Contacts of the helix formed by residues 279 - 292 (chain D) in PDB entry 2G1T
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 279 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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296A PRO* 3.9 11.7 - - - +
316A GLU* 3.9 4.5 - - - +
318A MET* 5.2 1.7 - - - +
376A LEU* 3.6 26.3 - - + +
378A LYS* 3.0 37.0 + - - +
277D THR 4.2 2.2 - - - +
278D MET* 1.3 76.7 - - - +
280D VAL* 1.3 66.7 + - - +
281D GLU* 3.4 5.6 - - + +
282D GLU* 2.9 33.4 + - + +
283D PHE* 3.0 22.3 + - - +
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Residues in contact with VAL 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A PRO* 4.2 11.8 - - + +
297A ASN* 5.2 5.4 - - - +
342A TYR* 6.1 0.7 - - - +
226D GLY 5.3 7.2 - - - +
227D HIS* 4.0 22.2 - - + -
278D MET 3.9 0.4 + - - -
279D GLU* 1.3 71.8 - - - +
281D GLU* 1.3 64.5 + - - +
283D PHE* 3.2 2.4 + - - +
284D LEU* 2.9 38.0 + - + +
306D THR* 3.7 31.0 - - - +
309D PRO* 5.7 0.4 - - + -
311D PHE* 3.9 25.6 - - + -
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Residues in contact with GLU 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342A TYR* 4.6 8.4 + - - +
373A GLU 5.9 0.2 - - - -
374A ASN* 3.4 41.4 + - - +
227D HIS* 5.5 12.1 - - + +
228D MET* 4.6 15.8 + - - +
229D SER 6.3 0.4 - - - +
230D PRO* 5.5 18.6 - - + +
232D TYR* 5.3 0.5 + - - -
279D GLU* 3.4 4.5 - - + +
280D VAL* 1.3 79.9 - - - +
282D GLU* 1.3 62.7 + - - +
284D LEU* 3.4 7.0 + - + +
285D LYS* 3.0 23.8 + - - +
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Residues in contact with GLU 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277D THR 4.6 0.2 - - - +
278D MET* 3.4 27.3 - - + +
279D GLU* 2.9 58.5 + - + +
281D GLU* 1.3 74.1 - - - +
283D PHE* 1.3 65.3 + - - +
285D LYS* 3.4 9.0 + - - +
286D GLU* 3.1 23.4 + - - +
389D THR* 4.5 7.2 + - - +
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Residues in contact with PHE 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273D LEU* 3.9 9.0 - - + -
278D MET* 3.8 13.2 - - - -
279D GLU 3.0 19.0 + - - +
280D VAL 3.2 2.4 + - - +
282D GLU* 1.3 78.4 - - - +
284D LEU* 1.3 62.4 + - + +
286D GLU* 3.3 4.6 + - - +
287D ALA* 2.8 28.9 + - + +
304D VAL* 4.0 18.6 - - + -
306D THR* 3.6 32.3 - - + -
311D PHE* 3.4 35.0 - + + -
313D ILE* 3.4 26.7 - - + -
387D LEU* 3.6 47.4 - - + +
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Residues in contact with LEU 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227D HIS* 3.6 32.8 - - + +
230D PRO 4.7 0.9 - - - +
232D TYR* 3.7 19.0 + - + +
235D TRP* 3.7 14.9 - - + -
236D GLU* 3.6 16.2 - - + +
280D VAL* 2.9 34.3 + - + +
281D GLU* 3.8 6.1 - - + +
283D PHE* 1.3 85.4 - - + +
285D LYS* 1.3 60.8 + - - +
287D ALA* 3.7 2.8 - - - +
288D ALA* 2.8 29.8 + - - +
304D VAL* 3.8 29.2 - - + -
306D THR* 4.0 6.1 - - + +
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Residues in contact with LYS 285 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232D TYR* 4.0 13.8 + - - +
281D GLU 3.0 17.6 + - - +
282D GLU* 3.7 9.0 - - - +
284D LEU* 1.3 77.1 - - - +
