Contacts of the helix formed by residues 186 - 202 (chain A) in PDB entry 3C3C
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 GLY 186 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A LEU* 4.1 7.6 - - - -
45A SER* 3.9 5.6 - - - -
161A VAL* 3.9 12.3 - - - +
162A ASN 3.1 14.8 + - - -
163A ASP* 3.1 19.0 + - - -
184A ALA 3.6 2.0 + - - -
185A GLY* 1.3 77.0 - - - +
187A PHE* 1.3 63.7 + - - -
188A LEU 3.5 0.2 + - - -
189A MET* 3.5 1.4 - - - +
190A LYS* 3.2 19.8 + - - +
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Residues in contact with PHE 187 (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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8A LEU* 3.6 22.7 - - + -
9A ASP* 3.7 21.1 - - + -
44A PRO* 3.9 30.3 - - + -
45A SER* 3.2 12.6 + - - +
48A PHE* 3.5 54.5 - + + -
186A GLY* 1.3 71.0 - - - -
188A LEU* 1.3 60.4 + - - +
190A LYS* 3.5 13.2 + - + +
191A LYS* 2.8 30.9 + - - +
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Residues in contact with LEU 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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23A ASP* 6.2 2.2 - - + +
38A ARG 5.6 1.1 - - - +
41A ALA* 3.7 45.0 + - + +
42A ALA* 4.8 2.5 - - + +
163A ASP* 2.9 43.9 + - - +
165A PHE* 4.6 6.1 - - + +
166A GLY 5.7 0.2 - - - +
187A PHE* 1.3 70.1 - - - +
189A MET* 1.3 67.2 + - - +
191A LYS* 2.9 21.8 + - + -
192A GLU* 2.8 52.8 + - + +
393A THR* 3.9 16.4 - - + +
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Residues in contact with MET 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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2A LEU* 4.5 4.5 - - + -
162A ASN* 3.4 48.9 - - + +
163A ASP* 3.4 5.0 + - - +
164A ALA 3.6 20.2 - - - +
165A PHE* 4.0 28.0 - - - +
168A ALA* 4.3 8.3 - - + -
185A GLY* 4.4 9.9 - - - -
186A GLY 3.5 12.1 - - - +
188A LEU* 1.3 79.0 - - - +
190A LYS* 1.3 62.6 + - - +
192A GLU* 4.0 0.9 - - - +
193A LEU* 3.2 38.4 + - + +
409A GLY 4.8 6.1 - - - +
410A VAL* 4.0 22.0 - - + -
413A LEU* 5.0 5.4 - - + -
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Residues in contact with LYS 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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2A LEU* 3.7 22.7 - - + +
7A THR* 3.6 21.7 + - - -
9A ASP* 2.8 36.5 + - - -
186A GLY 3.2 11.0 + - - +
187A PHE* 3.6 17.1 - - + +
188A LEU 3.0 1.2 + - - -
189A MET* 1.3 75.8 - - - +
191A LYS* 1.3 66.1 + - - +
193A LEU* 3.4 1.7 + - - +
194A ASN* 3.0 41.9 + - - +
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Residues in contact with LYS 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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187A PHE 2.8 21.4 + - - +
188A LEU* 2.9 22.3 + - + +
190A LYS* 1.3 72.7 - - - +
192A GLU* 1.3 62.6 + - - +
194A ASN* 3.8 4.0 - - - +
195A TYR* 3.0 52.5 + - + -
389A SER 5.4 2.0 + - - -
390A HIS* 3.8 26.3 + - + -
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Residues in contact with GLU 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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165A PHE* 3.4 46.9 - - + -
188A LEU* 2.8 37.7 + - + +
189A MET 4.0 0.4 - - - +
191A LYS* 1.3 73.4 - - - +
193A LEU* 1.3 57.5 + - - +
195A TYR* 3.3 1.4 + - - +
196A PHE* 3.0 37.6 + - - -
390A HIS* 2.8 29.1 + - + -
391A VAL 4.5 0.7 - - - +
392A SER* 2.8 23.4 + - - -
393A THR* 2.8 29.6 + - - +
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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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1A SER 4.7 16.4 - - - +
2A LEU* 3.3 34.8 - - + -
165A PHE* 4.2 9.0 - - + -
189A MET* 3.2 22.9 + - + +
190A LYS* 4.2 2.0 - - - +
192A GLU* 1.3 78.3 - - - +
194A ASN* 1.3 61.1 + - - +
196A PHE* 3.9 3.3 - - - +
197A ALA* 2.9 32.9 + - - +
401A LEU* 3.9 23.5 - - + +
407A LEU* 3.9 24.0 - - + -
