Contacts of the helix formed by residues 257 - 269 (chain A) in PDB entry 1LVO
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 SER 257 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208A TYR* 3.2 0.7 - - - -
223A SER* 5.3 1.0 + - - -
251A ALA* 4.0 8.7 - - - -
255A GLY 3.8 3.8 + - - -
256A GLN* 1.3 75.8 - - - +
258A VAL* 1.3 66.8 + - - +
259A GLU* 4.4 8.6 + - - +
260A LYS* 3.0 40.1 + - - +
261A LEU* 3.8 2.4 + - - +
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Residues in contact with VAL 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A VAL* 4.6 6.3 - - + -
208A TYR* 2.8 24.8 + - + +
241A LEU* 4.9 2.7 - - + -
244A THR* 4.0 32.5 - - + +
247A PHE* 3.4 44.6 - - + -
251A ALA* 4.4 3.7 - - + +
257A SER* 1.3 73.1 - - - +
259A GLU* 1.3 64.6 + - + +
261A LEU* 3.0 15.2 + - - +
262A LEU* 3.0 33.1 + - + -
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Residues in contact with GLU 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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223A SER* 3.5 16.1 + - - +
224A MET 3.1 36.7 + - - +
225A SER* 3.3 11.3 - - - -
226A LEU* 2.7 34.3 + - + +
244A THR* 4.9 8.1 - - + -
257A SER* 3.2 7.0 + - - +
258A VAL* 1.3 79.9 - - + +
260A LYS* 1.3 61.8 + - - +
262A LEU* 3.4 9.8 + - + -
263A ASP 3.4 7.8 + - - -
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Residues in contact with LYS 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A VAL* 5.9 1.8 - - + -
220A THR 5.0 6.4 + - - +
221A ASN* 6.2 0.8 - - - +
222A THR 3.3 27.0 + - - +
223A SER* 4.2 10.2 - - - +
255A GLY 5.0 3.8 - - - -
256A GLN* 3.2 35.1 + - + +
257A SER* 3.0 37.3 + - - +
259A GLU* 1.3 75.5 - - - +
261A LEU* 1.3 68.9 + - - +
263A ASP* 3.0 19.6 + - - +
264A SER* 3.2 8.1 + - - -
267A ARG* 5.3 0.2 + - - -
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Residues in contact with LEU 261 (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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204A VAL* 3.9 19.7 - - + +
207A LEU* 4.1 17.6 - - + +
208A TYR* 3.2 61.9 - - + +
211A LEU* 4.0 19.7 - - + -
218A PHE* 4.2 12.6 - - + -
219A VAL* 4.3 11.4 - - + -
256A GLN* 4.7 5.8 - - + +
257A SER 3.8 0.4 + - - +
258A VAL 3.0 8.9 + - - +
260A LYS* 1.3 77.9 - - - +
262A LEU* 1.3 62.5 + - - +
264A SER* 3.0 17.7 + - - +
265A ILE* 3.2 16.6 + - - +
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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
----------------------------------------------------------
204A VAL* 3.6 26.7 - - + -
224A MET* 3.9 18.4 - - + +
226A LEU* 4.0 24.5 - - + -
229A TYR* 3.8 42.4 - - + -
241A LEU* 4.7 7.9 - - + -
258A VAL* 3.0 32.6 + - + +
259A GLU* 3.6 12.3 - - + +
260A LYS 3.1 0.6 - - - -
261A LEU* 1.3 75.7 - - - +
263A ASP* 1.3 62.2 + - - +
265A ILE* 3.5 10.2 + - + +
266A VAL* 3.3 27.5 + - - +
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Residues in contact with ASP 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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222A THR* 2.5 48.8 - - - +
223A SER* 4.2 5.4 - - - -
224A MET* 3.9 28.0 - - - +
259A GLU 3.4 1.8 + - - +
260A LYS 3.0 13.9 + - - +
262A LEU* 1.3 76.7 - - - +
264A SER* 1.3 63.2 + - - +
266A VAL* 3.3 5.0 + - - +
267A ARG* 3.2 42.2 + - - +
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Residues in contact with SER 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A LEU* 4.2 13.5 - - - -
218A PHE* 2.9 35.2 + - - -
219A VAL* 4.1 5.9 - - - +
220A THR 4.8 0.5 + - - -
260A LYS 3.2 7.3 + - - -
261A LEU* 3.0 16.7 + - - +
263A ASP* 1.3 79.1 - - - +
265A ILE* 1.3 62.9 + - - +
267A ARG* 3.1 15.9 + - - +
268A LEU* 2.8 32.2 + - - +
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Residues in contact with ILE 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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200A SER 4.4 2.5 - - - +
203A VAL* 3.7 31.9 - - + -
204A VAL* 3.9 26.7 - - + +
207A LEU* 3.8 9.4 - - + -
229A TYR* 4.0 23.8 - - + +
232A TRP* 4.1 9.2 - - + -
238A PHE* 3.8 31.2 - - + -
261A LEU 3.2 11.2 + - - +
262A LEU* 3.6 9.4 - - - +
263A ASP 3.3 0.2 - - - -
264A SER* 1.3 77.0 - - - +
266A VAL* 1.3 65.4 + - - +
268A LEU* 3.1 11.1 + - - +
269A ASN* 3.2 13.5 + - - +
283A LEU* 4.2 8.7 - - + +
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Residues in contact with VAL 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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224A MET* 3.4 30.7 - - + -
229A TYR* 3.7 13.7 - - + -
232A TRP* 3.8 40.4 - - + +
262A LEU 3.3 15.7 - - - +
263A ASP* 3.3 7.8 + - - +
264A SER 3.3 0.4 - - - -
265A ILE* 1.3 79.8 - - - +
267A ARG* 1.3 66.7 + - + +
269A ASN* 3.8 12.5 - - - +
270A LYS* 4.4 7.6 - - - +
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Residues in contact with ARG 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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218A PHE 4.3 8.5 + - - -
220A THR* 2.3 39.9 + - - +
222A THR* 5.0 3.2 + - - +
260A LYS 5.3 0.2 + - - -
263A ASP* 3.2 41.5 + - - +
264A SER* 3.1 23.2 + - - +
266A VAL* 1.3 82.7 - - + +
268A LEU* 1.3 70.5 + - + +
270A LYS* 4.2 13.2 + - - +
271A GLY 4.3 4.2 - - - +
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Residues in contact with LEU 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A LEU* 4.8 2.5 - - + -
217A TRP* 3.7 27.1 - - + -
218A PHE* 3.8 27.8 - - + +
264A SER* 2.8 28.6 + - - +
265A ILE 3.1 0.2 + - - -
267A ARG* 1.3 82.3 - - + +
269A ASN* 1.3 56.3 + - - +
270A LYS 3.0 3.4 - - - -
271A GLY* 2.7 38.1 + - - +
272A PHE* 3.6 23.8 - - + -
275A ARG* 5.5 1.3 - - - +
277A ILE* 3.8 20.2 - - + -
283A LEU* 4.1 19.7 - - + -
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Residues in contact with ASN 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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232A TRP* 3.9 23.8 - - + -
236A ASN* 4.5 13.3 - - - +
238A PHE* 3.5 24.1 - - - -
265A ILE 3.2 10.2 + - - +
266A VAL 3.8 13.2 - - - +
268A LEU* 1.3 75.2 - - - +
270A LYS* 1.3 67.4 + - + +
271A GLY 3.3 1.0 + - - -
283A LEU* 4.1 9.4 - - + +
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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