Contacts of the strand formed by residues 177 - 184 (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 LEU 177 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172N ARG* 4.3 2.2 - - - +
175N ARG 3.8 0.2 + - - -
176N PRO* 1.3 75.0 - - - +
178N LEU* 1.3 61.7 + - - +
179N LEU* 3.6 28.6 + - + +
201N LEU* 3.8 24.3 - - + +
206N ILE* 3.6 19.3 - - + -
207N PRO 2.8 7.4 + - - +
208N ASN* 3.6 9.5 - - - +
209N ALA* 2.8 25.3 + - - -
234N ASP* 3.3 33.9 - - + +
236N LEU* 3.8 21.1 - - + -
288N LEU* 4.2 20.0 - - + -
292N ILE* 4.2 8.5 - - + -
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Residues in contact with LEU 178 (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* 1.3 74.6 - - - +
179N LEU* 1.3 63.5 + - - +
180N THR* 3.7 16.2 - - + -
190N VAL* 4.5 9.6 - - + -
209N ALA* 4.0 10.1 - - + -
210N TRP* 3.9 39.9 - - + +
227N LEU* 4.0 25.6 - - + -
230N TYR* 4.2 20.9 - - + -
233N VAL* 4.7 1.3 - - + -
234N ASP 2.7 15.8 + - - +
235N VAL* 3.4 23.7 - - + +
236N LEU 2.9 27.5 + - - +
260N PHE* 4.7 4.3 - - + -
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Residues in contact with LEU 179 (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* 3.6 31.5 + - + +
178N LEU* 1.3 74.4 - - - +
180N THR* 1.3 67.7 + - - +
190N VAL* 3.4 2.6 - - - +
191N PHE* 3.1 45.1 + - + +
195N SER* 5.4 0.2 - - - +
197N PHE* 3.4 40.2 - - + -
201N LEU* 4.1 16.8 - - + -
208N ASN* 5.1 4.1 + - - +
236N LEU* 3.8 18.2 - - + -
238N PHE* 4.5 7.2 - - + -
284N PHE* 3.8 24.2 - - + -
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Residues in contact with THR 180 (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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178N LEU* 3.7 27.8 - - + +
179N LEU* 1.3 83.8 - - - +
181N THR* 1.3 62.4 + - - +
188N MET* 3.3 27.6 - - + +
189N LEU 3.0 11.2 - - - -
190N VAL* 3.7 14.4 - - + -
191N PHE* 4.0 6.7 - - - -
227N LEU* 4.9 4.0 - - + -
235N VAL* 4.1 6.8 - - + +
236N LEU 2.9 17.5 + - - +
237N CYS* 3.2 6.1 - - - +
238N PHE* 2.9 30.4 + - - -
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Residues in contact with THR 181 (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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1N DEF 5.4 0.7 - - + -
68N TRP* 5.0 2.2 - - + -
180N THR* 1.3 78.8 - - - +
182N LEU* 1.3 59.6 + - - +
183N ILE* 5.1 2.0 - - + +
188N MET* 3.3 4.6 - - - +
189N LEU* 2.8 53.3 + - + +
191N PHE* 4.0 2.9 - - + -
237N CYS* 3.8 7.4 - - - -
238N PHE* 2.8 25.2 + - - +
240N HIS* 3.1 20.8 + - + -
274N PHE* 3.8 28.6 - - + -
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Residues in contact with LEU 182 (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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181N THR* 1.3 73.8 + - - +
183N ILE* 1.3 61.4 + - - +
184N ASP* 3.3 28.3 - - - +
185N PRO* 4.6 1.3 - - + -
187N HIS 3.6 6.1 - - - +
188N MET* 3.6 17.5 - - + -
224N ILE* 4.3 4.9 - - + -
237N CYS* 3.8 4.2 - - - -
238N PHE 4.6 0.6 + - - -
240N HIS* 2.9 30.7 + - - -
242N ASN* 3.6 6.1 + - - +
245N ASP* 3.5 40.3 - - + +
246N MET* 3.5 32.5 - - - +
249N LEU* 3.7 27.6 - - + -
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Residues in contact with ILE 183 (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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1N DEF 4.9 13.7 - - + +
68N TRP* 6.0 2.9 - - - -
181N THR* 4.4 2.0 - - + +
182N LEU* 1.3 74.2 - - - +
184N ASP* 1.3 73.1 + - + +
187N HIS* 2.9 21.6 + - + +
189N LEU* 3.7 36.8 - - + +
221N ALA* 3.5 32.1 - - + -
240N HIS* 5.0 3.5 + - - -
245N ASP* 4.2 7.9 - - - +
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Residues in contact with ASP 184 (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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182N LEU* 3.3 12.0 - - - +
183N ILE* 1.3 86.1 - - + +
185N PRO* 1.3 77.5 - - + +
186N ARG* 2.7 11.6 + - - +
187N HIS* 2.7 52.8 + - - +
245N ASP* 4.2 7.0 - - - +
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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