Contacts of the helix formed by residues 192 - 208 (chain A) in PDB entry 3KVF
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 THR 192 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188A SER* 4.2 0.2 - - - -
189A SER* 2.9 35.5 + - - +
191A ASP* 1.3 78.9 - - + +
193A LEU* 1.3 53.9 + - - +
194A LEU 3.3 1.8 - - - -
195A LYS* 3.0 28.8 + - + +
196A ASP* 2.6 53.0 + - - +
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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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46A ALA 3.3 20.0 - - - +
47A CYS* 3.2 27.8 - - - +
48A ALA* 5.2 1.1 - - - +
49A LEU* 5.9 1.8 - - + +
165A PHE 4.7 4.5 - - - +
166A ASN* 4.0 5.2 - - - -
167A ASN* 3.6 36.1 - - + +
172A LEU* 3.5 25.4 - - + -
188A SER* 4.1 4.3 - - - +
189A SER 2.9 12.5 + - - +
190A GLU* 3.3 24.7 - - - +
191A ASP 3.2 1.2 - - - -
192A THR* 1.3 76.0 - - - +
194A LEU* 1.3 60.3 + - + +
196A ASP* 3.7 1.2 - - - +
197A ALA* 2.8 33.2 + - + +
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Residues in contact with LEU 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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31A VAL* 6.2 0.4 - - + -
39A LEU* 4.4 34.0 - - + +
42A VAL* 4.3 17.7 - - + +
43A PRO 5.3 0.4 - - - +
44A ALA* 6.5 0.7 - - + -
46A ALA* 3.7 34.5 - - + +
48A ALA 5.4 1.6 - - - +
49A LEU* 4.5 32.3 - - + +
191A ASP 4.4 7.6 + - - +
192A THR 3.3 0.4 - - - -
193A LEU* 1.3 77.0 - - + +
195A LYS* 1.3 56.6 + - - +
197A ALA* 3.7 3.8 - - - +
198A ALA* 2.8 38.3 + - - +
218A ALA* 4.6 8.1 - - + -
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Residues in contact with LYS 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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36A GLU* 3.4 32.4 + - - +
39A LEU* 5.1 4.0 - - - +
191A ASP 5.0 1.0 + - - +
192A THR* 3.0 31.4 + - + +
194A LEU* 1.3 76.7 - - - +
196A ASP* 1.3 69.9 + - - +
198A ALA* 4.1 5.1 - - - +
199A LYS* 3.4 21.3 + - - +
202A ARG* 5.4 1.9 + - - -
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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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172A LEU* 3.4 22.3 - - + +
187A ALA 3.5 7.4 - - - +
188A SER* 2.8 37.0 + - - +
192A THR* 2.6 35.3 + - - +
193A LEU 3.8 2.0 - - - +
195A LYS* 1.3 79.7 - - - +
197A ALA* 1.3 64.2 + - - +
199A LYS* 3.5 13.5 - - - +
200A VAL* 3.4 11.3 - - - +
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Residues in contact with ALA 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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49A LEU* 3.7 24.2 - - + -
165A PHE* 3.7 25.4 - - + -
172A LEU* 3.9 11.8 - - + +
193A LEU* 2.8 19.6 + - + +
194A LEU* 3.7 2.0 - - - +
196A ASP* 1.3 76.1 - - - +
198A ALA* 1.3 60.1 + - - +
199A LYS 3.2 0.2 - - - -
200A VAL* 3.0 10.0 + - - +
201A CYS* 2.9 28.6 + - - -
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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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34A LEU* 3.8 21.3 - - + +
39A LEU* 3.8 26.0 - - + -
49A LEU* 4.3 3.5 - - + +
194A LEU 2.8 19.8 + - - +
195A LYS* 4.1 4.3 - - - +
197A ALA* 1.3 71.2 - - - +
199A LYS* 1.3 59.4 + - - +
201A CYS* 3.5 10.7 - - - +
202A ARG* 3.0 39.7 + - - +
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Residues in contact with LYS 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 LYS 3.4 12.6 + - - +
196A ASP* 3.5 13.2 - - - +
197A ALA 3.2 0.4 - - - -
198A ALA* 1.3 78.8 - - - +
200A VAL* 1.3 67.3 - - - +
202A ARG* 3.8 29.6 + - - +
203A GLU* 3.6 30.6 + - + +
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Residues in contact with VAL 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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165A PHE* 3.6 23.8 - - + -
172A LEU* 3.9 17.3 - - + -
174A GLU* 3.9 5.4 - - - +
185A HIS* 3.7 33.4 - - + +
196A ASP 3.4 16.6 - - - +
197A ALA 3.0 6.6 + - - +
