Contacts of the helix formed by residues 187 - 201 (chain A) in PDB entry 3D14
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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1A AK1 3.3 36.6 - - - -
157A PHE* 4.0 13.7 - - + -
182A LEU* 3.1 28.7 + - + +
185A ALA* 3.7 17.0 - - + +
186A GLY* 1.3 77.6 - - - +
188A GLU* 1.3 64.2 + - - +
189A HIS* 3.3 3.1 - - - -
190A GLN* 3.1 32.2 + - - +
191A LEU* 3.1 18.2 + - - +
290A TRP* 4.5 11.0 - - + -
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Residues in contact with GLU 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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179A LYS* 5.1 6.3 + - - -
182A LEU* 3.9 28.5 - - + +
183A GLU* 2.7 39.9 - - - +
186A GLY* 3.7 2.0 - - - -
187A VAL* 1.3 78.4 - - - +
189A HIS* 1.3 61.3 + - - +
191A LEU* 3.3 8.8 + - - +
192A ARG* 3.2 20.6 + - - +
212A TYR* 5.5 0.5 + - - -
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Residues in contact with HIS 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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186A GLY 3.2 26.9 + - - -
187A VAL 4.2 0.2 - - - -
188A GLU* 1.3 76.4 + - - +
190A GLN* 1.3 83.7 + - + +
192A ARG* 3.4 9.8 + - - +
193A ARG* 2.9 36.3 + - + +
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Residues in contact with GLN 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A AK1 3.5 13.1 - - - -
186A GLY 4.3 1.2 + - - -
187A VAL* 3.1 34.8 + - - +
189A HIS* 1.3 101.4 + - + +
191A LEU* 1.3 58.6 + - - +
193A ARG* 3.4 7.4 + - - +
194A GLU* 2.9 27.7 + - - +
288A PHE 4.8 0.2 - - - +
289A GLY 3.0 22.7 - - - +
290A TRP* 3.3 28.6 - - - -
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Residues in contact with LEU 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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1A AK1 3.3 39.0 - - + -
177A LEU* 4.4 8.1 - - + -
182A LEU* 4.1 20.9 - - + -
187A VAL 3.1 7.3 + - - +
188A GLU* 3.6 10.1 - - - +
189A HIS 3.3 0.2 - - - -
190A GLN* 1.3 75.6 - - - +
192A ARG* 1.3 65.1 + - - +
194A GLU* 3.3 11.8 + - - +
195A VAL* 3.1 28.6 + - + +
212A TYR* 4.1 13.2 - - + -
219A VAL* 3.8 30.3 - - + -
221A LEU* 3.9 25.4 - - + -
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Residues in contact with ARG 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A GLU 3.2 13.4 + - - +
189A HIS* 3.6 11.7 - - - +
191A LEU* 1.3 77.0 - - - +
193A ARG* 1.3 56.3 + - + +
195A VAL* 3.4 3.8 + - - +
196A GLU* 3.0 28.6 + - + +
212A TYR* 3.8 26.7 + - + +
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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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189A HIS* 2.9 23.2 + - + +
190A GLN* 3.6 8.5 - - - +
192A ARG* 1.3 74.2 - - + +
194A GLU* 1.3 54.4 + - - +
196A GLU* 3.3 10.0 + - + +
197A ILE* 2.8 49.0 + - + +
291A SER 5.6 3.4 - - - +
293A HIS* 6.2 3.4 - - + -
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Residues in contact with GLU 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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1A AK1 2.8 56.9 + - - -
190A GLN 2.9 13.5 + - - +
191A LEU* 3.3 14.9 + - - +
193A ARG* 1.3 75.6 - - - +
195A VAL* 1.3 58.2 + - + +
