Contacts of the helix formed by residues 280 - 296 (chain B) in PDB entry 2GQ3
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 ASP 280 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B VAL* 1.3 87.4 - - + +
281B ALA* 1.3 62.3 + - - +
282B ALA* 3.7 9.1 + - - +
283B ASP* 3.0 39.1 + - - +
284B LYS* 3.1 22.3 + - - +
347B ASN* 3.6 9.7 - - - +
348B ASP* 3.5 18.6 - - - +
719B ARG* 5.4 4.2 - - + +
722B LYS* 5.0 10.4 - - - +
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Residues in contact with ALA 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ALA* 3.8 21.8 - - + -
15B VAL* 4.1 11.4 - - + -
16B LEU* 4.8 5.6 - - + -
280B ASP* 1.3 72.7 - - - +
282B ALA* 1.3 56.4 + - - +
284B LYS* 3.8 1.3 - - - +
285B VAL* 2.7 38.1 + - - +
347B ASN* 4.2 0.8 + - - -
348B ASP* 3.9 6.0 + - - +
349B ALA* 3.6 32.8 - - + -
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Residues in contact with ALA 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B VAL* 3.8 20.8 - - + +
280B ASP* 3.4 10.5 + - - +
281B ALA* 1.3 77.1 - - - +
283B ASP* 1.3 62.6 + - - +
285B VAL* 3.8 2.3 - - - +
286B LEU* 2.9 32.7 + - + +
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Residues in contact with ASP 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B LEU* 3.4 9.9 - - + +
277B ALA 4.5 5.1 - - - +
278B ALA* 3.4 29.1 + - + -
279B VAL* 3.0 24.6 + - - +
280B ASP* 3.0 27.8 + - - +
282B ALA* 1.3 78.1 - - - +
284B LYS* 1.3 56.4 + - - +
286B LEU* 3.1 15.0 + - - +
287B GLY 3.0 24.4 + - - -
718B ARG* 5.3 6.7 + - - +
6000B EPE 4.4 16.7 + - - -
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Residues in contact with LYS 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LEU* 6.1 0.7 - - + -
272B PHE* 4.0 24.0 + - - -
278B ALA* 4.5 13.3 + - + +
280B ASP 3.1 9.1 + - - +
281B ALA* 3.8 7.0 - - - +
283B ASP* 1.3 79.4 - - - +
285B VAL* 1.3 56.9 + - + +
287B GLY* 3.2 3.1 + - - +
288B TYR* 2.8 64.2 + - + +
341B VAL* 4.0 7.7 - - - +
347B ASN* 3.8 24.5 - - - +
349B ALA* 4.8 6.7 - - + -
360B GLU* 2.7 34.6 + - + +
363B MET* 5.5 3.8 - - + -
364B ASP* 3.2 32.4 + - - +
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Residues in contact with VAL 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B VAL* 3.6 36.8 - - + +
16B LEU* 3.6 29.8 - - + -
19B PHE* 4.1 15.2 - - + -
281B ALA 2.7 23.1 + - - +
282B ALA 4.0 2.2 - - - +
284B LYS* 1.3 70.2 - - + +
286B LEU* 1.3 61.7 + - - +
288B TYR* 3.9 3.9 - - - +
289B ARG* 2.8 57.0 + - - +
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Residues in contact with LEU 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B LEU* 3.6 37.5 - - + +
282B ALA* 2.9 16.2 + - + +
283B ASP* 3.1 16.4 + - - +
285B VAL* 1.3 79.3 - - - +
287B GLY* 1.3 62.9 + - - +
289B ARG* 3.5 10.1 + - - +
290B ASN* 3.4 27.3 + - - +
6000B EPE 4.0 33.4 - - - +
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Residues in contact with GLY 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B VAL* 4.0 8.1 - - - +
122B LEU* 3.2 19.5 - - - +
272B PHE* 3.5 22.3 - - - -
283B ASP 3.0 11.9 + - - -
284B LYS 3.2 2.9 + - - -
286B LEU* 1.3 75.0 - - - +
288B TYR* 1.3 65.2 + - - +
289B ARG 3.3 0.3 + - - -
290B ASN* 3.3 5.9 + - - +
291B TRP 3.1 17.2 + - - -
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Residues in contact with TYR 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LEU* 4.0 22.9 - - + -
19B PHE* 3.4 21.1 - + + -
272B PHE* 3.6 21.1 - + - -
284B LYS* 2.8 47.6 + - + +
285B VAL* 3.9 3.6 - - - +
287B GLY* 1.3 70.8 - - - +
289B ARG* 1.4 58.3 + - - +
291B TRP 3.2 1.6 + - - -
292B LEU* 2.8 26.5 + - - +
363B MET* 3.8 4.2 - - - +
364B ASP* 2.8 33.6 + - - -
367B PHE* 3.5 40.8 - + + -
368B THR* 3.9 21.1 - - + -
371B ILE* 3.1 17.6 - - + +
