Contacts of the helix formed by residues 259 - 270 (chain A) in PDB entry 2GWU
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 259 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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256A LYS* 2.6 45.8 + - - +
258A LEU* 1.3 76.1 - - - +
260A GLU* 1.3 58.2 + - - +
261A GLU* 2.9 9.9 - - - +
262A GLU* 2.8 45.2 + - - +
263A ILE* 3.6 9.4 + - - +
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Residues in contact with GLU 260 (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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237A PHE* 5.4 1.6 - - - +
256A LYS 3.6 1.6 - - - +
257A THR* 2.6 29.6 - - - +
258A LEU 3.3 2.0 + - - -
259A SER* 1.3 73.1 - - - +
261A GLU* 1.3 64.3 + - - +
262A GLU 3.1 0.9 - - - -
263A ILE* 2.7 29.9 - - - +
264A GLU* 2.8 8.2 + - - +
284A GLY* 4.1 9.8 - - - +
287A PHE* 2.7 48.0 - - + +
288A PHE* 2.9 50.4 - - + +
290A ILE 4.7 1.9 - - - +
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Residues in contact with GLU 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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259A SER* 4.4 6.7 - - - -
260A GLU* 1.3 80.7 - - - +
262A GLU* 1.3 75.1 + - - +
264A GLU* 3.2 16.7 - - - +
265A LYS* 3.0 35.7 + - + +
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Residues in contact with GLU 262 (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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255A PHE* 3.9 20.9 - - + -
256A LYS* 4.9 4.3 - - - +
259A SER* 2.8 34.5 + - - +
260A GLU 3.1 0.2 - - - -
261A GLU* 1.3 92.0 - - - +
263A ILE* 1.4 64.9 + - - +
265A LYS* 2.9 26.4 + - - +
266A VAL* 3.0 15.9 + - - +
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Residues in contact with ILE 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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234A LEU* 5.4 5.5 - - + +
236A GLY 3.8 10.1 - - - +
237A PHE* 4.1 4.7 - - - -
255A PHE* 3.9 23.1 - - + -
259A SER 3.9 10.1 - - - +
260A GLU* 2.7 22.1 + - - +
262A GLU* 1.4 75.9 - - - +
264A GLU* 1.3 89.7 + - + +
266A VAL* 3.0 11.5 + - - +
267A LEU* 2.9 24.1 + - + +
283A HIS* 4.9 3.1 - - + +
287A PHE* 2.9 71.1 - - + -
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Residues in contact with GLU 264 (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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260A GLU 2.8 11.7 + - - +
261A GLU* 3.2 22.2 - - - +
263A ILE* 1.3 83.3 - - - +
265A LYS* 1.3 66.2 + - + +
267A LEU* 3.1 6.5 + - - +
268A LYS* 3.0 21.5 + - - +
275A LEU* 3.0 34.6 - - + +
283A HIS* 3.2 40.8 + - - +
284A GLY* 4.5 11.0 + - - -
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Residues in contact with LYS 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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261A GLU* 3.0 31.6 + - + +
262A GLU* 2.9 25.1 + - - +
264A GLU* 1.3 80.6 - - + +
266A VAL* 1.3 52.9 + - + +
268A LYS* 5.0 7.6 - - - +
269A ASN* 2.6 67.3 + - - +
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Residues in contact with VAL 266 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232A HIS* 4.7 2.9 - - - +
234A LEU* 5.2 7.6 - - + -
239A LEU* 5.0 3.8 - - + -
255A PHE* 2.9 48.7 - - + -
262A GLU 3.0 7.5 + - - +
263A ILE* 3.0 8.0 + - - +
265A LYS* 1.3 75.2 - - + +
267A LEU* 1.3 62.7 + - - +
269A ASN* 4.9 0.4 - - - -
270A ILE* 2.8 53.5 + - + +
271A PHE* 2.9 28.0 + - + -
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Residues in contact with LEU 267 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A LEU* 3.0 31.9 - - + -
223A CYS* 3.5 25.4 - - - -
263A ILE* 2.9 15.1 + - + +
264A GLU* 3.1 11.4 + - - +
266A VAL* 1.3 76.1 - - - +
268A LYS* 1.3 60.5 + - - +
271A PHE* 3.0 29.3 - - + +
273A ILE* 3.0 46.2 + - + -
275A LEU* 3.0 25.6 - - + -
283A HIS* 3.6 13.5 - - + +
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Residues in contact with LYS 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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63A ASN* 5.6 0.4 - - - -
264A GLU 3.0 13.9 + - - +
265A LYS* 4.0 8.7 - - - +
267A LEU* 1.3 77.7 - - - +
269A ASN* 1.3 69.8 + - - +
272A ASN* 2.8 38.0 - - - +
273A ILE 2.9 28.0 - - - +
274A SER* 4.0 17.7 - - - +
275A LEU* 4.2 18.3 - - + +
276A GLN* 5.0 10.6 + - - +
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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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265A LYS* 2.6 58.6 + - - +
268A LYS* 1.3 86.1 - - - +
270A ILE* 1.4 71.7 + - + +
272A ASN* 3.7 8.7 + - - +
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Residues in contact with ILE 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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225A LEU* 5.0 8.2 - - + +
232A HIS* 3.8 31.9 - - + +
239A LEU* 5.8 2.7 - - + -
255A PHE* 6.1 0.2 - - + -
266A VAL* 2.8 38.1 + - + +
269A ASN* 1.4 79.6 - - + +
271A PHE* 1.3 61.0 + - - +
272A ASN* 4.6 1.7 - - - +
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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