Contacts of the helix formed by residues 187 - 200 (chain A) in PDB entry 4YON
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 187 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176A MET* 4.0 5.6 - - + -
185A ASP 3.5 5.1 - - - +
186A ILE* 1.3 103.5 - - + +
188A LEU* 1.3 67.5 + - - +
189A GLU* 3.2 9.0 - - + +
190A GLY 2.9 14.5 + - - +
191A TYR* 3.5 4.9 - - - -
41B SER* 5.9 0.4 - - - +
56B TRP* 4.6 14.1 - - + -
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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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71A LEU* 4.0 13.5 - - + -
75A PHE* 3.7 43.5 - - + -
99A LEU* 4.8 5.6 - - + -
100A PHE* 4.7 2.5 - - + -
159A LEU* 4.0 27.6 - - + -
172A LEU* 4.4 15.7 - - + -
176A MET* 3.8 23.7 - - + +
187A PRO* 1.3 72.3 - - - +
189A GLU* 1.3 62.4 + - - +
191A TYR* 3.0 7.0 + - + +
192A LEU* 2.9 43.2 + - + +
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Residues in contact with GLU 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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152A HIS* 2.8 32.4 + - - -
156A LEU* 3.3 34.6 - - + +
159A LEU* 4.1 19.8 - - + +
187A PRO* 3.1 8.1 + - + +
188A LEU* 1.3 79.1 - - - +
190A GLY* 1.3 63.0 + - - +
192A LEU* 3.3 5.1 + - - +
193A LEU* 3.0 24.9 + - - +
5B LYS* 5.3 5.8 - - - +
56B TRP* 4.4 13.5 - - + -
70B LEU 4.5 2.6 - - - +
73B PRO 6.1 0.4 - - - +
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Residues in contact with GLY 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 ILE* 3.6 11.0 - - - -
187A PRO* 2.9 11.1 + - - +
189A GLU* 1.3 79.8 - - - +
191A TYR* 1.3 61.7 + - - +
193A LEU* 3.3 3.3 + - - +
194A SER* 3.3 15.2 + - - -
39B ASN* 3.2 19.1 + - - -
56B TRP* 3.4 27.4 - - - -
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Residues in contact with TYR 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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67A THR* 3.8 26.9 - - + -
70A PHE* 4.0 14.1 - + + -
71A LEU* 3.7 29.5 - - + +
176A MET* 4.3 1.8 - - + -
181A ARG* 3.0 46.2 + - - -
185A ASP* 4.4 7.6 + - - +
186A ILE* 3.2 32.3 + - + +
187A PRO 3.5 14.6 - - - -
188A LEU* 3.0 10.1 + - - +
190A GLY* 1.3 75.7 - - - +
192A LEU* 1.3 62.5 + - - +
194A SER* 2.7 26.9 + - - -
195A PRO* 3.9 0.7 - - - +
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Residues in contact with LEU 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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71A LEU* 4.2 16.8 - - + -
99A LEU* 3.9 38.6 - - + +
100A PHE* 3.8 31.0 - - + -
103A ILE* 5.9 0.9 - - + -
148A TYR* 2.6 39.0 + - - +
152A HIS* 3.5 19.1 - - + -
155A ALA* 5.5 1.8 - - + -
159A LEU* 4.2 8.7 - - + -
188A LEU* 2.9 34.2 + - + +
189A GLU* 3.3 7.8 + - - +
191A TYR* 1.3 77.8 - - - +
193A LEU* 1.3 57.7 + - - +
194A SER 3.3 0.2 - - - -
195A PRO* 3.2 8.5 - - - +
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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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152A HIS* 3.8 24.7 - - + +
189A GLU* 3.0 21.5 + - - +
190A GLY 3.6 5.6 - - - +
191A TYR 3.2 0.4 - - - -
192A LEU* 1.3 74.7 - - - +
194A SER* 1.3 65.2 + - - +
195A PRO* 3.2 2.7 - - - -
196A ILE* 3.0 28.9 + - + +
197A GLN* 3.2 23.4 + - + +
56B TRP* 3.6 30.3 - - + -
70B LEU* 3.9 24.7 - - + +
71B SER* 3.6 26.2 - - - +
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Residues in contact with SER 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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64A TYR* 4.1 12.3 - - - -
