Contacts of the helix formed by residues 187 - 200 (chain A) in PDB entry 2PHG
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 SER 187 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155A ALA* 4.0 11.8 - - - +
157A ASP* 2.6 24.7 + - - -
158A ALA* 3.2 13.5 - - - +
186A ILE* 1.3 78.5 - - - +
188A LYS* 1.3 65.0 + - - +
189A LYS* 3.0 5.2 - - - +
190A GLU* 3.1 17.7 + - - +
191A ILE* 3.1 12.8 + - - +
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Residues in contact with LYS 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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181A CYS* 5.4 0.4 - - - -
184A SER* 2.8 37.2 + - - +
185A ARG* 3.7 16.1 - - - +
186A ILE 3.1 3.9 - - - +
187A SER* 1.3 77.8 - - - +
189A LYS* 1.3 61.7 + - - +
191A ILE* 3.5 10.3 - - + -
192A GLY 3.3 4.7 + - - -
315A GLN* 4.4 0.8 + - - +
474B GLU 4.3 0.5 - - - +
477B GLN* 2.8 61.6 + - + +
478B MET* 3.5 29.4 + - + +
481B ASP* 2.6 39.4 + - - -
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Residues in contact with LYS 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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187A SER* 3.0 2.6 - - - +
188A LYS* 1.3 79.6 - - - +
190A GLU* 1.3 64.9 + - + +
193A ARG* 3.2 30.6 + - - +
474B GLU* 2.6 52.7 + - + +
475B PHE* 5.0 1.2 - - - -
478B MET* 3.6 27.2 - - + +
479B PHE* 3.6 22.7 - - - -
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Residues in contact with GLU 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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151A LEU* 5.2 6.1 - - - +
154A ARG* 2.7 48.9 + - - +
155A ALA* 4.2 16.2 - - + +
158A ALA* 3.4 21.8 - - + -
159A ILE* 5.9 0.9 - - + -
187A SER* 3.1 7.0 + - - +
189A LYS* 1.3 78.4 - - + +
191A ILE* 1.3 64.8 + - - +
193A ARG* 2.7 47.0 + - - +
194A CYS* 3.0 35.1 + - - -
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Residues in contact with ILE 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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158A ALA* 3.4 23.1 - - - +
161A SER* 3.7 21.8 - - - +
162A ALA* 3.2 36.4 - - - +
165A TYR* 5.6 1.6 - - + -
184A SER* 4.1 8.7 - - - -
186A ILE 3.6 12.8 - - - +
187A SER 3.1 12.3 + - - +
188A LYS* 3.5 23.3 - - + -
189A LYS 3.2 0.2 - - - -
190A GLU* 1.3 77.6 - - - +
192A GLY* 1.3 56.4 + - - +
195A PHE* 3.0 25.9 + - + +
477B GLN* 3.3 33.7 - - + +
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Residues in contact with GLY 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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188A LYS 3.3 7.5 + - - -
191A ILE* 1.3 77.6 - - - +
193A ARG* 1.3 63.5 + - - +
196A LYS 3.3 9.5 + - - -
470B MET 3.1 11.5 - - - +
473B PHE* 3.2 48.4 - - - +
474B GLU* 3.8 7.4 - - - -
477B GLN* 3.8 3.2 - - - +
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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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151A LEU* 5.3 5.8 - - + -
154A ARG* 5.3 1.8 - - - +
189A LYS* 3.2 23.5 + - - +
190A GLU* 2.7 51.2 + - - +
192A GLY* 1.3 79.5 - - - +
194A CYS* 1.3 64.3 + - - +
196A LYS 3.8 2.6 + - - -
470B MET* 3.2 58.6 - - + +
471B ALA* 3.2 27.2 - - - +
474B GLU* 2.7 31.1 + - - +
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Residues in contact with CYS 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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145A VAL* 4.4 9.2 - - + -
