Contacts of the helix formed by residues 190 - 200 (chain A) in PDB entry 1W6J
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 PRO 190 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152A PHE* 3.8 14.8 - - + +
188A ALA 3.7 5.6 - - - +
189A ILE* 1.3 93.8 - - + +
191A SER* 1.3 56.4 + - - +
192A TRP* 4.5 2.9 - - + +
193A GLY* 2.8 25.5 + - - -
194A LYS* 2.9 9.4 + - - -
280A VAL* 3.8 19.1 - - + -
284A GLU* 3.2 29.4 - - - +
518A SER 4.8 1.6 - - - +
519A GLU* 3.8 9.4 - - + +
520A VAL* 3.7 30.3 - - + -
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Residues in contact with SER 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A ILE 3.7 0.8 + - - -
190A PRO* 1.3 72.0 - - - +
192A TRP* 1.3 69.2 + - - +
194A LYS* 3.2 19.8 + - - +
195A PHE* 2.9 28.1 + - - +
208A LEU* 5.2 5.1 - - - +
209A ASN* 6.2 4.7 - - - -
237A TYR* 4.7 1.7 + - - -
277A ARG 6.0 0.9 - - - -
280A VAL* 4.5 0.6 - - - +
517A PRO* 3.5 12.5 + - - +
518A SER* 4.1 2.1 + - - -
519A GLU* 2.8 33.0 + - - -
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Residues in contact with TRP 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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103A PHE* 4.0 16.4 - + + -
152A PHE* 3.8 20.4 - + + -
190A PRO* 3.1 3.2 + - + +
191A SER* 1.3 88.8 + - - +
193A GLY* 1.3 62.1 + - - +
195A PHE* 3.5 8.0 - - - +
196A TRP* 3.2 33.6 + - + -
236A VAL* 4.1 13.7 - - + -
237A TYR* 3.1 32.3 + + - -
240A MET* 3.9 22.7 - - + +
338A ILE* 3.7 27.8 - - + -
518A SER* 4.1 11.2 + - - +
520A VAL* 5.9 1.3 - - + -
521A PHE* 3.6 35.2 - + - -
1733A R71 3.6 43.1 - + + -
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Residues in contact with GLY 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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152A PHE* 3.4 14.8 - - - -
156A LEU* 4.3 7.9 - - - -
189A ILE* 3.5 25.4 - - - -
190A PRO 2.8 9.6 + - - -
192A TRP* 1.3 76.1 - - - +
194A LYS* 1.3 63.0 + - - -
195A PHE 3.2 0.2 - - - -
196A TRP* 4.0 0.9 - - - +
197A LEU* 3.0 29.8 + - - +
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Residues in contact with LYS 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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187A VAL 3.9 3.8 - - - -
189A ILE* 3.0 33.4 + - + +
190A PRO 2.9 8.4 + - - +
191A SER* 3.4 17.8 - - - +
193A GLY* 1.3 74.9 - - - +
195A PHE* 1.3 58.4 + - - +
197A LEU* 3.4 1.7 + - - +
198A ALA* 2.8 31.2 + - - +
203A TYR* 3.1 37.8 - - + +
207A GLY 3.8 7.9 - - - +
208A LEU* 3.7 24.3 - - + +
276A GLN 2.9 16.0 + - - -
277A ARG 3.1 16.7 + - - +
279A ASN 2.8 24.4 + - - -
280A VAL* 3.5 11.3 - - - +
519A GLU* 5.3 0.4 + - - -
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Residues in contact with PHE 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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191A SER 2.9 12.7 + - - +
192A TRP* 3.5 11.2 - - - +
193A GLY 3.2 0.2 - - - -
194A LYS* 1.3 76.7 - - - +
196A TRP* 1.3 82.5 + + - +
198A ALA* 3.2 4.1 + - - +
199A VAL* 3.0 47.5 + - + +
205A TRP* 3.6 27.6 - + - -
208A LEU* 3.9 11.8 - - + +
