Contacts of the helix formed by residues 288 - 302 (chain B) in PDB entry 2COG
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 GLY 288 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119B ARG* 3.7 0.9 - - - -
262B ASN* 3.2 16.8 - - - +
286B LEU* 2.8 12.2 + - - -
287B PRO* 1.3 74.6 - - - +
289B VAL* 1.3 65.6 + - - -
290B THR 3.3 1.8 - - - -
291B ARG* 3.5 6.5 + - - +
292B ARG* 3.2 21.0 + - - +
410B PLP 3.1 24.2 - - - -
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Residues in contact with VAL 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B PHE* 4.3 9.6 - - + +
112B GLN* 3.8 32.8 - - + +
115B LEU* 4.1 29.8 - - + +
116B ASN* 4.3 19.3 - - - +
119B ARG* 3.9 11.0 - - - +
287B PRO 5.1 0.7 - - - +
288B GLY* 1.3 70.3 - - - -
290B THR* 1.3 66.7 + - - +
292B ARG* 3.3 6.1 + - - +
293B CYS* 3.0 26.6 + - - -
333B THR* 5.3 4.0 - - - +
410B PLP 2.8 20.2 + - - +
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Residues in contact with THR 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B PHE* 5.7 3.5 - - + -
289B VAL* 1.3 79.1 - - - +
291B ARG* 1.3 56.5 + - - +
293B CYS* 3.1 8.2 + - - +
294B ILE* 2.9 40.4 + - + +
331B SER* 3.8 8.3 - - - -
332B GLY 3.2 25.8 - - - +
333B THR* 3.3 5.5 + - - -
336B VAL* 3.5 45.4 - - + +
369B LEU* 4.2 4.0 - - + -
410B PLP 2.8 14.8 + - - -
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Residues in contact with ARG 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B ASN* 3.4 42.4 - - + +
264B PHE* 3.8 27.6 - - + -
278B THR* 4.0 11.4 + - - +
279B PRO 3.2 25.7 + - - -
281B LEU* 3.3 36.8 - - - +
285B ILE* 4.5 3.0 - - - +
287B PRO* 5.4 1.2 - - - +
288B GLY 3.5 13.7 + - - +
290B THR* 1.3 80.5 - - - +
292B ARG* 1.3 77.2 + - - +
294B ILE 3.3 0.5 + - - -
295B LEU* 3.1 41.9 + - + +
308B GLU* 2.7 28.7 + - - -
331B SER* 4.0 2.0 + - - -
410B PLP 4.3 0.4 + - - -
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Residues in contact with ARG 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B GLN* 6.0 0.7 - - - +
115B LEU* 5.3 12.8 - - + -
281B LEU* 5.3 5.3 - - - +
288B GLY 3.2 11.0 + - - +
289B VAL* 3.7 9.6 - - - +
290B THR 3.3 0.2 - - - -
291B ARG* 1.3 89.0 - - - +
293B CYS* 1.3 60.1 + - - +
295B LEU* 3.3 37.6 + - - +
296B ASP* 2.9 52.2 + - - +
299B HIS* 4.9 7.5 + - - -
308B GLU* 3.5 20.0 + - - -
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Residues in contact with CYS 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B PHE* 3.7 30.1 - - - -
112B GLN* 3.9 18.4 - - - -
115B LEU* 5.9 0.2 - - - -
289B VAL* 3.0 20.6 + - - +
290B THR* 3.1 10.1 + - - +
292B ARG* 1.3 79.4 - - - +
294B ILE* 1.3 57.3 + - - +
296B ASP* 3.2 6.0 + - - +
297B LEU* 2.9 34.4 + - - +
369B LEU* 4.2 12.3 - - + -
381B TRP* 3.7 25.7 - - + -
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Residues in contact with ILE 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B PHE* 3.7 29.2 - - + -
276B LEU* 4.3 7.9 - - + -
290B THR* 2.9 24.1 + - + +
291B ARG 3.8 4.3 - - - +
293B CYS* 1.3 72.5 - - - +
295B LEU* 1.3 61.2 + - - +
297B LEU* 3.4 7.2 + - - +
298B ALA* 2.9 29.0 + - + +
329B PHE* 4.3 9.2 - - + -
331B SER* 3.7 30.1 - - - -
336B VAL 4.2 4.5 - - - +
337B VAL* 4.9 0.2 - - + -
365B ILE* 3.8 45.1 - - + -
369B LEU* 4.1 9.2 - - + -
