Contacts of the helix formed by residues 187 - 202 (chain A) in PDB entry 2P3L
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 MET 187 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A THR* 5.2 0.4 - - - -
11A GLU* 3.6 43.3 - - - +
154A PRO* 3.7 19.3 - - + +
155A THR* 4.0 31.2 - - + +
158A ALA* 3.9 18.4 - - + -
184A ASN* 3.2 27.9 + - - +
185A PRO 3.6 0.4 - - - -
186A TYR* 1.3 80.1 - - + +
188A SER* 1.3 60.9 + - - +
189A SER* 3.3 2.9 - - - +
190A VAL* 2.8 27.5 + - + -
191A ILE* 3.0 10.5 + - - -
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Residues in contact with SER 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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8A THR* 4.4 13.5 - - - +
11A GLU* 4.7 4.7 + - - -
186A TYR 3.6 2.6 + - - -
187A MET* 1.3 74.8 - - - +
189A SER* 1.3 61.5 + - - +
191A ILE* 3.4 10.8 + - - +
192A GLU* 3.1 23.7 + - - +
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Residues in contact with SER 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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158A ALA* 3.7 23.6 - - - +
162A LEU* 3.6 24.2 - - - +
187A MET* 4.5 1.2 + - - +
188A SER* 1.3 78.5 - - - +
190A VAL* 1.3 62.3 + - - +
192A GLU* 3.7 12.7 + - - +
193A LYS* 3.2 22.3 + - - +
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Residues in contact with VAL 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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158A ALA* 4.0 25.1 - - + +
161A THR* 3.7 31.6 - - + -
162A LEU* 4.2 10.8 - - + -
165A LEU* 4.1 9.0 - - + -
182A VAL* 4.0 12.6 - - + -
184A ASN 3.4 28.0 - - - +
185A PRO* 4.0 7.0 - - + +
187A MET* 2.8 15.7 + - + +
189A SER* 1.3 73.4 + - - +
191A ILE* 1.3 59.0 + - - +
193A LYS* 3.3 1.1 + - - +
194A MET* 2.9 31.2 + - + +
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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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185A PRO 3.2 23.8 - - - +
186A TYR* 3.9 14.4 - - - +
187A MET 3.0 19.6 + - - +
188A SER* 3.6 8.7 - - - +
190A VAL* 1.3 76.1 - - - +
192A GLU* 1.3 57.6 + - - +
194A MET* 3.2 3.1 + - - +
195A GLU* 2.9 52.7 + - - +
228A ILE* 4.0 18.3 - - + +
229A VAL* 3.7 21.3 - - + -
232A VAL* 4.4 12.3 - - + -
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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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188A SER 3.1 13.8 + - - +
189A SER* 3.8 12.9 - - - +
191A ILE* 1.3 78.9 - - - +
193A LYS* 1.3 63.2 + - - +
195A GLU* 3.6 14.6 + - - +
196A ALA* 3.3 21.1 + - - +
199A ARG* 5.3 0.9 + - - -
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Residues in contact with LYS 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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162A LEU* 3.8 16.6 - - + -
165A LEU* 3.7 25.1 - - + -
166A ASN* 3.3 27.7 + - - +
169A GLU* 2.7 31.8 + - - -
189A SER 3.2 14.7 + - - +
190A VAL 3.8 4.0 - - - +
191A ILE 3.3 0.2 - - - -
192A GLU* 1.3 79.8 - - - +
194A MET* 1.3 57.0 + - - +
196A ALA* 3.4 9.6 + - + +
197A LEU* 2.9 47.9 + - + +
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Residues in contact with MET 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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165A LEU* 3.8 35.0 - - + -
182A VAL* 4.3 4.3 - - + -
185A PRO* 6.1 0.9 - - + +
190A VAL* 2.9 27.3 + - + +
191A ILE* 3.7 3.4 - - - +
193A LYS* 1.3 74.0 - - - +
195A GLU* 1.3 61.3 + - - +
