Contacts of the helix formed by residues 257 - 269 (chain C) in PDB entry 2GVG
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 HIS 257 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253C TRP* 3.5 37.9 - - + +
254C GLY* 2.9 9.6 + - - -
256C ASP* 1.3 90.7 + - + +
258C GLU* 1.3 60.7 + - - +
259C LYS* 3.4 3.1 - - - +
260C ASP* 2.9 30.3 + - + +
261C ALA 3.4 14.4 + - - -
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Residues in contact with GLU 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250C ILE* 4.0 13.0 - - + +
254C GLY 3.6 3.0 + - - -
255C LYS 4.0 10.8 - - - +
256C ASP 3.4 4.2 + - - -
257C HIS* 1.3 75.1 - - - +
259C LYS* 1.3 66.4 + - - +
260C ASP 3.1 0.2 - - - -
261C ALA* 3.1 8.6 + - - +
262C PHE* 3.1 54.1 + - + -
278C SER* 4.7 7.3 - - - -
280C SER* 4.9 4.1 + - - -
281C TYR* 2.8 38.7 + - + +
282C ASP 5.2 2.4 + - - +
286C ALA* 4.3 10.6 - - - +
290C ILE* 4.2 14.4 - - + +
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Residues in contact with LYS 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256C ASP 4.9 7.0 - - - +
257C HIS 4.9 0.9 - - - -
258C GLU* 1.3 81.7 - - - +
260C ASP* 1.3 74.1 + - - +
262C PHE* 3.4 3.4 + - - +
263C GLU* 3.0 30.2 + - - +
290C ILE* 4.2 29.7 - - + +
294C ASP* 3.3 40.1 + - - +
295C LEU* 3.6 20.4 - - - +
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Residues in contact with ASP 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253C TRP* 3.7 21.5 - - + -
257C HIS* 2.9 41.7 + - - +
258C GLU 3.1 0.8 - - - -
259C LYS* 1.3 90.3 - - - +
261C ALA* 1.3 65.4 + - - +
263C GLU* 3.3 14.4 + - - +
264C HIS* 2.9 26.2 + - - +
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Residues in contact with ALA 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249C THR 4.2 0.9 - - - +
250C ILE* 3.9 28.7 - - + +
253C TRP* 3.7 40.3 - - + +
257C HIS 3.4 4.6 + - - +
258C GLU 3.1 10.9 + - - +
260C ASP* 1.3 78.6 - - - +
262C PHE* 1.3 64.3 + - - +
264C HIS* 3.3 1.6 + - - +
265C ILE* 3.0 29.8 + - - +
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Residues in contact with PHE 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250C ILE* 3.7 28.7 - - + -
258C GLU* 3.1 42.3 + - + -
259C LYS 3.5 8.1 - - - +
261C ALA* 1.3 80.3 - - - +
263C GLU* 1.3 56.6 + - - +
265C ILE* 3.3 4.8 + - - +
266C VAL* 2.9 36.2 + - - +
276C VAL* 3.9 9.9 - - + -
277C VAL 4.0 3.1 - - - -
278C SER* 3.5 23.6 - - - -
286C ALA* 4.5 3.4 - - + -
290C ILE* 3.5 28.5 - - + -
291C TRP* 3.2 46.4 - + + -
295C LEU* 3.6 5.8 - - + -
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Residues in contact with GLU 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259C LYS* 3.0 17.7 + - - +
260C ASP* 3.7 13.8 - - - +
262C PHE* 1.3 76.7 - - - +
264C HIS* 1.3 64.7 + - - +
266C VAL* 3.1 8.7 - - - +
267C THR* 2.9 33.6 + - - +
295C LEU* 3.9 20.2 - - + +
297C HIS* 4.7 6.2 + - - -
298C LEU* 3.4 27.0 - - + +
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Residues in contact with HIS 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A LYS 2.9 30.2 + - - -
25A GLN* 4.3 6.4 + - - -
26A TYR 4.4 5.8 + - - -
28A PRO* 4.4 18.8 - - + +
253C TRP* 3.4 40.7 - + + -
260C ASP 2.9 13.1 + - - +
261C ALA 3.6 1.6 - - - +
263C GLU* 1.3 75.2 - - - +
265C ILE* 1.3 60.9 + - - +
267C THR* 3.4 5.3 + - - -
268C GLN* 2.9 50.0 + - + +
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Residues in contact with ILE 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A GLN* 4.1 28.9 - - + +
245C ALA* 3.7 9.2 - - + +
249C THR* 3.1 34.3 - - + +
250C ILE* 3.6 20.9 - - + -
261C ALA 3.0 16.6 + - - +
262C PHE* 3.7 3.8 - - - +
264C HIS* 1.3 74.2 - - - +
266C VAL* 1.3 66.0 - - - +
267C THR 3.0 1.5 + - - -
268C GLN* 3.2 4.4 + - - -
269C PHE* 3.0 32.8 + - + +
274C VAL* 3.8 22.7 - - + -
276C VAL* 4.1 12.3 - - + -
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Residues in contact with VAL 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262C PHE 2.9 18.8 + - - +
263C GLU* 3.1 18.8 - - - +
265C ILE* 1.3 73.9 - - - +
267C THR* 1.3 60.3 + - - +
269C PHE 3.2 11.3 - - - -
270C SER* 3.2 5.2 + - - -
274C VAL* 4.6 2.0 - - + -
276C VAL* 4.3 6.5 - - + -
291C TRP* 3.5 29.8 - - + -
298C LEU* 4.1 25.6 - - + +
299C ILE* 6.0 1.3 - - + -
302C ARG* 2.5 37.6 + - - +
308C LEU* 4.0 17.9 - - + -
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Residues in contact with THR 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263C GLU* 2.9 30.5 + - - +
264C HIS* 3.5 5.8 - - - +
266C VAL* 1.3 78.4 - - - +
268C GLN* 1.3 69.1 - - + +
269C PHE 3.1 2.1 + - - -
270C SER* 3.3 22.4 + - - -
298C LEU* 4.6 8.5 - - - +
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Residues in contact with GLN 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A LYS* 2.9 42.7 + - - +
264C HIS* 2.9 46.9 + - + +
265C ILE* 3.6 5.4 - - - +
267C THR* 1.3 79.2 - - + +
269C PHE* 1.3 82.6 + - + +
270C SER* 3.9 1.4 + - - -
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Residues in contact with PHE 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A THR* 3.6 19.1 - - - -
24A LYS* 3.6 31.4 - - + -
25A GLN* 4.0 25.6 - - + -
95A VAL* 4.0 14.1 - - + -
243C PRO* 3.5 31.4 - - + -
265C ILE* 3.0 24.9 + - + +
266C VAL 3.2 4.0 - - - -
268C GLN* 1.3 91.9 - - + +
270C SER* 1.3 54.4 + - - +
271C SER 3.4 2.7 - - - +
272C VAL* 3.2 25.8 - - + +
274C VAL* 3.9 13.0 - - + +
302C ARG* 2.8 27.2 + - - -
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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