Contacts of the helix formed by residues 332 - 343 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167F GLU* 5.8 0.4 - - - +
330F PRO 3.7 0.8 + - - -
331F PRO* 1.3 71.6 - - - +
333F MET* 1.3 64.5 + - + +
334F LEU* 2.8 21.2 + - - +
335F GLY* 2.6 25.5 + - - -
336F ARG* 2.8 36.2 + - - +
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Residues in contact with MET 333 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332F ASP* 1.3 79.7 - - - +
334F LEU* 1.3 88.8 + - + +
336F ARG* 3.2 20.6 + - - +
337F LYS* 3.0 29.1 + - + -
356F GLU* 3.3 42.6 - - + +
359F ALA* 3.2 26.3 - - + +
360F LYS* 4.0 20.2 - - + -
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Residues in contact with LEU 334 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167F GLU* 5.8 3.8 - - - +
332F ASP* 2.8 20.1 + - - +
333F MET* 1.3 98.6 - - + +
335F GLY* 1.3 60.9 + - - +
337F LYS* 3.1 10.6 + - + +
338F LYS* 2.8 48.4 + - - +
356F GLU* 5.6 0.2 - - - +
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Residues in contact with GLY 335 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165F GLY* 3.2 30.1 + - - -
167F GLU* 5.3 2.6 + - - -
331F PRO* 3.8 11.2 - - - -
332F ASP* 2.6 19.2 + - - -
334F LEU* 1.3 70.0 - - - +
336F ARG* 1.3 64.3 + - - +
338F LYS* 3.0 15.5 + - - +
339F ILE* 3.0 16.8 + - - +
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Residues in contact with ARG 336 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331F PRO* 3.7 28.6 + - + +
332F ASP* 2.8 32.4 + - - +
333F MET* 3.6 16.1 - - - +
335F GLY* 1.3 74.2 - - - +
337F LYS* 1.3 62.6 + - - +
339F ILE* 4.5 0.2 - - - -
340F LEU* 3.0 23.3 + - - +
359F ALA* 2.5 38.4 + - + -
360F LYS* 4.0 8.1 + - - +
362F THR* 2.8 36.0 + - - +
363F PRO* 3.4 17.2 - - - +
364F GLY 3.7 5.3 - - - +
365F PHE* 3.7 19.7 + - - +
370F LEU* 3.2 24.2 - - + +
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Residues in contact with LYS 337 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333F MET* 3.0 28.3 + - + +
334F LEU* 3.1 10.8 - - + +
335F GLY 3.1 0.2 - - - -
336F ARG* 1.3 78.3 - - - +
338F LYS* 1.3 82.0 + - - +
340F LEU* 3.3 7.4 + - - +
341F GLU* 3.0 46.4 + - + +
355F LEU* 4.6 16.3 - - + +
356F GLU* 4.2 22.6 + - - +
359F ALA* 3.8 14.5 - - + +
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Residues in contact with LYS 338 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164F GLY* 3.8 15.9 - - - -
165F GLY* 4.1 5.4 - - - +
167F GLU* 5.7 3.4 - - - +
334F LEU* 2.8 38.5 + - - +
335F GLY* 3.0 10.5 + - - +
337F LYS* 1.3 100.5 - - - +
339F ILE* 1.3 63.1 + - - +
341F GLU* 3.1 23.7 + - - +
342F ILE* 3.0 27.8 + - + +
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Residues in contact with ILE 339 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164F GLY* 4.0 13.0 - - - +
331F PRO* 4.3 12.8 - - + -
335F GLY 3.0 13.4 + - - +
336F ARG 3.6 0.4 - - - +
337F LYS 3.3 0.2 - - - -
338F LYS* 1.3 72.8 - - - +
340F LEU* 1.3 60.4 + - - +
342F ILE* 2.8 25.9 + - - +
343F HIS* 3.0 33.8 + - + +
367F GLY* 3.5 18.6 - - - +
370F LEU* 3.3 35.2 - - + -
1607F ADP 3.0 44.2 - - + +
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Residues in contact with LEU 340 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336F ARG 3.0 18.4 + - - +
337F LYS* 3.3 5.6 + - - +
339F ILE* 1.3 75.6 - - - +
341F GLU* 1.3 62.1 + - - +
343F HIS* 3.6 4.3 + - + +
344F THR* 3.1 26.2 + - - -
355F LEU* 3.9 20.3 - - + +
358F ILE* 3.3 48.0 - - + -
359F ALA* 4.4 4.7 - - - +
370F LEU* 4.0 41.3 - - + +
373F LEU* 5.4 2.9 - - + -
374F VAL* 4.8 15.6 - - + +
394F PHE* 5.0 9.9 - - + -
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Residues in contact with GLU 341 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337F LYS* 3.0 47.4 + - + +
338F LYS* 3.1 24.6 + - - +
340F LEU* 1.3 76.4 - - - +
342F ILE* 1.3 62.0 + - + +
344F THR* 2.7 29.4 - - - +
345F ARG* 3.0 9.3 + - - +
355F LEU* 3.7 13.9 - - + +
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Residues in contact with ILE 342 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161F LYS 4.0 9.2 - - - +
162F ASP* 3.0 65.1 - - + +
163F VAL 3.3 6.3 - - - +
164F GLY* 3.4 20.4 - - - +
338F LYS* 3.0 15.0 + - + +
339F ILE* 2.8 16.1 + - - +
341F GLU* 1.3 72.1 - - + +
343F HIS* 1.3 68.5 + - + +
344F THR 3.0 3.3 + - - -
345F ARG* 2.9 39.9 + - - +
346F ASN* 5.3 0.3 + - - -
1607F ADP 4.5 2.9 - - + -
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Residues in contact with HIS 343 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162F ASP 5.6 0.2 + - - -
339F ILE* 3.0 36.3 + - + +
340F LEU* 3.9 4.3 - - - +
342F ILE* 1.3 81.8 - - + +
344F THR* 1.3 56.2 + - - +
345F ARG 3.6 0.2 - - - -
346F ASN 5.3 0.4 - - - -
347F LYS* 3.7 15.6 - - - +
370F LEU 5.4 0.7 - - - +
371F GLU* 3.3 38.2 - - + +
374F VAL* 3.6 32.8 - - + +
1607F ADP 2.8 51.2 + + - -
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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