67A THR* 3.7 22.1 - - - +
68A LEU* 4.9 1.9 - - - +
71A LEU* 4.9 0.2 - - - +
190A GLY 3.3 8.2 + - - -
191A TYR* 2.7 22.2 + - - -
193A LEU* 1.3 77.9 - - - +
195A PRO* 1.4 64.6 - - - +
197A GLN* 3.3 15.7 + - - +
198A ARG* 2.8 30.8 + - - +
39B ASN* 5.4 1.1 - - - -
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Residues in contact with PRO 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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64A TYR* 3.3 24.0 - - + +
68A LEU* 4.6 0.9 - - + -
103A ILE* 3.7 23.3 - - + -
106A ILE* 4.5 4.0 - - + -
145A TYR* 3.3 24.1 - - + -
148A TYR* 3.6 26.2 - - + -
191A TYR 3.9 1.1 - - - +
192A LEU* 3.2 17.0 - - - +
193A LEU 3.2 2.0 - - - -
194A SER* 1.4 98.8 - - - +
196A ILE* 1.3 62.0 + - - +
199A ILE* 3.1 20.1 + - - +
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Residues in contact with ILE 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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148A TYR* 3.7 33.2 - - + -
149A CYS* 3.7 20.4 - - - -
152A HIS* 4.1 22.9 - - + -
192A LEU 4.3 0.9 - - - +
193A LEU* 3.0 26.4 + - + +
195A PRO* 1.3 77.1 - - - +
197A GLN* 1.3 66.0 + - - +
199A ILE* 3.4 18.9 - - - +
200A CYS* 3.6 9.8 + - - -
61B GLN* 4.8 11.7 - - - +
67B LEU* 4.3 32.3 - - + +
70B LEU* 3.7 15.9 - - + -
71B SER* 5.8 0.4 - - - +
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Residues in contact with GLN 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* 3.2 32.7 + - + +
194A SER* 3.6 18.2 + - - +
196A ILE* 1.3 79.6 - - + +
198A ARG* 1.3 61.9 + - - +
200A CYS* 3.4 4.3 + - - +
201A LYS* 3.2 35.9 + - - +
39B ASN* 2.9 43.0 + - - +
56B TRP* 4.4 4.0 - - - +
57B ASP 3.8 18.0 + - - +
61B GLN* 4.1 22.3 + - - +
71B SER* 4.9 2.0 + - - -
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Residues in contact with ARG 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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57A ILE* 3.7 5.1 + - - +
60A THR* 2.9 42.9 + - - -
61A GLU* 2.8 34.3 + - - +
64A TYR* 3.6 42.2 - - + +
145A TYR* 4.7 0.9 - - - +
194A SER 2.8 17.7 + - - +
195A PRO 3.9 2.9 - - - +
197A GLN* 1.3 76.0 - - - +
199A ILE* 1.3 61.4 + - - +
201A LYS* 2.8 32.9 + - - +
202A TYR* 3.1 37.8 + - + +
205A LEU* 4.0 15.2 - - - +
36B VAL* 4.3 9.9 - - - +
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Residues in contact with ILE 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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142A PHE* 4.4 6.1 - - + -
145A TYR* 3.8 37.2 - - + -
149A CYS* 5.2 2.2 - - - -
195A PRO 3.1 13.2 + - - +
196A ILE* 3.4 16.2 - - - +
198A ARG* 1.3 78.7 - - - +
200A CYS* 1.3 70.8 + - - +
202A TYR* 3.6 28.1 + - + +
203A PRO* 3.4 9.7 - - - +
230A MET* 4.3 7.9 - - + +
233A VAL* 4.2 18.6 - - + -
234A CYS* 3.2 19.6 - - - -
237A ILE* 3.8 26.7 - - + -
67B LEU* 5.1 4.9 - - + -
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Residues in contact with CYS 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 ILE 3.6 12.8 - - - +
197A GLN 3.4 10.0 + - - +
198A ARG 3.1 1.2 - - - -
199A ILE* 1.3 84.6 - - - +
201A LYS* 1.3 62.2 + - - +
202A TYR 3.4 0.2 - - - -
203A PRO* 3.5 10.4 - - - +
204A LEU* 4.0 4.2 - - - +
234A CYS* 3.9 8.7 - - - -
59B ALA 4.9 0.9 - - - +
60B GLY* 3.6 34.1 - - - +
61B GLN* 3.9 19.3 - - + -
64B TYR* 4.1 15.3 - - - -
67B LEU* 3.7 29.2 - - - -
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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