211A LEU* 4.0 12.3 - - + -
240A MET* 3.4 56.1 - - + -
243A CYS* 3.8 9.6 - - + -
342A ILE* 4.0 25.1 - - + -
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Residues in contact with TRP 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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103A PHE 4.9 6.8 + - - -
107A GLY* 3.4 46.7 - - - +
110A ILE* 3.7 40.0 - - + +
111A THR* 3.5 14.8 - - - -
152A PHE* 5.7 0.9 - + - -
156A LEU* 4.3 21.1 - - + -
192A TRP* 3.2 30.2 + + + +
193A GLY 3.3 3.1 + - - +
195A PHE* 1.3 97.7 - + - +
197A LEU* 1.3 61.8 + - - +
199A VAL* 3.4 7.8 + - + +
200A LEU* 3.1 21.8 + - - +
240A MET* 5.2 6.0 - - + +
338A ILE* 5.1 10.0 - - + +
341A THR* 3.9 7.0 - - + -
342A ILE* 3.7 35.8 - - + +
345A LEU* 4.6 11.4 - - + -
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Residues in contact with LEU 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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110A ILE* 5.0 0.9 - - + -
155A ALA* 4.8 3.4 - - + +
156A LEU* 4.0 18.6 - - + -
159A VAL* 4.1 22.2 - - + -
186A ALA* 4.0 22.9 - - + -
189A ILE* 3.8 27.1 - - + -
193A GLY 3.0 17.9 + - - +
194A LYS 3.9 0.2 - - - +
196A TRP* 1.3 77.3 - - - +
198A ALA* 1.3 59.3 + - - +
200A LEU* 3.3 6.9 + - + -
201A ASN 3.2 4.0 + - - -
202A VAL* 3.0 45.7 + - + +
203A TYR* 3.2 18.3 + - + -
263A LEU* 4.3 5.8 - - + -
264A TYR* 4.5 8.1 - - - +
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Residues in contact with ALA 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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194A LYS 2.8 18.3 + - - +
195A PHE 3.2 5.4 + - - +
197A LEU* 1.3 75.4 - - - +
199A VAL* 1.3 64.1 + - - +
201A ASN* 3.1 14.0 + - - -
203A TYR* 3.1 22.4 + - - +
205A TRP* 3.6 47.3 + - + +
208A LEU* 4.0 7.6 - - + -
249A SER* 3.9 4.7 + - - -
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Residues in contact with VAL 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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110A ILE* 3.9 17.3 - - + -
114A VAL* 4.1 10.0 - - + +
195A PHE* 3.0 44.9 + - + +
196A TRP* 3.6 13.5 - - + +
197A LEU 3.4 0.2 - - - -
198A ALA* 1.3 76.1 - - - +
200A LEU* 1.3 57.7 + - - +
201A ASN 3.3 0.2 + - - -
205A TRP* 3.9 12.1 - - + -
243A CYS* 4.8 3.8 - - + -
248A LEU* 3.5 15.5 - - + +
249A SER* 3.4 1.4 - - - -
250A ALA* 2.8 28.1 + - - +
345A LEU* 3.8 27.4 - - + -
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Residues in contact with LEU 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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110A ILE* 4.1 20.6 - - + +
113A HIS* 3.9 28.7 - - + +
114A VAL* 5.1 0.9 - - + -
159A VAL* 3.4 33.7 - - + -
163A ILE* 4.2 12.1 - - + -
196A TRP 3.1 15.8 + - - +
197A LEU* 3.6 8.7 - - + +
198A ALA 3.2 0.4 - - - -
199A VAL* 1.3 73.5 - - - +
201A ASN* 1.3 71.7 + - - +
202A VAL* 3.3 17.1 + - + +
250A ALA* 4.0 5.6 - - + -
255A LEU* 5.9 0.9 - - + -
256A VAL* 3.4 21.5 - - + +
259A LEU* 3.8 18.8 - - + -
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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