Contacts of the helix formed by residues 332 - 338 (chain A) in PDB entry 1CEC
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 GLN 332 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A ALA* 6.3 0.2 - - - +
329A PRO* 3.7 22.2 - - + +
331A SER* 1.3 70.9 + - - +
333A GLU* 1.3 74.5 + - - +
335A VAL* 3.4 11.9 + - - +
336A ASN* 2.7 72.8 + - - +
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Residues in contact with GLU 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293A ILE* 4.6 12.5 - - + +
331A SER* 3.3 13.7 + - - +
332A GLN* 1.3 89.3 + - - +
334A LEU* 1.3 61.5 + - - +
336A ASN* 3.3 9.6 + - - +
337A ILE* 3.0 36.1 + - + +
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Residues in contact with LEU 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289A LEU* 5.2 2.2 - - + -
292A ARG* 4.1 25.1 - - + +
293A ILE* 4.3 23.0 - - + +
296A HIS* 3.6 40.2 - - + +
322A ILE* 4.0 21.5 - - + -
330A VAL* 5.2 7.4 - - + -
331A SER* 3.3 26.8 + - - +
332A GLN 3.2 0.4 - - - -
333A GLU* 1.3 78.0 - - - +
335A VAL* 1.3 63.2 + - + +
337A ILE* 3.1 10.0 + - + +
338A LEU* 2.9 39.2 + - + +
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Residues in contact with VAL 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ALA* 3.9 21.5 - - + +
42A PHE* 4.1 7.4 - - + -
322A ILE* 3.8 23.8 - - + -
323A TYR* 3.7 22.0 - - + +
329A PRO* 3.5 30.3 - - + -
331A SER 3.2 7.8 + - - +
332A GLN* 3.9 16.8 - - - +
334A LEU* 1.3 75.3 - - - +
336A ASN* 1.3 60.0 + - - +
338A LEU* 3.1 7.3 + - - +
339A ALA* 2.8 29.3 + - - +
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Residues in contact with ASN 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ALA 5.4 3.8 + - - -
332A GLN* 2.7 58.5 + - - +
333A GLU* 3.6 9.0 - - - +
335A VAL* 1.3 76.7 - - - +
337A ILE* 1.3 64.3 + - + +
339A ALA* 3.6 10.5 + - - +
340A ARG* 3.6 10.0 + - - -
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Residues in contact with ILE 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293A ILE* 3.9 22.7 - - + +
296A HIS* 4.2 4.3 - - + +
297A GLU* 3.9 53.8 - - + +
300A ILE* 3.9 27.9 - - + +
333A GLU* 3.0 22.2 + - + +
334A LEU* 3.3 9.0 - - + +
336A ASN* 1.3 79.5 - - + +
338A LEU* 1.3 61.5 + - + +
340A ARG* 3.1 20.3 + - - -
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Residues in contact with LEU 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ALA* 3.8 15.1 - - - +
7A GLY 5.0 1.6 + - - +
42A PHE* 3.8 19.8 - - + -
281A PHE* 4.2 4.4 - - + -
296A HIS* 3.7 28.7 - - + -
300A ILE* 4.2 22.9 - - + +
312A VAL* 3.9 24.2 - - + -
322A ILE* 3.7 39.3 - - + -
334A LEU* 2.9 30.8 + - + +
335A VAL* 3.6 4.3 - - - +
337A ILE* 1.3 72.6 - - + +
339A ALA* 1.3 57.0 + - - +
340A ARG* 3.1 12.5 + - - +
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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