Contacts of the helix formed by residues 312 - 324 (chain B) in PDB entry 2B7O
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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310B ASN 3.6 7.6 + - - +
311B MSE 1.3 81.6 - - - +
313B PRO* 1.4 68.1 - - + +
314B GLU* 3.6 14.1 + - - +
315B LEU* 3.1 27.0 + - + +
316B ALA* 2.8 31.0 + - - +
350B ILE* 4.1 3.6 - - - -
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Residues in contact with PRO 313 (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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311B MSE 4.4 1.3 - - - +
312B THR* 1.4 87.0 - - + +
314B GLU* 1.3 67.1 + - - +
316B ALA* 3.4 3.1 + - + +
317B VAL* 3.0 35.7 + - - +
349B PRO* 3.7 35.4 - - + +
350B ILE* 3.9 17.0 - - + +
353B LYS* 3.4 27.5 - - + +
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Residues in contact with GLU 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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312B THR* 3.6 18.4 - - - +
313B PRO* 1.3 81.5 - - - +
315B LEU* 1.3 65.8 + - - +
317B VAL* 3.2 9.4 + - - +
318B GLU* 3.0 21.7 + - - +
353B LYS* 4.3 20.9 + - - +
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Residues in contact with LEU 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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286B ARG* 3.8 26.0 - - - +
288B ILE* 4.3 29.6 - - + -
310B ASN* 5.8 1.8 - - - +
311B MSE 3.8 12.1 - - + -
312B THR* 3.1 21.2 + - + +
314B GLU* 1.3 75.7 - - - +
316B ALA* 1.3 66.2 + - - +
318B GLU* 3.1 9.5 + - + +
319B TYR* 3.0 43.6 + - + +
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Residues in contact with ALA 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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307B LEU* 4.5 8.3 - - + -
311B MSE 3.6 14.9 - - + -
312B THR 2.8 21.4 + - - +
313B PRO 3.6 4.9 - - - +
315B LEU* 1.3 73.1 - - - +
317B VAL* 1.3 62.1 + - - +
319B TYR* 3.3 8.5 + - - +
320B VAL* 3.1 24.8 + - - +
334B LEU* 4.8 2.2 - - + +
350B ILE* 3.9 26.9 - - + -
354B VAL* 4.1 10.8 - - + -
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Residues in contact with VAL 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B PRO 3.0 19.2 + - - +
314B GLU* 3.6 9.4 - - - +
315B LEU 3.2 0.2 - - - -
316B ALA* 1.3 71.9 - - - +
318B GLU* 1.3 61.4 + - - +
320B VAL* 3.2 8.4 + - - +
321B GLU* 2.9 46.9 + - - +
353B LYS* 3.8 41.7 - - + +
354B VAL* 4.0 5.8 - - + +
357B THR* 3.8 22.7 - - + -
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Residues in contact with GLU 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B ILE* 3.8 23.1 - - + -
314B GLU 3.0 13.6 + - - +
315B LEU* 3.1 15.2 + - + +
317B VAL* 1.3 78.3 - - - +
319B TYR* 1.3 55.7 + - - +
321B GLU* 3.4 14.8 + - - +
322B ARG* 2.7 71.2 + - - +
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Residues in contact with TYR 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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286B ARG* 2.5 57.8 + - + -
287B GLN* 4.8 0.3 - - - -
288B ILE* 3.5 26.0 + - + -
293B ILE* 3.8 23.6 - - + -
305B VAL* 4.5 6.1 - - + -
307B LEU* 4.3 10.5 - - + -
311B MSE 3.9 11.7 - - + -
315B LEU* 3.0 48.7 + - + +
316B ALA* 3.4 12.1 - - - +
318B GLU* 1.3 73.9 - - - +
320B VAL* 1.3 58.1 + - - +
322B ARG* 4.8 0.9 - - - -
323B LEU* 2.8 46.4 + - + +
332B LEU* 4.3 2.5 - - - -
334B LEU* 4.8 11.7 - - + -
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Residues in contact with VAL 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 ALA 3.1 14.6 + - - +
317B VAL* 3.2 9.2 + - + +
319B TYR* 1.3 75.8 - - - +
321B GLU* 1.3 58.3 + - + +
324B ASP* 2.7 31.9 + - + +
332B LEU* 3.5 20.6 - - + -
334B LEU* 3.9 12.6 - - + -
354B VAL* 3.8 24.9 - - + -
357B THR* 4.6 5.8 - - + +
359B HIS* 3.6 40.4 - - + +
361B VAL* 3.9 8.3 - - + -
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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 VAL* 2.9 42.3 + - + +
318B GLU* 4.0 17.4 - - - +
320B VAL* 1.3 76.3 - - + +
322B ARG* 1.3 61.4 + - + +
325B PRO* 3.5 21.8 - - - +
357B THR* 4.6 9.1 - - + +
359B HIS* 4.6 20.0 + - + +
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Residues in contact with ARG 322 (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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32B LYS* 5.7 1.8 - - - +
288B ILE* 3.3 39.7 + - - +
289B ASP* 3.0 31.9 + - - +
293B ILE* 4.8 4.5 - - + -
297B GLN* 3.0 48.2 + - - +
318B GLU* 2.7 47.4 + - - +
319B TYR* 3.9 3.8 - - - +
321B GLU* 1.3 79.1 - - + +
323B LEU* 1.3 65.5 + - + +
324B ASP 3.6 0.2 - - - -
325B PRO* 3.6 13.1 - - - +
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Residues in contact with LEU 323 (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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281B ILE* 5.5 0.2 - - + -
293B ILE* 3.7 31.0 - - + +
296B ALA* 3.6 31.9 - - + +
297B GLN* 3.8 13.9 - - + +
303B VAL* 4.7 6.3 - - + -
305B VAL* 3.5 31.6 - - + -
319B TYR* 2.8 26.6 + - + +
322B ARG* 1.3 75.4 - - + +
324B ASP* 1.3 57.9 + - - +
325B PRO* 3.3 6.9 - - - +
331B ARG* 2.8 37.7 + - - +
332B LEU* 3.9 20.1 - - + +
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Residues in contact with ASP 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B VAL* 2.7 18.3 + - + +
323B LEU* 1.3 79.0 - - - +
325B PRO* 1.4 60.7 - - - +
326B HIS 3.1 2.8 + - - -
327B ASN* 3.5 2.8 + - - -
328B LYS* 2.7 47.3 + - - +
331B ARG* 3.9 8.1 - - + +
332B LEU* 4.3 20.0 - - + -
359B HIS* 2.8 46.0 + - - +
360B GLN 4.6 6.5 + - - +
361B VAL* 5.4 1.7 - - + +
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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