Contacts of the helix formed by residues 277 - 293 (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 ALA 277 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44N LEU* 3.8 14.6 - - + -
47N GLU* 2.8 24.1 + - + +
48N LEU* 3.9 18.8 - - + -
131N LEU* 4.2 3.8 - - - +
134N ALA* 3.6 24.9 - - + +
196N LEU* 4.1 3.9 - - - +
276N GLY* 1.3 75.3 - - - +
278N THR* 1.3 62.5 + - + +
280N SER* 3.6 1.6 - - - -
281N ALA* 3.0 26.2 + - - +
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Residues in contact with THR 278 (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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47N GLU* 5.5 0.2 - - - +
48N LEU* 6.0 0.5 - - - +
51N ALA* 4.8 2.3 - - - +
131N LEU* 4.6 2.7 - - + -
134N ALA* 4.3 16.6 - - + +
135N ARG* 4.7 7.2 - - + +
138N LEU* 4.9 5.4 - - + +
154N HIS* 2.6 34.5 - - + -
155N LEU* 4.7 13.5 - - + -
158N TYR* 3.7 36.7 - - + -
277N ALA* 1.3 79.5 - - + +
279N LEU* 1.3 65.7 + - - +
281N ALA* 3.6 3.1 - - - +
282N MET* 2.9 30.2 + - - +
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Residues in contact with LEU 279 (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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47N GLU* 2.5 45.4 + - + +
50N LEU* 4.2 6.3 - - + -
51N ALA* 4.0 20.2 - - + +
71N GLU* 5.6 0.2 - - - +
72N PRO* 4.0 34.1 - - + +
154N HIS* 3.3 28.5 - - + +
278N THR* 1.3 73.5 + - - +
280N SER* 1.3 54.7 + - - +
282N MET* 3.4 16.4 + - + +
283N HIS* 2.9 27.9 + - - +
286N ARG* 4.7 2.3 + - - -
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Residues in contact with SER 280 (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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47N GLU* 2.7 30.2 + - - -
69N VAL* 5.0 4.0 - - - +
72N PRO* 5.6 1.5 - - - +
196N LEU* 3.8 9.4 - - - -
272N VAL* 3.5 7.8 - - - +
273N TRP* 3.3 42.4 + - - +
276N GLY* 3.5 1.3 - - - -
277N ALA 3.6 8.3 - - - -
279N LEU* 1.3 73.2 - - - +
281N ALA* 1.3 57.2 + - - +
283N HIS* 3.1 9.6 + - - +
284N PHE* 2.8 26.2 + - - +
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Residues in contact with ALA 281 (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* 3.7 25.6 - - + -
158N TYR* 3.6 25.6 - - + +
196N LEU* 4.4 8.0 - - + +
197N PHE* 5.9 1.3 - - - -
200N ILE* 4.4 6.2 - - + +
277N ALA 3.0 6.5 + - - +
278N THR 3.6 7.9 - - - +
280N SER* 1.3 78.0 - - - +
282N MET* 1.3 63.2 + - - +
284N PHE* 3.0 11.1 + - - +
285N VAL* 3.0 25.8 + - - +
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Residues in contact with MET 282 (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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154N HIS* 3.6 17.7 - - + +
157N GLN* 4.5 16.6 - - - +
158N TYR* 3.4 34.5 - - + -
161N PHE* 3.6 39.2 - - + -
162N ILE* 4.7 0.7 - - + -
278N THR 2.9 18.9 + - - +
279N LEU* 3.4 36.3 - - + +
281N ALA* 1.3 73.2 - - - +
283N HIS* 1.3 64.9 - - - +
285N VAL* 3.2 3.4 + - - -
286N ARG* 3.2 36.7 + - - +
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Residues in contact with HIS 283 (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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69N VAL 3.9 8.1 - - - -
70N SER* 5.0 1.6 + - - -
71N GLU* 3.1 55.7 + - + +
72N PRO* 5.2 0.9 - - + -
270N PRO* 5.1 4.9 - - + -
271N ALA 3.0 24.5 + - - -
272N VAL* 4.0 11.9 - - + -
273N TRP 5.1 0.7 - - - -
279N LEU 2.9 15.0 + - - +
280N SER* 3.1 12.8 + - - +
282N MET* 1.3 76.2 - - - +
284N PHE* 1.3 63.1 + - - +
286N ARG* 3.2 18.8 + - + +
287N VAL* 3.1 38.6 + - + +
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Residues in contact with PHE 284 (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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179N LEU* 3.8 37.5 - - + -
197N PHE* 3.4 42.4 - + + -
200N ILE* 3.7 39.5 - - + -
201N LEU* 4.3 8.1 - - + -
236N LEU* 5.1 3.6 - - + -
238N PHE* 3.9 17.0 - + - -
272N VAL* 3.8 9.6 - - + +
280N SER 2.8 12.7 + - - +
281N ALA* 3.0 9.8 + - - +
283N HIS* 1.3 78.9 - - - +
285N VAL* 1.3 53.2 + - - +
287N VAL* 3.2 2.8 + - + +
288N LEU* 2.6 66.9 + - + +