199A LYS* 1.3 83.1 - - + +
201A CYS* 1.3 63.7 + - - +
203A GLU* 3.2 29.4 + - - +
204A PHE* 3.1 25.5 - - + -
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Residues in contact with CYS 201 (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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34A LEU* 3.7 24.0 - - + +
49A LEU* 3.9 20.4 - - - -
51A LEU* 3.7 24.4 - - + +
165A PHE* 3.6 24.7 - - - -
197A ALA 2.9 16.4 + - - +
198A ALA* 3.3 9.4 + - - +
200A VAL* 1.3 77.6 - - - +
202A ARG* 1.3 61.1 + - - +
204A PHE* 3.2 26.4 + - - +
205A THR* 3.3 8.7 + - - -
214A PHE* 5.8 0.3 - - - -
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Residues in contact with ARG 202 (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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34A LEU* 2.8 52.0 + - + -
35A GLU* 4.7 3.6 - - - +
36A GLU* 5.7 4.4 + - - -
39A LEU* 5.8 0.2 - - - +
195A LYS 5.4 1.4 + - - -
198A ALA* 3.0 28.9 + - - +
199A LYS* 3.8 30.4 + - - +
200A VAL 3.3 0.2 - - - -
201A CYS* 1.3 73.6 - - - +
203A GLU* 1.3 54.5 + - + +
205A THR* 3.1 12.8 + - - -
206A GLU* 2.8 50.5 + - - +
9B THR 6.0 1.3 - - - +
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Residues in contact with GLU 203 (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 HIS* 5.5 2.3 - - - -
199A LYS* 3.6 33.1 + - + +
200A VAL* 3.2 22.9 + - - +
202A ARG* 1.3 73.0 - - + +
204A PHE* 1.3 59.2 + - - +
206A GLU* 3.6 17.6 - - - +
207A ARG* 2.9 56.4 + - + +
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Residues in contact with PHE 204 (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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51A LEU* 4.1 9.6 - - + -
53A PHE* 4.2 28.9 - + - -
59A HIS* 4.3 6.5 - + - -
62A PHE* 5.3 0.4 - + - -
63A ARG* 4.0 12.1 - - - -
163A ILE* 3.5 24.7 - - + -
165A PHE* 4.0 9.2 - + - -
174A GLU* 3.8 16.2 - - - -
200A VAL* 3.1 43.7 - - + -
201A CYS* 3.2 12.9 + - - +
203A GLU* 1.3 75.9 - - - +
205A THR* 1.3 63.3 + - - +
207A ARG* 3.5 30.2 + - - +
208A GLU* 3.2 20.4 + - - +
214A PHE* 3.8 21.4 - + + -
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Residues in contact with THR 205 (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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34A LEU* 3.9 13.0 - - - +
201A CYS 3.3 10.9 + - - -
202A ARG* 3.1 14.3 + - - -
204A PHE* 1.3 77.0 - - - +
206A GLU* 1.3 59.9 + - + +
208A GLU 2.8 29.1 - - - +
209A GLN 3.7 7.8 + - - +
211A GLU 4.8 4.0 - - - +
214A PHE* 4.2 13.3 - - - -
9B THR* 3.6 45.7 + - + +
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Residues in contact with GLU 206 (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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202A ARG* 2.8 35.9 + - - +
203A GLU* 3.2 22.5 + - - +
205A THR* 1.3 76.1 - - + +
207A ARG* 1.3 60.9 + - + +
209A GLN* 3.9 14.5 + - - +
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Residues in contact with ARG 207 (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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58A GLN* 4.2 20.5 - - + +
59A HIS* 4.7 4.6 - - - +
62A PHE* 3.3 64.9 - - - +
203A GLU* 2.9 48.6 + - + +
204A PHE* 3.5 44.2 - - - +
205A THR 3.3 0.2 - - - -
206A GLU* 1.3 77.6 - - + +
208A GLU* 1.3 70.8 + - + +
209A GLN* 3.5 3.6 + - - +
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Residues in contact with GLU 208 (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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53A PHE* 6.2 1.8 - - + -
54A PRO* 4.5 9.4 - - + +
56A THR* 2.7 41.3 + - - +
58A GLN* 3.5 25.7 - - - +
59A HIS* 3.9 6.9 + - + +
204A PHE 3.2 10.3 + - - +
205A THR 2.8 10.7 - - - +
207A ARG* 1.3 78.7 - - + +
209A GLN* 1.3 66.7 + - - +
210A GLY 3.7 1.1 - - - -
211A GLU* 3.1 33.6 + - + +
214A PHE* 3.8 19.0 - - + -
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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