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Residues in contact with LEU 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B PHE* 3.9 22.4 - - + -
276B LEU* 4.8 2.5 - - + +
278B THR* 3.9 10.8 - - + -
291B ARG* 3.1 38.7 + - - +
292B ARG* 3.5 40.6 - - - +
294B ILE* 1.3 75.5 - - - +
296B ASP* 1.3 57.6 + - - +
298B ALA* 3.8 3.4 - - - +
299B HIS* 2.8 42.2 + - + +
306B VAL* 3.7 23.1 - - + -
307B SER 5.2 2.0 - - - +
308B GLU* 3.7 20.0 - - + +
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Residues in contact with ASP 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B GLN* 5.5 0.7 - - - +
292B ARG* 2.9 47.8 + - - +
293B CYS* 3.2 8.7 + - - +
295B LEU* 1.3 75.5 - - - +
297B LEU* 1.3 63.2 + - - +
299B HIS* 3.2 9.6 + - - +
300B GLN* 3.0 25.2 + - - +
379B ARG* 5.2 2.2 - - - +
381B TRP* 3.8 26.2 + - + -
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Residues in contact with LEU 297 (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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293B CYS 2.9 23.0 + - - +
294B ILE* 3.8 7.0 - - + +
296B ASP* 1.3 72.7 - - - +
298B ALA* 1.3 63.8 + - - +
300B GLN* 3.2 15.4 - - - +
301B TRP* 3.0 45.1 + - + -
365B ILE* 4.8 6.7 - - + +
368B LYS* 3.7 36.3 - - + -
369B LEU* 3.9 27.4 - - + -
372B ILE* 4.7 0.2 - - + -
379B ARG* 3.5 27.8 - - - +
381B TRP* 3.8 15.3 - - + -
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Residues in contact with ALA 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B LEU* 4.3 14.6 - - + -
294B ILE* 2.9 19.0 + - + +
295B LEU 3.8 3.1 - - - +
297B LEU* 1.3 76.8 - - - +
299B HIS* 1.3 62.6 + - - +
301B TRP* 4.0 15.9 - - + +
302B GLY* 3.1 19.8 + - - -
303B GLU 4.6 1.2 + - - -
304B PHE* 4.0 18.8 - - + -
306B VAL* 3.6 26.1 - - + +
365B ILE* 6.2 1.8 - - + -
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Residues in contact with HIS 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B ARG* 4.9 7.9 + - - -
295B LEU* 2.8 35.1 + - + +
296B ASP* 3.5 8.3 - - - +
298B ALA* 1.3 78.1 - - - +
300B GLN* 1.3 62.0 + - - +
302B GLY* 3.3 14.0 + - - -
306B VAL* 3.5 40.8 + - + +
308B GLU* 5.3 6.3 + - - +
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Residues in contact with GLN 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B ASP 3.0 13.3 + - - +
297B LEU* 3.2 25.4 - - - +
299B HIS* 1.3 72.4 - - - +
301B TRP* 1.3 80.5 + - + +
302B GLY* 3.1 2.6 + - - -
368B LYS* 5.4 3.2 + - - +
379B ARG* 2.7 46.6 + - - +
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Residues in contact with TRP 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B LEU* 3.0 36.1 + - + +
298B ALA* 4.0 12.6 - - + +
300B GLN* 1.3 91.3 + - + +
302B GLY* 1.3 66.1 + - - +
303B GLU* 3.0 28.4 + - + +
304B PHE* 4.7 6.7 - + + -
361B LEU* 4.0 18.6 - - + -
364B ARG* 3.6 57.7 - - + +
365B ILE* 4.0 24.5 - - + -
368B LYS* 4.2 31.8 - - + +
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Residues in contact with GLY 302 (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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298B ALA 3.1 12.7 + - - -
299B HIS 3.6 11.9 - - - -
300B GLN 3.1 4.3 - - - -
301B TRP* 1.3 77.7 - - - +
303B GLU* 1.3 59.7 + - - +
304B PHE 3.4 8.0 + - - -
306B VAL* 6.2 0.2 - - - -
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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