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Residues in contact with ALA 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 GLY 2.9 19.1 + - - +
193A THR 3.4 2.4 + - - +
195A LEU* 1.4 77.5 - - - +
197A GLU* 1.3 62.1 + - + +
199A LEU* 3.4 8.9 + - - +
200A LYS* 3.2 35.7 + - - +
417B ASN* 3.7 27.1 - - + +
419B ILE* 4.2 16.5 - - + +
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Residues in contact with GLU 197 (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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193A THR* 3.0 22.2 + - + +
194A HIS* 4.2 3.6 - - + +
196A ALA* 1.3 76.2 - - + +
198A VAL* 1.3 62.8 + - + +
200A LYS* 4.0 26.1 + - - +
201A ARG* 3.4 33.5 + - - +
176B LYS* 3.4 32.5 + - + +
177B PRO* 5.5 1.0 - - - +
347B TYR* 2.6 43.7 + - + +
417B ASN* 4.7 2.0 + - - +
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Residues in contact with VAL 198 (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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157A ILE* 4.0 23.6 - - + -
185A HIS* 3.9 38.6 - - + -
186A PHE 4.6 7.0 - - - +
187A VAL* 3.8 17.9 - - + -
194A HIS* 3.5 14.7 + - + +
195A LEU* 3.0 8.5 + - + +
197A GLU* 1.3 78.3 - - + +
199A LEU* 1.3 61.6 + - + +
201A ARG* 2.9 33.7 + - - +
202A LEU* 3.4 10.9 - - + +
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Residues in contact with LEU 199 (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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195A LEU* 2.9 48.3 + - + +
196A ALA* 3.4 7.6 + - - +
198A VAL* 1.3 75.3 - - + +
200A LYS* 1.3 63.1 + - + +
202A LEU* 3.0 38.3 + - + +
209A PHE* 3.9 15.5 - - + -
227A SER 4.8 1.3 - - - +
228A ALA* 4.7 4.5 - - + -
231A TRP* 3.7 64.6 + - + +
419B ILE* 6.0 2.2 - - + -
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Residues in contact with LYS 200 (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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196A ALA* 3.2 22.8 + - - +
197A GLU* 4.1 26.2 + - - +
198A VAL 3.2 0.4 - - - -
199A LEU* 1.3 76.4 - - + +
201A ARG* 1.3 58.9 + - + +
202A LEU 3.3 2.4 + - - +
347B TYR* 5.7 0.2 + - - -
417B ASN* 4.4 14.5 + - - -
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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