Contacts of the helix formed by residues 332 - 345 (chain B) in PDB entry 2CEA
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 332 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330B PRO 3.7 3.0 + - - -
331B PRO* 1.3 73.4 - - - +
333B MET* 1.3 67.5 + - + +
334B LEU* 4.3 8.3 - - - +
335B GLY* 3.1 18.2 + - - -
336B ARG* 2.8 29.5 + - - +
444B SER* 4.8 2.0 - - - +
446B ILE* 4.1 9.9 - - + -
590B GLU* 3.8 8.1 - - + +
591B THR* 3.6 30.9 + - - +
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Residues in contact with MET 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B ASP* 1.3 77.7 - - + +
334B LEU* 1.3 68.8 + - + +
336B ARG* 3.1 16.9 + - - +
337B LYS* 2.8 28.0 + - + +
356B GLU* 5.5 6.3 - - + +
359B ALA* 3.7 10.0 - - + +
360B LYS* 3.7 40.8 - - + +
588B GLU 3.8 10.1 - - - +
589B LYS* 2.7 47.6 - - + +
590B GLU* 3.0 21.1 + - + +
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Residues in contact with LEU 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B ASP* 3.4 9.6 + - - +
333B MET* 1.3 88.4 - - + +
335B GLY* 1.3 58.2 + - - +
337B LYS* 3.0 21.4 - - + +
338B LYS* 3.0 60.8 + - - +
356B GLU* 5.5 4.9 - - - +
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Residues in contact with GLY 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B GLY* 3.9 23.0 + - - -
167B GLU* 6.1 0.4 - - - -
331B PRO* 4.1 10.3 - - - -
332B ASP* 3.1 17.0 + - - -
334B LEU* 1.3 76.4 - - - +
336B ARG* 1.3 63.9 + - - +
338B LYS* 3.1 6.4 + - - +
339B ILE* 3.0 27.8 + - - +
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Residues in contact with ARG 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B PRO* 3.0 37.3 + - + +
332B ASP* 2.8 21.3 + - - +
333B MET* 3.4 15.6 - - - +
335B GLY* 1.3 69.0 - - - +
337B LYS* 1.3 68.2 + - - +
339B ILE* 3.1 2.1 + - - +
340B LEU* 2.9 30.0 + - - +
359B ALA* 2.8 33.3 + - + -
360B LYS* 4.5 1.6 - - - +
362B THR* 2.9 28.8 + - - +
363B PRO* 3.4 20.8 - - - +
364B GLY 4.4 1.6 - - - +
365B PHE* 4.2 11.2 - - - -
370B LEU* 3.8 17.9 - - + +
446B ILE* 3.7 7.7 - - - +
590B GLU* 2.5 37.0 + - - -
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Residues in contact with LYS 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B MET* 2.8 12.0 + - + +
334B LEU* 3.0 25.6 - - + +
336B ARG* 1.3 79.3 - - - +
338B LYS* 1.3 74.1 + - - +
340B LEU* 3.3 7.2 + - - +
341B GLU* 3.1 49.3 + - - +
355B LEU* 4.5 4.7 - - + +
356B GLU* 3.9 44.5 - - + +
359B ALA* 3.9 10.1 - - + +
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Residues in contact with LYS 338 (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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164B GLY* 4.7 4.0 - - - -
165B GLY* 4.5 13.2 - - - +
167B GLU* 5.8 1.8 + - - -
334B LEU* 3.0 59.6 + - - +
335B GLY* 3.1 8.2 + - - +
337B LYS* 1.3 91.6 - - - +
339B ILE* 1.3 57.6 + - - +
341B GLU* 3.1 19.5 + - - +
342B ILE* 2.8 36.2 + - + +
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Residues in contact with ILE 339 (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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164B GLY 4.0 11.4 - - - +
331B PRO* 3.9 23.1 - - + -
335B GLY 3.0 20.3 + - - +
336B ARG 3.7 4.0 - - - +
338B LYS* 1.3 75.6 - - - +
340B LEU* 1.3 57.8 - - - +
342B ILE* 3.3 6.5 + - - +
343B HIS* 2.9 49.3 + - + +
367B GLY* 4.3 10.1 - - - -
370B LEU* 3.8 33.7 - - + -
1607B ADP 3.6 38.8 - - + +
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Residues in contact with LEU 340 (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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336B ARG 2.9 21.0 + - - +
337B LYS* 3.6 5.2 - - - +
339B ILE* 1.3 74.1 - - - +
341B GLU* 1.3 66.5 + - - +
343B HIS* 3.1 5.1 + - - +
344B THR* 2.9 28.5 + - - +
355B LEU* 3.7 44.4 - - + +
358B ILE* 4.1 12.3 - - + -
359B ALA* 3.9 17.0 - - - +
370B LEU* 4.1 28.7 - - + -
373B LEU* 4.3 12.3 - - + -
374B VAL* 3.9 22.8 - - + +
394B PHE* 5.2 2.9 - - + -
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Residues in contact with GLU 341 (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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337B LYS* 3.1 44.2 + - + +
338B LYS* 3.1 32.0 + - - +
340B LEU* 1.3 74.6 - - - +
342B ILE* 1.3 63.9 + - + +
344B THR* 3.0 6.2 + - - +
345B ARG* 3.0 23.4 + - - +
355B LEU* 3.8 22.0 - - + -
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Residues in contact with ILE 342 (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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161B LYS 3.7 19.5 - - - +
162B ASP* 3.7 15.7 - - + +
163B VAL 3.5 34.1 - - - +
164B GLY* 3.7 10.1 - - - +
338B LYS* 2.8 14.3 + - + +
339B ILE* 3.5 8.5 - - - +
341B GLU* 1.3 77.9 - - + +
343B HIS* 1.3 77.4 + - + +
344B THR 2.9 4.5 + - - -
345B ARG* 2.5 47.2 - - + +
1607B ADP 4.5 2.2 - - + -
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Residues in contact with HIS 343 (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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162B ASP 5.5 0.9 - - - -
339B ILE* 2.9 41.8 + - + +
340B LEU 3.6 2.7 - - - +
342B ILE* 1.3 83.3 - - + +
344B THR* 1.3 58.1 + - - +
346B ASN 5.2 0.8 + - - -
347B LYS* 4.0 11.4 - - - +
370B LEU 5.1 0.2 - - - -
371B GLU* 3.7 33.2 + - + +
374B VAL* 3.7 32.6 - - + +
1607B ADP 2.8 54.7 + + - -
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Residues in contact with THR 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B LEU 2.9 20.6 + - - -
341B GLU* 3.3 7.4 - - - +
342B ILE 2.9 0.4 - - - -
343B HIS* 1.3 79.5 + - - +
345B ARG* 1.3 67.7 + - - +
346B ASN 2.7 5.5 + - - -
347B LYS* 2.9 22.0 + - + +
349B LEU* 3.5 40.6 - - + +
355B LEU* 4.3 13.9 - - + +
374B VAL* 4.5 13.0 - - - +
394B PHE* 4.8 1.6 - - - -
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Residues in contact with ARG 345 (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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161B LYS* 2.9 33.5 + - - +
162B ASP* 3.1 22.5 + - - -
341B GLU 3.0 14.0 + - - +
342B ILE* 2.5 42.9 + - + +
344B THR* 1.3 76.9 - - - +
346B ASN* 1.3 81.1 + - - +
347B LYS 3.6 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