Contacts of the helix formed by residues 257 - 269 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253E TRP* 2.9 38.6 + - + +
254E GLY* 2.8 12.9 + - - -
256E ASP* 1.3 102.1 - - + +
258E GLU* 1.3 64.0 + - - +
259E LYS* 3.2 3.6 - - - +
260E ASP* 3.0 35.7 + - + +
261E ALA 3.2 8.7 + - - -
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Residues in contact with GLU 258 (chain E).
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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250E ILE* 3.8 15.8 - - + +
254E GLY 3.8 3.7 + - - -
255E LYS 4.2 3.1 + - - +
256E ASP 3.7 2.2 - - - -
257E HIS* 1.3 75.1 - - - +
259E LYS* 1.3 64.1 + - - +
261E ALA* 3.1 9.7 + - - +
262E PHE* 3.0 55.8 + - + -
278E SER 4.1 11.6 - - - +
280E SER* 4.1 13.0 + - - -
281E TYR* 3.6 36.7 + - + +
282E ASP 5.1 3.2 + - - +
285E ASN* 4.8 9.9 + - - -
286E ALA* 4.6 8.7 - - - +
290E ILE* 4.8 6.0 - - + +
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Residues in contact with LYS 259 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257E HIS* 3.2 1.5 - - - -
258E GLU* 1.3 79.1 - - - +
260E ASP* 1.3 74.5 + - - +
262E PHE* 3.3 2.5 + - - +
263E GLU* 2.9 36.7 + - - +
290E ILE* 4.1 26.3 - - + +
294E ASP* 3.5 38.4 - - + +
295E LEU* 3.7 20.7 - - + +
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Residues in contact with ASP 260 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253E TRP* 3.9 21.9 - - + -
257E HIS* 3.0 34.2 + - + +
259E LYS* 1.3 95.7 + - - +
261E ALA* 1.3 56.1 + - - +
263E GLU* 3.9 10.0 - - - +
264E HIS* 2.9 31.7 + - - +
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Residues in contact with ALA 261 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249E THR 4.2 0.9 - - - +
250E ILE* 3.9 28.3 - - + +
253E TRP* 3.5 41.4 - - + +
257E HIS 3.2 6.7 + - - +
258E GLU 3.1 9.3 + - - +
260E ASP* 1.3 74.5 - - - +
262E PHE* 1.3 66.8 + - - +
264E HIS* 3.2 1.9 + - - +
265E ILE* 2.9 31.8 + - - +
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Residues in contact with PHE 262 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250E ILE* 3.9 10.8 - - + -
258E GLU* 3.0 48.2 + - + -
259E LYS 3.4 8.1 - - - +
261E ALA* 1.3 76.5 - - - +
263E GLU* 1.3 62.9 + - - +
265E ILE* 3.9 4.1 - - - +
266E VAL* 3.1 30.5 + - - +
276E VAL* 3.8 15.5 - - + -
277E VAL 3.8 16.2 - - - -
278E SER* 4.0 19.3 - - - -
286E ALA* 3.9 11.7 - - + -
290E ILE* 3.3 28.5 - - + -
291E TRP* 3.3 36.3 - + + -
295E LEU* 3.5 11.7 - - + -
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Residues in contact with GLU 263 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259E LYS* 2.9 26.6 + - - +
260E ASP* 3.9 10.4 - - - +
262E PHE* 1.3 74.7 - - - +
264E HIS* 1.3 62.9 + - - +
266E VAL* 3.4 7.8 - - - +
267E THR* 2.6 37.6 + - - +
295E LEU* 3.6 20.4 - - + +
297E HIS* 5.0 3.8 + - - -
298E LEU* 3.6 26.7 - - + +
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Residues in contact with HIS 264 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D LYS 2.9 32.8 + - - -
25D GLN* 3.8 7.0 + - - -
26D TYR 3.9 14.0 + - - -
28D PRO* 4.3 16.6 - - + +
253E TRP* 3.3 31.7 - + + -
260E ASP 2.9 19.7 + - - +
261E ALA 3.7 1.3 - - - +
263E GLU* 1.3 77.9 - - - +
265E ILE* 1.3 59.3 + - - +
267E THR* 3.8 4.9 - - - -
268E GLN* 3.0 53.3 + - + +
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Residues in contact with ILE 265 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D GLN* 3.9 35.2 - - + +
245E ALA* 4.0 4.9 - - + -
249E THR* 3.5 35.2 - - + +
250E ILE* 3.5 21.3 - - + -
261E ALA 2.9 21.3 + - - +
262E PHE* 3.9 3.8 - - - +
264E HIS* 1.3 75.5 - - - +
266E VAL* 1.3 66.0 + - - +
267E THR 3.1 1.3 - - - -
268E GLN* 3.3 4.1 + - - -
269E PHE* 3.1 27.4 + - + +
274E VAL* 4.1 21.5 - - + -
276E VAL* 4.2 13.5 - - + -
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Residues in contact with VAL 266 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262E PHE 3.1 15.6 + - - +
263E GLU* 3.4 15.0 - - - +
265E ILE* 1.3 76.7 - - - +
267E THR* 1.3 64.4 + - - +
270E SER* 3.1 17.8 + - - -
274E VAL* 4.6 2.2 - - + -
276E VAL* 4.3 7.0 - - + -
291E TRP* 3.6 31.0 - - + -
295E LEU* 5.5 0.7 - - + -
298E LEU* 4.3 22.2 - - + +
299E ILE* 4.6 5.8 - - + -
302E ARG* 3.0 36.6 + - - +
308E LEU* 4.1 14.6 - - + -
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Residues in contact with THR 267 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263E GLU* 2.6 33.0 + - - +
264E HIS* 3.8 5.4 - - - -
266E VAL* 1.3 80.8 - - - +
268E GLN* 1.3 65.5 + - - +
269E PHE 3.5 0.2 + - - -
270E SER* 3.7 18.7 + - - -
298E LEU* 4.4 7.4 - - - +
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Residues in contact with GLN 268 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D LYS* 2.9 63.6 + - - +
264E HIS* 3.0 43.1 + - + +
265E ILE* 3.3 6.3 + - - +
267E THR* 1.3 79.4 - - + +
269E PHE* 1.3 76.1 + - + +
270E SER* 3.8 1.4 + - - -
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Residues in contact with PHE 269 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D THR* 3.8 15.5 - - - -
24D LYS* 3.5 41.3 - - + -
25D GLN* 3.6 28.7 - - + -
93D ASP* 6.1 0.2 - - - -
95D VAL* 4.2 14.6 - - + -
243E PRO* 3.6 27.6 - - + -
265E ILE* 3.1 20.1 + - + +
266E VAL 3.2 3.8 - - - -
268E GLN* 1.3 84.4 - - + +
270E SER* 1.3 54.1 + - - +
271E SER 3.4 3.1 - - - +
272E VAL* 3.4 25.4 - - + +
274E VAL* 4.0 21.7 - - + +
302E ARG* 2.5 25.3 + - - -
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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