Contacts of the helix formed by residues 188 - 199 (chain A) in PDB entry 2N8A
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 ALA 188 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A TYR* 3.1 18.2 + - + +
186A LEU 4.0 0.8 + - - -
187A LEU* 1.3 73.7 - - - +
189A THR* 1.3 67.9 + - - +
190A GLU* 4.4 6.5 - - + +
191A ASP* 3.0 21.0 + - - +
192A LYS 3.0 9.5 + - - -
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Residues in contact with THR 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 LEU 3.6 1.2 + - - -
188A ALA* 1.3 71.4 - - - +
190A GLU* 1.3 64.0 + - - +
192A LYS* 3.1 21.2 + - - +
193A GLU* 3.0 34.3 + - - +
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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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188A ALA* 3.2 5.5 - - + +
189A THR* 1.3 79.9 - - - +
191A ASP* 1.3 72.1 + - - +
193A GLU* 3.3 6.9 + - - +
194A ALA* 3.2 20.8 + - - +
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Residues in contact with ASP 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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117A TYR* 2.5 37.6 + - + +
137A VAL* 2.9 26.3 - - + +
187A LEU* 4.2 7.0 - - + -
188A ALA* 3.0 15.7 + - - +
190A GLU* 1.3 88.9 - - - +
192A LYS* 1.3 63.1 + - - +
194A ALA* 3.4 8.1 + - - +
195A LEU* 3.3 28.5 + - + +
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Residues in contact with LYS 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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184A PHE* 3.6 47.6 - - + +
185A SER* 4.3 12.3 + - - +
187A LEU* 3.5 38.0 + - + +
188A ALA 3.0 2.0 + - - +
189A THR* 3.4 25.0 + - + +
191A ASP* 1.3 76.3 - - - +
193A GLU* 1.3 63.7 + - - +
195A LEU* 3.3 4.5 + - - +
196A LYS* 3.0 32.7 + - + +
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Residues in contact with GLU 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 THR* 3.0 22.1 + - - +
190A GLU* 3.6 10.5 - - - +
191A ASP 3.3 0.2 - - - -
192A LYS* 1.3 77.8 - - - +
194A ALA* 1.3 64.4 + - - +
196A LYS* 3.3 15.0 + - - +
197A LYS* 3.0 34.4 + - + +
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Residues in contact with ALA 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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190A GLU* 3.2 9.8 + - + +
191A ASP* 3.6 12.3 - - - +
193A GLU* 1.3 78.8 - - - +
195A LEU* 1.3 64.6 + - + +
197A LYS* 3.1 19.7 - - - +
198A GLN* 3.4 10.9 + - - +
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Residues in contact with LEU 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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115A ALA* 4.7 6.3 - - + -
137A VAL* 4.6 16.2 - - + -
139A LEU* 3.9 22.7 - - + -
160A PRO* 4.3 9.6 - - + -
178A ALA* 3.5 17.5 - - + +
181A LEU* 5.0 3.8 - - + -
184A PHE* 4.0 10.5 - - + -
187A LEU* 3.8 28.3 - - + -
191A ASP* 3.3 16.3 + - + +
192A LYS 3.6 5.6 - - - +
193A GLU 3.2 0.4 - - - -
194A ALA* 1.3 74.9 - - + +
196A LYS* 1.3 63.7 + - - +
197A LYS 2.8 4.7 + - - -
198A GLN* 2.9 27.2 + - - +
199A LEU* 2.8 23.1 + - + +
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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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177A SER* 6.2 1.3 - - - -
178A ALA* 3.3 19.5 - - + +
179A SER* 4.2 15.7 - - - +
184A PHE* 3.8 23.4 - - + -
192A LYS* 3.0 23.4 + - + +
193A GLU* 3.7 15.7 - - - +
195A LEU* 1.3 78.7 - - - +
197A LYS* 1.3 61.1 + - - +
199A LEU 3.9 2.7 - - - -
200A PRO* 3.3 26.6 - - + +
204A SER* 6.3 3.1 - - - -
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Residues in contact with LYS 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 GLU* 3.0 22.2 + - + +
194A ALA* 3.1 16.8 - - - +
195A LEU 2.8 0.4 + - - -
196A LYS* 1.3 80.7 - - - +
198A GLN* 1.3 60.1 + - + +
200A PRO* 4.0 8.8 - - - +
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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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139A LEU* 3.9 3.3 - - - +
160A PRO* 3.7 22.8 + - - +
161A GLY* 4.2 3.4 - - - +
164A VAL* 2.9 44.8 - - + +
194A ALA 3.6 9.8 + - - +
195A LEU* 2.9 33.0 - - - +
197A LYS* 1.3 77.2 - - - +
199A LEU* 1.3 81.7 + - + +
200A PRO* 3.1 9.1 - - - +
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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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139A LEU* 4.5 13.9 - - + -
163A PHE* 4.6 4.5 - - + -
164A VAL* 4.5 17.3 - - + -
167A ARG* 5.3 6.5 - - + -
172A PHE* 3.4 44.9 - - + -
176A TYR 4.7 1.1 - - - +
177A SER* 3.5 1.5 - - - -
178A ALA* 3.0 31.7 + - + +
181A LEU* 4.5 9.6 - - + -
195A LEU* 2.8 10.6 + - + +
196A LYS* 3.4 7.7 - - - +
198A GLN* 1.3 105.8 - - + +
200A PRO* 1.3 64.8 - - + +
201A GLY 3.4 1.8 - - - +
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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