Contacts of the helix formed by residues 257 - 271 (chain A) in PDB entry 1K86
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 GLU 257 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A LEU* 1.3 73.8 - - - +
258A ILE* 1.3 91.2 + - - +
259A MET* 2.7 37.7 + - - +
260A GLN* 2.9 30.9 + - + +
261A ILE* 3.3 7.0 + - - +
295A LEU* 4.9 0.9 - - - +
297A LYS 4.6 1.7 - - - +
298A GLU* 3.6 29.8 - - + +
299A LEU* 2.7 37.0 + - - +
300A TYR* 3.0 22.5 - - + +
259B MET* 5.5 0.7 - - - +
260B GLN* 6.2 0.7 - - + -
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Residues in contact with ILE 258 (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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180A LEU* 5.5 2.0 - - + -
182A PHE* 4.9 13.0 - - + -
220A LEU* 4.3 11.0 - - + -
245A LEU* 6.5 0.2 - - + -
249A LEU* 5.5 1.6 - - + -
256A LEU 3.7 0.6 + - - -
257A GLU* 1.3 94.1 - - - +
259A MET* 1.3 60.0 + - + +
261A ILE* 3.3 16.9 - - + +
262A LEU* 3.1 51.1 + - + +
295A LEU* 3.8 19.7 - - + -
299A LEU* 2.8 38.8 + - + +
301A PHE* 4.0 28.3 - - + -
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Residues in contact with MET 259 (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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220A LEU* 4.1 15.9 - - + -
257A GLU* 2.7 25.6 + - - +
258A ILE* 1.3 77.3 - - + +
260A GLN* 1.3 56.6 + - + +
262A LEU* 4.2 6.0 - - + +
263A THR* 2.6 41.4 + - - +
291A VAL* 3.8 35.0 - - + +
293A SER* 4.6 4.9 - - - +
295A LEU* 5.6 2.0 - - + -
259B MET* 3.3 59.0 - - + -
263B THR* 5.5 3.4 - - - +
291B VAL 6.1 0.2 - - - +
293B SER* 4.1 14.1 - - - +
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Residues in contact with GLN 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A ASP 5.0 0.3 - - - +
256A LEU* 3.6 29.6 - - + +
257A GLU* 2.9 36.3 + - + +
259A MET* 1.3 75.9 - - + +
261A ILE* 1.3 67.2 + - - +
263A THR* 3.3 1.3 + - - -
264A ARG* 3.0 39.9 + - - +
300A TYR* 4.2 6.4 + - - -
257B GLU* 6.5 0.2 - - - -
298B GLU* 2.9 42.2 + - - +
300B TYR* 5.7 0.4 + - - -
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Residues in contact with ILE 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A LEU* 4.6 1.6 - - + -
248A ILE* 4.2 16.9 - - + +
249A LEU* 3.7 33.2 - - + -
252A HIS* 3.7 23.6 - - + +
253A GLY* 4.4 3.8 - - - +
256A LEU* 3.6 35.4 - - + +
257A GLU 3.6 13.0 - - - +
258A ILE* 3.3 17.0 - - + +
260A GLN* 1.3 79.3 - - - +
262A LEU* 1.3 66.3 + - + +
264A ARG* 3.2 4.2 + - - +
265A VAL* 3.0 35.5 + - + +
301A PHE* 5.5 2.2 - - + -
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Residues in contact with LEU 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A PHE* 4.5 8.7 - - + -
220A LEU* 3.9 22.9 - - + -
222A ALA* 4.4 17.7 - - + -
241A PHE* 5.3 5.2 - - + -
245A LEU* 4.3 23.3 - - + -
258A ILE* 3.1 36.2 + - + +
259A MET* 4.2 7.6 - - + +
261A ILE* 1.3 81.8 - - + +
263A THR* 1.3 66.5 + - - +
265A VAL* 3.1 10.3 + - + +
266A ASN* 2.9 27.4 + - - +
291A VAL* 4.0 29.8 - - + -
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Residues in contact with THR 263 (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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259A MET* 2.6 32.7 + - - +
260A GLN* 3.8 5.6 - - - -
262A LEU* 1.3 76.0 - - - +
264A ARG* 1.3 65.1 + - + +
266A ASN* 3.0 15.1 + - - +
267A ASP 3.0 18.2 + - - -
291A VAL* 5.5 0.4 - - - +
257B GLU* 5.6 2.1 + - - +
259B MET* 5.4 3.6 - - - +
293B SER* 5.1 2.9 + - - -
295B LEU* 3.5 13.4 + - + +
296B THR 3.4 5.4 - - - +
297B LYS* 3.2 43.5 - - - +
298B GLU* 4.6 6.5 + - - +
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Residues in contact with ARG 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A ILE* 3.6 21.8 - - + -
252A HIS* 3.7 29.3 + - - -
256A LEU* 3.6 33.2 - - - +
260A GLN* 3.0 25.8 + - - +
