Contacts of the helix formed by residues 197 - 204 (chain N) in PDB entry 1K2V
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 PHE 197 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179N LEU* 3.4 32.8 - - + -
191N PHE* 3.7 38.8 - + + -
195N SER* 3.1 4.4 - - - +
196N LEU* 1.3 85.7 - - + +
198N GLN* 1.3 64.8 + - - +
199N GLU 3.3 0.2 - - - -
200N ILE* 3.0 19.0 + - + +
201N LEU* 3.1 14.1 + - + +
238N PHE* 3.8 17.7 - + - -
272N VAL* 4.1 12.1 - - + -
273N TRP 4.4 2.5 - - - -
274N PHE* 3.7 35.7 - + + -
280N SER 5.3 0.2 - - - -
281N ALA* 5.9 0.9 - - - -
284N PHE* 3.4 45.1 - + + -
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Residues in contact with GLN 198 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192N GLY 4.1 1.1 - - - +
193N PRO* 3.0 43.4 - - + +
195N SER* 3.3 13.8 + - - +
197N PHE* 1.3 75.8 - - - +
199N GLU* 1.3 65.8 + - - +
201N LEU* 2.9 13.6 + - - +
202N ASP* 2.8 51.5 + - - +
206N ILE 4.8 0.5 - - - +
207N PRO* 5.7 0.2 - - - +
208N ASN* 2.7 50.7 + - - +
211N GLN* 5.5 1.0 + - - -
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Residues in contact with GLU 199 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129N GLN* 4.1 23.0 + - + +
131N LEU* 3.4 37.4 - - + +
132N ALA* 4.1 4.9 + - - +
135N ARG* 2.5 39.3 + - - -
158N TYR* 4.4 0.9 + - - -
195N SER 4.6 1.0 + - - -
196N LEU 4.1 2.1 + - - +
197N PHE 3.3 0.6 - - - -
198N GLN* 1.3 78.6 - - - +
200N ILE* 1.3 64.6 + - + +
202N ASP* 3.2 11.5 + - + +
203N GLU* 3.1 27.4 + - - +
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Residues in contact with ILE 200 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131N LEU* 3.8 12.1 - - + -
158N TYR* 3.4 26.7 - - - +
162N ILE* 3.6 24.7 - - + -
196N LEU 4.5 3.6 - - - +
197N PHE* 3.0 11.1 + - + +
199N GLU* 1.3 79.2 - - + +
201N LEU* 1.3 63.4 + - - +
203N GLU* 3.1 14.1 + - - +
204N TYR* 3.1 41.2 + - + -
281N ALA* 4.4 8.7 - - + -
284N PHE* 3.7 29.4 - - + -
285N VAL* 3.8 10.5 - - + -
288N LEU* 4.5 1.3 - - + -
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Residues in contact with LEU 201 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177N LEU* 3.8 18.6 - - + +
179N LEU* 4.1 17.7 - - + -
197N PHE 3.1 15.1 + - - +
198N GLN* 2.9 14.9 + - - +
200N ILE* 1.3 75.5 - - - +
202N ASP* 1.3 57.5 + - - +
204N TYR* 3.2 3.4 + - - -
205N GLY 3.0 8.7 + - - -
206N ILE* 2.9 68.7 + - + +
207N PRO 4.9 0.7 - - - +
208N ASN* 3.9 40.8 - - + +
284N PHE* 4.3 14.6 - - + -
288N LEU* 4.6 2.2 - - + -
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Residues in contact with ASP 202 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198N GLN* 2.8 44.8 + - - +
199N GLU* 3.5 13.3 - - + +
201N LEU* 1.3 78.3 - - - +
203N GLU* 1.3 61.7 + - - +
204N TYR 3.4 0.2 + - - -
205N GLY* 3.4 10.7 + - - -
206N ILE 4.9 2.4 - - - +
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Residues in contact with GLU 203 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159N GLU 5.3 0.2 - - - +
162N ILE* 3.7 26.5 - - + +
163N ARG* 3.9 13.0 + - - +
166N LYS* 3.5 44.6 + - - +
199N GLU* 3.1 17.5 + - - +
200N ILE* 3.1 7.8 + - - +
202N ASP* 1.3 77.1 - - - +
204N TYR* 1.3 69.6 + - + +
205N GLY 3.4 0.6 + - - -
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Residues in contact with TYR 204 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162N ILE* 2.6 43.0 + - + +
165N MET* 3.3 16.2 - - + +
166N LYS* 3.7 26.5 - - + -
169N PHE* 3.5 50.3 - + + +
200N ILE* 3.1 33.0 + - + +
201N LEU 3.2 0.9 + - - +
202N ASP 3.2 0.2 - - - -
203N GLU* 1.3 96.0 - - + +
205N GLY* 1.3 61.5 + - - +
206N ILE* 3.3 20.6 + - + +
285N VAL* 3.5 14.9 - - + +
288N LEU* 3.9 10.5 - - + -
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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