197A LEU* 3.8 7.2 - - - +
198A GLN* 2.8 26.2 + - + +
205A LEU* 3.7 31.4 - - + +
220A TRP* 3.5 42.4 - - + +
228A ILE* 3.2 31.4 - - + +
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Residues in contact with GLU 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 ILE* 2.9 37.0 + - - +
192A GLU* 3.6 14.4 - - - +
194A MET* 1.3 76.9 - - - +
196A ALA* 1.3 60.5 + - - +
198A GLN* 3.4 5.8 + - - +
199A ARG* 3.2 49.0 + - - +
227A ASN* 5.8 1.2 + - - -
228A ILE* 3.6 20.6 - - + +
229A VAL* 3.5 16.5 + - - +
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Residues in contact with ALA 196 (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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192A GLU 3.3 11.5 + - - +
193A LYS* 3.6 15.0 - - + +
195A GLU* 1.3 79.5 - - - +
197A LEU* 1.3 61.8 + - + +
199A ARG* 3.3 25.2 + - - +
200A LYS* 3.2 22.3 + - - +
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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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165A LEU* 3.8 43.7 - - + +
169A GLU* 3.5 43.5 - - + +
193A LYS* 2.9 36.8 + - + +
194A MET* 3.8 8.5 - - - +
196A ALA* 1.3 73.5 - - - +
198A GLN* 1.3 57.0 + - - +
200A LYS* 3.4 6.0 + - + +
201A HIS* 2.8 39.2 + - - +
220A TRP* 3.6 32.2 - - + -
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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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194A MET 2.8 20.6 + - - +
195A GLU* 3.7 6.7 + - - +
196A ALA 3.3 0.2 - - - -
197A LEU* 1.3 70.5 - - - +
199A ARG* 1.3 62.6 + - + +
202A GLY* 2.7 38.4 + - - +
203A GLY 2.9 28.0 - - - +
204A ALA* 4.0 4.0 - - - +
220A TRP* 4.5 4.0 - - - +
225A SER* 5.1 0.2 - - - -
226A GLY 2.9 28.6 + - - +
227A ASN* 4.9 2.2 - - - +
228A ILE* 3.2 28.1 - - + +
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Residues in contact with ARG 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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192A GLU 5.3 0.6 + - - -
195A GLU* 3.2 44.5 + - - +
196A ALA* 3.3 28.3 + - - +
198A GLN* 1.3 77.1 - - - +
200A LYS* 1.3 61.2 + - - +
202A GLY 4.6 0.9 + - - -
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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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169A GLU* 3.7 25.6 - - + +
196A ALA 3.2 13.7 + - - +
197A LEU* 3.8 4.3 - - + +
199A ARG* 1.3 82.5 - - + +
201A HIS* 1.3 90.6 + - + +
202A GLY 4.0 0.2 - - - -
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Residues in contact with HIS 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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169A GLU* 4.7 10.8 - - + -
172A LEU* 3.8 35.8 + - + +
173A SER 3.4 27.3 + - - -
174A ASN* 5.0 5.6 - - - -
176A THR* 5.6 0.4 - - + -
178A PHE* 3.7 19.6 - + + -
197A LEU* 2.8 17.3 + - - +
200A LYS* 1.3 115.5 + - + +
202A GLY* 1.3 64.3 + - - +
203A GLY 3.7 0.5 + - - -
220A TRP* 3.9 16.6 - - + -
222A SER* 5.2 1.0 - - - +
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Residues in contact with GLY 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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178A PHE* 4.4 0.2 - - - -
198A GLN* 2.7 34.1 + - - -
199A ARG 4.6 1.0 + - - -
200A LYS 4.0 0.2 - - - -
201A HIS* 1.3 76.6 - - - +
203A GLY* 1.3 67.1 + - - +
220A TRP* 3.2 17.8 + - - -
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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