Contacts of the helix formed by residues 312 - 321 (chain B) in PDB entry 2COJ
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 THR 312 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252B ASP* 3.2 43.7 - - + +
253B HIS 3.6 4.7 - - - -
254B GLN* 4.2 8.3 - - + -
255B ILE* 4.2 5.5 - - - +
310B TYR* 5.4 2.9 - - + -
311B LEU* 1.3 79.2 - - - +
313B MET* 1.3 65.8 + - - +
314B ASP* 3.4 8.9 + - - +
315B ASP* 2.8 44.7 + - - +
316B LEU* 3.0 12.0 + - - +
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Residues in contact with MET 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B LEU* 3.9 15.3 - - - -
248B LEU* 4.1 10.8 - - + -
252B ASP 4.5 0.6 + - - -
253B HIS* 3.3 19.7 + - + +
255B ILE* 3.7 21.7 - - - +
312B THR* 1.3 72.5 - - - +
314B ASP* 1.3 54.8 + - - +
316B LEU* 3.1 12.7 + - + +
317B THR* 2.7 44.7 + - + +
343B ILE* 4.2 13.5 - - + -
345B TYR* 3.4 71.6 - - + +
350B ILE* 4.4 9.0 - - + -
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Residues in contact with ASP 314 (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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252B ASP 5.2 4.7 + - - +
253B HIS* 5.3 8.1 - - - -
312B THR* 3.1 8.0 + - - +
313B MET* 1.3 75.2 - - - +
315B ASP* 1.3 62.8 + - - +
317B THR* 3.6 10.7 + - - -
318B THR* 2.6 37.8 + - - +
345B TYR* 6.0 2.1 - - - -
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Residues in contact with ASP 315 (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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265B LEU* 6.2 0.4 - - + -
267B TRP* 3.4 20.1 - - + -
270B GLU* 4.0 17.1 - - - +
309B ARG* 3.8 13.4 + - - -
310B TYR 4.0 1.7 - - - +
311B LEU* 3.8 7.6 - - + -
312B THR* 2.8 43.5 + - - +
314B ASP* 1.3 77.4 - - - +
316B LEU* 1.3 58.0 + - - +
318B THR* 4.0 3.5 - - - +
319B ALA* 3.1 27.9 + - - +
324B ARG* 4.9 1.0 + - - -
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Residues in contact with LEU 316 (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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255B ILE* 3.7 15.9 - - + -
265B LEU* 4.3 12.3 - - + +
267B TRP* 4.9 1.8 - - - -
312B THR 3.0 9.8 + - - +
313B MET* 3.4 15.0 - - + +
315B ASP* 1.3 75.2 - - - +
317B THR* 1.3 63.5 + - + +
318B THR 3.2 1.1 - - - -
319B ALA* 3.0 5.6 + - - +
320B LEU* 2.8 47.2 + - + +
325B VAL* 4.0 22.2 - - + -
328B MET* 3.5 34.8 - - + -
343B ILE* 3.7 22.7 - - + -
350B ILE* 6.2 0.9 - - + -
352B ILE* 4.5 4.5 - - + -
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Residues in contact with THR 317 (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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313B MET* 2.7 33.8 + - + +
314B ASP* 3.6 15.6 + - - -
316B LEU* 1.3 73.0 - - + +
318B THR* 1.3 65.2 + - - +
320B LEU* 3.8 8.9 - - + +
321B GLU* 3.2 39.6 + - - +
345B TYR* 5.0 5.8 - - + -
348B GLU* 5.8 0.9 - - - +
350B ILE* 3.7 34.1 - - + -
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Residues in contact with THR 318 (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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314B ASP* 2.6 28.7 + - - +
315B ASP* 4.0 3.1 - - - +
317B THR* 1.3 81.2 + - - +
319B ALA* 1.3 62.4 + - - +
321B GLU* 3.5 13.4 + - - +
322B GLY* 3.6 8.7 + - - -
324B ARG* 3.9 16.7 + - - +
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Residues in contact with ALA 319 (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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267B TRP* 3.3 29.6 - - + -
315B ASP 3.1 18.2 + - - +
316B LEU 3.0 6.3 + - - +
318B THR* 1.3 78.2 - - - +
320B LEU* 1.3 63.0 + - - +
322B GLY 3.2 5.9 + - - -
324B ARG* 2.9 46.9 + - + +
325B VAL* 3.7 9.6 - - + -
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Residues in contact with LEU 320 (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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316B LEU* 2.8 35.9 + - + +
317B THR* 3.8 8.7 - - + +
319B ALA* 1.3 72.1 - - - +
321B GLU* 1.3 60.3 + - + +
322B GLY 2.9 5.6 - - - -
323B ASN* 2.9 24.9 + - - +
324B ARG 4.8 1.3 - - - +
325B VAL* 4.0 20.4 - - + +
350B ILE* 3.4 32.8 - - + -
351B HIS 3.6 18.2 - - - +
352B ILE* 4.3 8.7 - - + -
353B PRO* 3.7 23.3 - - + -
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Residues in contact with GLU 321 (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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317B THR* 3.2 27.6 + - - +
318B THR* 3.5 7.1 + - - +
319B ALA 3.4 0.2 - - - -
320B LEU* 1.3 77.2 - - + +
322B GLY* 1.3 56.6 + - - +
323B ASN* 3.4 6.0 + - - -
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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