Contacts of the helix formed by residues 187 - 198 (chain A) in PDB entry 2WWA
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 VAL 187 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A GLY* 5.2 11.0 - - - +
43A TYR* 3.4 33.6 - - + -
183A ILE* 3.1 25.3 + - + +
184A ILE* 3.7 12.3 - - - +
186A THR* 1.4 81.3 - - - +
188A VAL* 1.4 62.4 + - - +
189A ILE 3.3 0.7 - - - -
190A ALA* 3.6 10.0 - - + +
191A THR* 3.2 26.0 + - - -
64B ILE* 3.9 25.1 - - + -
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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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43A TYR* 3.6 11.9 - - - +
69A ARG 3.9 4.5 - - - +
70A GLY 4.0 21.1 - - - +
73A GLY* 3.6 7.2 - - - -
74A CYS 3.3 39.0 - - - +
184A ILE 3.2 13.2 + - - +
185A ASN* 3.3 17.7 + - - +
187A VAL* 1.4 77.4 - - - +
189A ILE* 1.4 66.5 + - + +
191A THR 3.5 0.7 + - - -
192A ASN* 2.9 51.8 + - - +
449A LYS* 4.7 3.4 - - + -
452A GLY* 5.0 0.4 - - - -
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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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185A ASN 3.7 11.0 - - - +
186A THR* 3.5 19.7 - - - +
188A VAL* 1.4 80.2 - - + +
190A ALA* 1.4 59.5 + - - +
193A LEU* 2.9 38.7 + - + +
449A LYS* 4.4 13.2 - - + -
452A GLY* 3.3 34.3 - - - +
453A ILE* 3.7 13.0 - - + +
456A GLY* 3.9 30.5 - - - +
457A ILE* 4.2 13.7 - - + -
57B GLY 5.4 1.3 - - - +
61B VAL* 4.2 14.8 - - + +
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Residues in contact with ALA 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 THR 4.3 4.0 - - - +
187A VAL* 3.5 15.0 + - + +
188A VAL 3.2 0.4 - - - -
189A ILE* 1.4 79.7 - - - +
191A THR* 1.4 62.9 + - - +
194A VAL 4.0 6.4 + - - -
60B ALA* 4.0 2.5 - - + +
61B VAL* 3.1 41.0 - - + +
64B ILE* 3.5 37.5 - - + -
65B GLY* 3.4 6.2 + - - -
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Residues in contact with THR 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A TYR* 3.6 17.9 - - - +
46A ALA* 5.3 0.7 - - + -
69A ARG* 4.4 3.8 - - - +
75A GLU* 3.9 25.1 - - + +
187A VAL 3.2 15.1 + - - -
188A VAL 3.8 1.6 - - - -
190A ALA* 1.4 76.8 - - - +
192A ASN* 1.4 74.4 + - - +
195A ALA* 3.3 23.8 + - + +
64B ILE* 3.7 8.9 - - - +
65B GLY* 3.7 8.0 - - - -
68B ILE* 3.6 31.0 - - + +
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Residues in contact with ASN 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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69A ARG* 3.0 46.7 + - - +
74A CYS 4.6 0.9 - - - +
75A GLU* 4.6 0.2 - - - +
188A VAL* 2.9 38.9 + - - +
191A THR* 1.4 84.4 - - - +
193A LEU* 1.4 63.4 + - - +
195A ALA* 3.7 2.8 + - - +
196A ASP* 3.2 24.6 + - - +
448A GLY 3.0 29.8 + - - +
449A LYS* 3.8 15.6 + - + +
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Residues in contact with LEU 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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189A ILE* 2.9 22.1 + - + +
192A ASN* 1.4 78.0 - - - +
194A VAL* 1.4 57.4 + - - +
196A ASP* 3.4 3.0 + - + +
197A THR* 3.1 39.0 + - + +
253A VAL* 3.6 37.0 - - + -
449A LYS* 3.7 20.8 - - + +
453A ILE* 4.0 19.5 - - + -
58B PHE* 4.0 20.9 - - + -
61B VAL* 3.8 27.4 - - + -
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Residues in contact with VAL 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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190A ALA 4.0 2.8 + - - -
193A LEU* 1.4 74.0 - - - +
195A ALA* 1.4 61.5 + - - +
196A ASP 3.3 0.2 - - - -
197A THR* 4.2 1.8 - - + -
198A PHE* 3.2 26.7 + - + +
199A GLY* 3.0 24.9 + - - -
58B PHE* 4.2 20.2 - - + -
61B VAL* 3.4 39.5 - - + +
62B GLY* 3.9 19.3 - - - +
65B GLY* 3.7 3.3 - - - +
66B TYR* 3.5 30.0 - - + +
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Residues in contact with ALA 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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69A ARG* 5.6 4.5 - - - +
191A THR* 3.3 24.4 + - + +
192A ASN* 3.8 5.8 - - - +
193A LEU 3.4 0.2 - - - -
194A VAL* 1.4 81.1 - - - +
196A ASP* 1.4 59.1 + - - +
199A GLY* 3.5 15.3 - - - +
214A GLN* 3.1 29.7 - - - +
65B GLY* 4.4 13.2 - - - +
69B LYS* 3.6 7.9 + - + -
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Residues in contact with ASP 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 ASN 3.2 15.5 + - - +
193A LEU* 3.5 6.0 - - + +
195A ALA* 1.4 80.2 - - - +
197A THR* 1.4 60.5 + - - +
214A GLN* 3.5 21.1 + - - +
215A GLY 3.2 20.1 + - - -
216A ALA* 3.4 6.6 + - - +
249A THR* 3.3 28.4 + - - +
356A PHE* 5.7 4.7 - - - +
446A LEU* 4.5 2.9 - - - +
447A LYS 5.1 2.6 - - - +
449A LYS* 3.3 20.4 + - - +
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Residues in contact with THR 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 LEU* 3.1 27.2 + - + +
194A VAL* 4.2 3.4 - - + -
196A ASP* 1.4 78.3 - - - +
198A PHE* 1.4 66.9 + - + +
215A GLY 3.3 0.5 - - - -
216A ALA* 3.1 11.8 + - - +
217A LEU* 2.8 51.7 + - + +
249A THR* 5.2 3.7 + - - +
250A THR* 4.3 12.5 + - - +
253A VAL* 5.7 5.3 - - + +
58B PHE* 3.9 32.3 - - + -
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Residues in contact with PHE 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 VAL* 3.2 30.2 + - + +
197A THR* 1.4 79.3 - - + +
199A GLY* 1.4 77.8 + - - +
215A GLY* 3.3 11.8 - - - -
217A LEU* 4.7 14.4 - - + -
218A ILE* 3.2 44.8 - - + +
58B PHE* 6.0 1.6 - + + -
62B GLY 6.0 0.9 - - - -
66B TYR* 3.7 38.6 - + + -
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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