197A ILE* 3.3 5.4 + - - +
198A GLN* 2.9 32.9 + - + +
209A LEU* 3.7 19.1 - - + +
221A LEU* 4.9 0.9 - - - -
287A ASP* 3.6 1.6 + - - -
288A PHE* 3.0 41.6 + - + +
289A GLY 3.4 9.6 + - - +
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Residues in contact with VAL 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 LEU 3.1 15.2 + - - +
192A ARG 3.7 7.0 - - - +
194A GLU* 1.3 75.2 - - + +
196A GLU* 1.3 58.1 + - - +
198A GLN* 3.8 1.6 - - - +
199A SER* 3.0 29.4 + - - -
209A LEU* 4.1 24.8 - - + +
211A GLY* 4.4 15.5 - - - -
212A TYR* 3.7 52.5 - - + -
221A LEU* 4.3 5.4 - - + -
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Residues in contact with GLU 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 ARG* 3.0 19.1 + - + +
193A ARG* 3.5 11.0 - - + +
195A VAL* 1.3 75.7 - - - +
197A ILE* 1.3 67.5 + - + +
199A SER* 2.6 27.0 + - - -
200A HIS* 2.7 41.5 + - + -
293A HIS* 6.4 1.3 - - + -
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Residues in contact with ILE 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 ARG* 2.8 34.0 + - + +
194A GLU* 3.7 4.5 - - - +
196A GLU* 1.3 75.1 - - + +
198A GLN* 1.3 59.3 + - - +
200A HIS* 3.1 23.7 + - - +
201A LEU* 3.3 32.6 + - + +
265A VAL* 3.9 24.5 - - + -
288A PHE* 4.3 13.0 - - + +
291A SER* 4.0 33.2 - - - +
292A VAL* 5.0 0.7 - - - +
293A HIS* 4.1 29.8 - - + +
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Residues in contact with GLN 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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1A AK1 5.6 2.8 + - - -
194A GLU* 2.9 22.0 + - + +
195A VAL 3.9 3.4 - - - +
197A ILE* 1.3 71.7 - - - +
199A SER* 1.3 57.3 + - - +
200A HIS 3.0 6.3 + - - -
201A LEU* 3.4 20.9 + - + +
202A ARG* 3.0 21.7 + - - -
206A ILE* 3.7 15.9 - - - +
207A LEU* 3.0 24.3 + - - +
208A ARG* 4.4 2.5 + - - -
209A LEU* 3.7 45.7 + - + +
223A LEU* 5.9 0.6 - - - +
286A ALA* 5.3 1.2 - - - +
287A ASP 5.1 4.4 - - - +
288A PHE* 3.5 36.2 - - + -
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Residues in contact with SER 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 VAL* 3.0 15.2 + - - -
196A GLU* 2.6 26.5 + - - -
198A GLN* 1.3 76.0 - - - +
200A HIS* 1.3 72.5 + - - +
202A ARG* 3.3 23.4 + - - +
209A LEU 4.8 3.6 + - - -
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Residues in contact with HIS 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A GLU* 2.7 46.7 + - + -
197A ILE* 3.1 8.8 + - - +
198A GLN 3.0 0.6 - - - -
199A SER* 1.3 89.8 + - - +
201A LEU* 1.3 65.9 + - + +
202A ARG* 3.6 8.8 + - - +
259A TYR* 3.7 7.1 + - - -
263A LYS* 5.3 8.9 - - + +
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Residues in contact with LEU 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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197A ILE* 3.3 31.1 + - + +
198A GLN* 3.4 27.1 + - - +
200A HIS* 1.3 78.4 - - + +
202A ARG* 1.3 81.3 + - - +
203A HIS 4.3 0.2 - - - -
206A ILE* 4.3 12.5 - - + +
208A ARG* 4.4 5.7 - - - -
259A TYR* 3.7 24.0 - - + -
260A CYS* 4.4 7.6 - - - -
263A LYS* 4.3 21.5 - - + -
265A VAL* 4.5 11.9 - - + -
288A PHE* 3.7 28.0 - - + -
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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