261A ILE 3.4 7.0 - - - +
263A THR* 1.3 74.1 - - + +
265A VAL* 1.3 62.3 + - - +
267A ASP* 3.2 7.4 + - - +
268A ARG* 2.8 31.7 + - - +
58B TYR* 3.5 66.2 + - + +
296B THR 5.0 1.3 - - - -
298B GLU* 5.9 3.0 + - - +
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Residues in contact with VAL 265 (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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241A PHE* 3.7 37.0 - - + -
244A ALA* 3.8 15.9 - - + -
245A LEU* 3.8 30.1 - - + +
248A ILE* 3.6 20.2 - - + -
261A ILE* 3.0 20.0 + - + +
262A LEU* 3.1 12.5 + - + +
264A ARG* 1.3 75.5 - - - +
266A ASN* 1.3 58.4 + - - +
268A ARG* 3.3 2.4 + - - +
269A VAL* 2.8 36.9 + - + +
289A PRO* 4.8 0.7 - - + -
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Residues in contact with ASN 266 (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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241A PHE* 5.5 0.2 - - - -
262A LEU 2.9 17.6 + - - +
263A THR* 3.1 12.2 + - - +
265A VAL* 1.3 76.6 - - - +
267A ASP* 1.3 57.8 + - - +
269A VAL* 3.1 2.6 + - - +
270A ALA* 2.8 29.6 + - - +
288A ILE* 3.4 14.2 - - + +
289A PRO* 3.1 39.9 + - - +
290A CYS 4.5 0.5 + - - -
291A VAL* 4.2 12.2 - - - +
293B SER* 4.0 21.2 + - - -
294B MET* 4.1 3.6 - - - +
295B LEU 2.9 24.8 + - - +
296B THR* 4.4 0.2 - - + -
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Residues in contact with ASP 267 (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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263A THR 3.0 3.5 + - - +
264A ARG* 3.6 8.9 - - - +
266A ASN* 1.3 78.0 - - - +
268A ARG* 1.3 54.5 + - - +
270A ALA* 2.8 5.7 + - - +
271A ARG* 2.4 74.1 + - - +
58B TYR* 6.0 3.3 - - - -
296B THR* 3.1 43.4 + - - +
297B LYS* 4.9 9.8 - - - +
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Residues in contact with ARG 268 (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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243A GLN 5.5 0.2 - - - -
244A ALA* 3.8 22.9 - - + +
247A SER* 3.6 29.1 + - - -
248A ILE* 3.3 29.7 - - + +
264A ARG 2.8 20.1 + - - +
265A VAL* 3.4 7.4 - - - +
267A ASP* 1.3 74.3 + - - +
269A VAL* 1.3 56.4 + - - +
271A ARG* 2.9 48.2 - - - +
272A HIS* 4.9 1.0 - - - +
273A PHE* 3.9 18.3 + - + -
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Residues in contact with VAL 269 (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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224A SER 5.7 1.3 - - - +
240A TRP* 4.0 23.8 - - + +
241A PHE* 3.9 28.7 - - + +
244A ALA* 4.1 5.8 - - + -
265A VAL* 2.8 24.7 + - + +
266A ASN 3.6 3.6 - - - +
268A ARG* 1.3 72.7 - - - +
270A ALA* 1.3 64.8 + - - +
271A ARG 3.2 3.5 - - - +
273A PHE* 3.6 21.8 - - - +
286A LYS* 3.7 6.0 + - - +
287A GLN* 4.1 14.4 - - + +
288A ILE* 4.7 0.7 - - - -
289A PRO* 3.7 28.9 - - + -
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Residues in contact with ALA 270 (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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266A ASN 2.8 16.7 + - - +
267A ASP* 2.8 7.7 + - - +
269A VAL* 1.3 74.2 - - - +
271A ARG* 1.3 69.7 + - - +
272A HIS 3.9 0.2 - - - +
273A PHE 2.8 14.6 - - - +
286A LYS* 4.0 8.6 - - - +
287A GLN 4.5 6.7 - - - +
288A ILE* 3.4 21.3 - - + -
217B ALA* 4.8 6.5 - - + -
296B THR* 4.3 7.4 - - + -
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Residues in contact with ARG 271 (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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267A ASP* 2.4 50.7 + - - +
268A ARG* 2.9 48.2 - - - +
269A VAL 3.2 1.0 - - - +
270A ALA* 1.3 85.4 - - - +
272A HIS* 1.3 87.9 - - + +
273A PHE 2.7 5.4 + - - -
58B TYR* 5.8 8.3 + - - -
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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