410A VAL* 3.6 21.8 - - + -
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Residues in contact with ASN 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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2A LEU* 6.1 3.8 - - - +
190A LYS* 3.0 40.1 + - - +
191A LYS* 3.8 4.7 - - - +
193A LEU* 1.3 78.2 + - - +
195A TYR* 1.3 60.2 + - + +
197A ALA* 4.2 5.2 - - - +
198A LYS* 3.0 31.0 + - - +
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Residues in contact with TYR 195 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191A LYS* 3.0 46.8 + - + +
192A GLU 3.8 3.1 - - - +
194A ASN* 1.3 75.2 - - + +
196A PHE* 1.3 58.9 + - + +
198A LYS* 3.9 3.3 - - - +
199A ALA* 2.8 32.3 + - - +
367A ILE* 5.4 6.3 - - + -
369A ILE* 4.4 15.5 - - + +
389A SER* 3.4 31.3 + - - -
390A HIS* 3.7 47.6 - + + -
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Residues in contact with PHE 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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165A PHE* 4.5 3.8 - + - -
192A GLU* 3.0 31.0 + - - +
193A LEU 4.5 0.7 - - - +
195A TYR* 1.3 77.4 - - - +
197A ALA* 1.3 60.3 + - - +
199A ALA* 3.9 5.4 - - + -
200A LEU* 3.2 35.0 + - + +
334A VAL* 4.5 12.8 - - + -
336A ASN* 5.8 2.2 - - - -
369A ILE* 3.8 31.9 - - + -
370A ILE 6.1 0.4 - - - -
371A GLY* 6.2 0.7 - - - -
390A HIS* 4.6 4.9 - + - -
392A SER* 3.4 22.0 - - - -
398A SER* 3.1 31.6 - - - -
401A LEU* 3.3 32.3 - - + -
402A LEU* 4.1 26.0 - - + -
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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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1A SER 5.4 8.5 - - - +
193A LEU 2.9 22.3 + - - +
194A ASN* 4.2 6.3 - - - +
195A TYR 3.3 0.2 - - - -
196A PHE* 1.3 73.9 - - - +
198A LYS* 1.3 62.5 + - - +
200A LEU* 4.9 2.7 - - - -
201A GLU* 3.0 39.2 + - + +
401A LEU* 5.5 0.4 - - - +
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Residues in contact with LYS 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 ASN 3.0 19.2 + - - +
195A TYR* 4.0 3.4 - - - +
197A ALA* 1.3 76.6 - - - +
199A ALA* 1.3 62.5 + - - +
202A SER* 3.0 62.0 + - - +
204A GLU* 4.6 15.4 + - - -
332A GLN* 5.8 1.8 - - - +
367A ILE* 6.4 1.1 - - - -
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Residues in contact with ALA 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 TYR 2.8 21.4 + - - +
196A PHE* 4.1 8.3 - - + +
198A LYS* 1.3 75.0 - - - +
200A LEU* 1.3 60.3 + - + +
203A PRO* 3.2 14.4 - - - +
207A PHE* 3.7 5.1 - - + -
332A GLN* 2.8 38.2 + - - +
334A VAL* 4.5 8.1 - - + -
367A ILE* 5.9 0.7 - - + -
369A ILE* 3.6 26.0 - - + -
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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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196A PHE* 3.2 26.8 + - + +
197A ALA* 4.4 2.0 - - - +
198A LYS 3.2 0.8 - - - -
199A ALA* 1.3 82.7 - - + +
201A GLU* 1.3 75.2 + - + +
202A SER 3.7 0.2 - - - -
203A PRO* 4.0 8.0 - - - +
207A PHE* 4.7 9.6 - - + -
226A MET* 3.8 21.5 - - + -
229A LYS* 3.7 44.3 + - + +
334A VAL* 6.0 1.3 - - + -
401A LEU* 4.5 17.0 - - + +
402A LEU* 3.8 25.4 - - + -
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Residues in contact with GLU 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 ALA* 3.0 23.4 + - + +
200A LEU* 1.3 88.4 - - + +
202A SER* 1.3 67.0 + - - +
203A PRO* 3.5 5.4 - - - +
229A LYS* 4.4 13.1 + - - -
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Residues in contact with SER 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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197A ALA 4.2 0.2 + - - -
198A LYS* 3.0 47.5 + - - +
201A GLU* 1.3 83.6 + - - +
203A PRO* 1.4 65.6 - - - +
204A GLU* 3.5 5.0 + - - +
332A GLN* 4.6 0.5 - - - +
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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