286D GLU* 1.3 63.9 + - - +
288D ALA* 3.3 16.0 + - - +
289D VAL* 3.6 12.5 + - + +
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Residues in contact with GLU 286 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278D MET* 4.6 3.4 - - + -
282D GLU 3.1 13.6 + - - +
283D PHE 3.6 6.7 - - - +
285D LYS* 1.3 75.6 - - - +
287D ALA* 1.3 65.0 + - - +
289D VAL* 3.0 31.3 + - - +
290D MET* 3.4 11.2 + - - +
359D PHE* 5.1 3.5 - - - -
383D GLY 5.1 0.3 - - - +
386D ARG* 3.2 56.6 + - + +
387D LEU* 3.6 20.0 - - + -
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Residues in contact with ALA 287 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235D TRP* 3.8 20.2 - - + -
283D PHE* 2.8 22.6 + - + +
284D LEU* 3.3 7.2 + - - +
286D GLU* 1.3 76.8 - - - +
288D ALA* 1.3 62.0 + - - +
290D MET* 3.1 10.9 + - - +
291D LYS* 2.9 23.2 + - - +
301D LEU* 3.6 7.2 - - + +
304D VAL* 4.4 13.7 - - + -
387D LEU* 3.9 14.3 - - + +
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Residues in contact with ALA 288 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232D TYR* 3.7 25.6 - - + +
235D TRP* 3.6 13.7 - - + -
284D LEU 2.8 14.5 + - - +
285D LYS* 3.4 12.3 - - - +
286D GLU 3.1 0.4 - - - -
287D ALA* 1.3 77.2 - - - +
289D VAL* 1.3 61.0 + - + +
291D LYS* 3.3 14.3 + - - +
292D GLU* 3.5 14.6 + - - +
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Residues in contact with VAL 289 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285D LYS* 3.7 15.0 - - + +
286D GLU* 3.0 19.7 + - - +
288D ALA* 1.3 74.8 - - + +
290D MET* 1.3 64.6 + - - +
292D GLU* 3.2 19.9 + - + +
293D ILE* 3.7 9.7 - - + +
359D PHE* 3.9 23.8 - - + -
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Residues in contact with MET 290 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286D GLU* 3.8 11.4 - - - +
287D ALA* 3.1 10.7 + - - +
289D VAL* 1.3 74.6 - - - +
291D LYS* 1.3 65.1 + - - +
293D ILE* 3.0 29.7 + - - +
301D LEU* 4.0 30.3 + - + +
313D ILE* 5.3 5.2 - - + -
315D THR* 6.3 0.9 - - + -
359D PHE* 3.7 22.7 - - + -
381D ASP* 6.2 2.0 - - - -
382D PHE* 4.2 30.0 - - + +
383D GLY 4.6 6.3 - - - +
384D LEU* 5.5 4.3 - - + -
387D LEU* 3.5 42.4 - - + -
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Residues in contact with LYS 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235D TRP* 3.5 52.0 - - + +
287D ALA 2.9 12.9 + - - +
288D ALA* 3.4 15.0 - - - +
289D VAL 3.2 0.4 - - - -
290D MET* 1.3 76.8 - - - +
292D GLU* 1.3 67.2 + - - +
293D ILE 3.2 2.9 + - - +
294D LYS* 3.6 22.2 - - - +
300D GLN* 4.1 16.3 + - - +
301D LEU* 3.2 45.6 + - + +
302D LEU* 3.8 10.4 + - - +
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Residues in contact with GLU 292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288D ALA 3.6 13.7 - - - +
289D VAL* 3.2 12.5 + - + +
290D MET 3.1 1.0 - - - -
291D LYS* 1.3 85.5 - - - +
293D ILE* 1.3 61.6 + - + +
294D LYS* 3.1 29.0 + - - +
353D TYR* 3.3 9.5 + - - -
357D LYS* 5.2 2.9 - - - +
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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