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Residues in contact with ARG 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B VAL 5.8 0.2 + - - -
19B PHE* 3.5 17.2 - - + +
23B GLU* 2.9 38.6 + - - +
285B VAL* 2.8 44.4 + - - +
286B LEU* 3.9 10.4 - - - +
287B GLY 3.2 0.4 - - - -
288B TYR* 1.4 76.5 - - - +
290B ASN* 1.3 55.2 + - - +
292B LEU* 3.3 5.0 + - + +
293B GLY* 2.8 30.5 + - - -
299B LEU* 4.9 1.5 - - + +
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Residues in contact with ASN 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B VAL* 2.7 31.0 + - + +
122B LEU* 3.3 23.6 + - - +
124B ALA* 3.7 19.7 - - - +
127B ALA* 5.7 0.4 - - + -
286B LEU* 3.4 13.6 + - - +
287B GLY 3.3 6.7 + - - +
289B ARG* 1.3 78.5 - - - +
291B TRP* 1.3 66.8 + - - +
293B GLY* 3.4 1.4 + - - -
294B LEU* 2.9 30.6 + - + +
299B LEU* 3.7 26.7 - - + +
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Residues in contact with TRP 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B VAL* 4.1 3.6 - - + +
270B MET* 3.6 39.0 - - + -
272B PHE* 3.9 15.0 - + + -
287B GLY 3.1 13.3 + - - +
288B TYR 3.7 5.4 - - - +
290B ASN* 1.3 74.8 - - - +
292B LEU* 1.3 56.2 + - - +
294B LEU* 3.1 11.3 + - + +
295B ASN* 2.9 61.3 + - - +
336B MET* 3.9 27.6 - - + -
337B PHE 4.0 3.8 - - - -
338B VAL* 3.6 34.3 - - + -
368B THR* 3.1 35.5 + - + -
371B ILE* 3.5 29.5 - - + +
372B ALA* 4.1 10.9 - - + +
387B ASN* 5.1 2.2 - - - -
393B ILE* 5.8 1.8 - - + -
394B TYR 5.4 1.3 - - - -
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Residues in contact with LEU 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B PHE* 3.6 27.1 - - + -
23B GLU* 3.7 31.0 - - + +
24B ALA* 4.2 2.2 - - - +
288B TYR 2.8 13.6 + - - +
289B ARG* 3.3 10.1 - - + +
291B TRP* 1.3 73.6 - - - +
293B GLY* 1.3 56.0 + - - +
295B ASN 3.1 0.9 + - - -
296B LYS* 2.8 50.2 + - + +
371B ILE* 3.1 26.2 - - + +
374B HIS* 3.5 33.2 - - + +
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Residues in contact with GLY 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289B ARG 2.8 17.3 + - - -
290B ASN 3.4 4.2 + - - -
292B LEU* 1.3 73.4 - - - +
294B LEU* 1.3 56.8 + - - +
297B GLY 3.1 4.5 + - - -
298B ASP* 3.0 28.4 + - - -
299B LEU* 2.9 37.8 + - - +
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Residues in contact with LEU 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B VAL* 4.5 3.8 - - + -
127B ALA* 4.2 11.4 - - + +
128B LEU* 4.9 0.2 - - - -
131B ALA* 4.2 11.4 - - + -
270B MET* 3.8 46.4 - - + -
290B ASN 2.9 22.4 + - - +
291B TRP* 3.3 17.7 - - + +
292B LEU 3.1 0.4 - - - -
293B GLY* 1.3 77.8 - - - +
295B ASN* 1.3 60.6 + - - +
297B GLY* 3.6 6.2 + - - -
299B LEU* 3.5 23.8 - - + -
314B LEU* 4.0 16.5 - - + +
336B MET* 3.6 29.2 - - + +
385B LEU* 3.6 12.8 - - - +
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Residues in contact with ASN 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291B TRP* 2.9 68.1 + - - +
292B LEU 4.0 2.2 - - - +
294B LEU* 1.3 75.8 - - - +
296B LYS* 1.3 65.0 + - - +
297B GLY 3.2 0.4 - - - -
336B MET* 4.1 10.9 - - - +
371B ILE* 3.5 26.0 - - + +
372B ALA* 3.9 9.8 - - - +
374B HIS* 3.1 21.9 - - + +
375B GLY* 3.4 21.7 + - - +
385B LEU* 3.9 7.7 - - - +
387B ASN* 4.4 5.5 + - - +
1003B MG 3.6 2.6 - - - -
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Residues in contact with LYS 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B GLU 4.0 13.5 + - - -
26B PRO* 4.8 6.1 + - - +
292B LEU* 2.8 32.9 + - + +
295B ASN* 1.3 77.2 - - - +
297B GLY* 1.3 59.5 + - - +
298B ASP* 3.4 25.3 + - - +
374B HIS* 3.8 32.1 - - + -
381B VAL* 3.2 28.3 + - - +
382B ASN 3.3 13.7 - - - +
383B GLY* 3.2 22.7 - - - +
384B PRO* 3.3 10.0 - - - +
385B LEU* 3.8 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
------------------------------------------------------------
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