151A LEU* 3.7 35.9 - - + -
159A ILE* 3.8 26.9 - - + -
162A ALA* 4.0 13.9 - - + -
190A GLU* 3.0 22.3 + - - +
193A ARG* 1.3 76.5 - - - +
195A PHE* 1.3 66.1 + - - +
197A LEU* 3.1 18.9 + - - +
198A ILE* 3.4 12.5 + - + +
470B MET* 4.4 7.4 - - - -
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Residues in contact with PHE 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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162A ALA* 3.5 21.7 - - + +
165A TYR* 3.4 35.9 - + + -
166A ILE* 3.3 34.5 - - + +
169A ARG* 5.4 5.4 - - + -
191A ILE* 3.0 19.2 + - + +
192A GLY 3.4 6.7 - - - +
193A ARG 3.3 0.2 - - - -
194A CYS* 1.3 77.6 - - - +
196A LYS* 1.3 59.9 + - - +
197A LEU 3.2 0.3 + - - -
198A ILE 3.2 2.3 + - - -
199A LEU* 2.8 63.0 + - + +
286A ARG* 6.4 0.4 - - - -
473B PHE* 3.6 45.5 - + + -
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Residues in contact with LYS 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 GLY 3.3 2.6 + - - -
194A CYS 3.4 0.4 - - - -
195A PHE* 1.3 80.1 - - - +
197A LEU* 1.3 58.4 + - - +
199A LEU* 3.8 26.9 - - + +
200A LYS* 2.7 35.0 + - + +
290A ARG* 4.2 9.4 - - - +
469B ASP* 2.6 47.0 + - - +
470B MET* 3.7 16.4 - - - +
472B ASP* 2.6 28.9 + - - -
473B PHE* 3.5 27.4 - - + +
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Residues in contact with LEU 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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145A VAL* 4.3 13.2 - - + -
148A GLN* 3.7 30.5 - - + +
151A LEU* 3.9 25.8 - - + -
193A ARG 4.0 1.6 + - - -
194A CYS 3.1 9.9 + - - +
195A PHE 3.1 0.6 - - - -
196A LYS* 1.3 80.9 - - - +
198A ILE* 1.3 62.2 + - + +
200A LYS* 3.5 25.0 - - - +
201A ALA* 3.9 8.3 + - - +
467B ALA* 5.6 7.6 - - + -
470B MET* 3.7 28.9 - - + -
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Residues in contact with ILE 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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141A LEU* 3.8 35.9 - - + +
144A GLN* 5.3 5.2 - - + +
145A VAL* 3.8 34.3 - - + -
162A ALA* 5.3 0.4 - - + -
163A CYS* 3.9 19.5 - - - +
166A ILE* 3.5 26.4 - - + +
194A CYS* 3.5 15.9 - - + +
195A PHE* 3.2 1.2 + - - -
197A LEU* 1.3 76.3 - - + +
199A LEU* 1.3 66.4 + - - +
200A LYS 3.2 2.0 - - - -
201A ALA* 2.9 20.3 + - + +
202A LEU* 3.4 16.5 - - + +
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Residues in contact with LEU 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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166A ILE* 4.2 10.7 - - + +
169A ARG* 3.8 32.8 + - - +
195A PHE* 2.8 49.4 + - + +
196A LYS* 3.8 30.7 - - + +
197A LEU 3.4 0.2 - - - -
198A ILE* 1.3 78.2 - - - +
200A LYS* 1.3 58.3 + - - +
201A ALA 3.2 0.9 + - - -
202A LEU 3.7 16.5 - - - +
203A GLU* 5.2 5.5 - - - +
283A VAL* 6.3 1.6 - - + -
286A ARG* 5.7 10.8 - - + +
473B PHE* 5.0 3.6 - - + -
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Residues in contact with LYS 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 LYS* 2.7 23.0 + - + +
197A LEU* 3.5 20.8 - - - +
199A LEU* 1.3 77.6 - - + +
201A ALA* 1.3 60.4 + - - +
202A LEU 3.6 0.9 - - - -
203A GLU* 6.4 0.9 - - - -
466B GLY* 2.9 33.4 - - - +
467B ALA* 4.4 5.2 - - - +
469B ASP* 2.6 48.2 + - + +
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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