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Residues in contact with VAL 285 (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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161N PHE* 3.8 9.9 - - + -
162N ILE* 3.6 25.1 - - + -
165N MET* 3.6 28.0 - - + -
169N PHE* 4.5 2.0 - - + -
200N ILE* 3.8 22.7 - - + -
204N TYR* 3.5 22.7 - - + +
281N ALA 3.0 14.6 + - - +
282N MET* 3.2 7.2 + - - +
284N PHE* 1.3 75.0 - - - +
286N ARG* 1.3 57.7 + - - +
288N LEU* 3.6 7.2 - - - +
289N ASP* 2.8 28.9 + - - +
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Residues in contact with ARG 286 (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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71N GLU* 2.9 47.0 + - - +
161N PHE* 3.9 20.2 - - + -
165N MET* 5.4 2.2 - - + -
279N LEU 4.7 2.4 + - - -
282N MET* 3.2 29.0 + - - +
283N HIS* 3.2 25.5 + - + +
285N VAL* 1.3 74.7 - - - +
287N VAL* 1.3 64.3 + - + +
289N ASP* 3.3 6.3 + - - +
290N ASN* 3.1 34.0 + - - +
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Residues in contact with VAL 287 (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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236N LEU* 5.5 2.0 - - + -
238N PHE* 4.4 7.6 - - + -
269N VAL* 3.5 39.4 - - + +
270N PRO* 4.0 21.3 - - + +
272N VAL* 3.6 19.3 - - + -
283N HIS* 3.1 28.0 + - + +
284N PHE* 3.6 7.6 - - + +
286N ARG* 1.3 72.5 - - + +
288N LEU* 1.3 67.5 + - - +
290N ASN* 3.3 10.1 + - - +
291N ALA* 3.0 22.6 + - + +
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Residues in contact with LEU 288 (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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169N PHE* 3.7 19.7 - - + -
177N LEU* 4.2 12.1 - - + -
200N ILE* 4.5 2.0 - - + -
201N LEU* 4.6 2.5 - - + -
204N TYR* 3.9 20.4 - - + -
206N ILE* 4.1 9.0 - - + -
236N LEU* 4.2 9.4 - - + -
284N PHE* 2.6 54.2 + - + +
285N VAL* 3.6 6.1 - - - +
287N VAL* 1.3 73.5 - - - +
289N ASP* 1.3 58.2 + - - +
291N ALA* 3.2 3.3 + - - +
292N ILE* 2.8 65.3 + - + +
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Residues in contact with ASP 289 (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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165N MET* 3.1 30.1 - - + +
168N ARG* 3.1 35.1 + - - +
169N PHE* 3.7 11.1 - - + -
285N VAL 2.8 19.0 + - - +
286N ARG* 3.5 6.1 - - - +
288N LEU* 1.3 77.5 - - - +
290N ASN* 1.3 66.1 + - - +
293N GLY* 2.6 36.5 + - - +
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Residues in contact with ASN 290 (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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267N GLN* 4.9 1.2 + - - -
286N ARG* 3.1 25.1 + - - +
287N VAL* 3.8 7.6 - - - +
289N ASP* 1.3 83.3 - - - +
291N ALA* 1.3 62.7 + - - +
293N GLY 4.9 0.7 + - - +
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Residues in contact with ALA 291 (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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236N LEU* 3.8 32.1 - - + -
267N GLN* 3.0 30.7 + - - +
269N VAL* 4.0 15.9 - - + -
287N VAL 3.0 17.6 + - - +
288N LEU 3.6 2.7 - - - +
289N ASP 3.2 0.2 - - - -
290N ASN* 1.3 79.2 - - - +
292N ILE* 1.3 59.6 + - - +
293N GLY 5.5 0.2 - - - -
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Residues in contact with ILE 292 (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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168N ARG 4.4 1.6 - - - +
169N PHE* 3.9 7.1 - - + -
172N ARG* 3.9 51.2 + - - +
177N LEU* 4.2 10.5 - - + -
206N ILE* 4.0 9.9 - - + -
234N ASP* 4.9 12.6 - - + -
236N LEU* 4.3 9.4 - - + -
267N GLN* 3.9 10.3 - - - +
288N LEU* 2.8 42.2 + - + +
291N ALA* 1.3 85.1 - - + +
293N GLY* 1.3 67.7 + - - +
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Residues in contact with GLY 293 (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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168N ARG* 3.3 52.0 + - - -
169N PHE* 4.0 7.4 - - - -
288N LEU 3.6 1.4 + - - -
289N ASP* 2.6 38.7 + - - +
290N ASN 5.4 0.9 - - - +
291N ALA 3.9 0.4 - - - -
292N ILE* 1.3 77.5 - - - +
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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