Contacts of the helix formed by residues 320 - 323 (chain A) in PDB entry 7ENL
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 320 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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295A GLU* 2.8 23.8 - - - +
296A ASP* 3.3 12.1 + - - +
318A VAL 4.0 0.6 - - - -
319A ALA* 1.3 70.1 - - - +
321A ASP* 1.3 65.5 + - - +
322A LEU 3.3 0.6 - - - +
323A THR* 3.5 2.3 + - - -
324A VAL* 2.8 34.0 + - - +
325A THR 4.6 0.2 + - - -
343A LEU* 3.3 16.3 - - + +
345A LYS* 2.8 29.5 + - - +
348A GLN* 3.9 5.2 + - - +
438A MG 2.0 30.0 - - - -
439A 2PG 3.0 5.7 + - - -
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Residues in contact with ASP 321 (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 THR* 2.9 40.3 + - - +
41A GLY* 4.5 0.4 - - - -
248A ALA* 5.3 7.8 - - - +
250A SER* 4.0 23.1 + - - +
251A GLU* 5.5 1.2 - - - +
296A ASP* 3.0 21.5 + - - +
300A GLU* 3.3 27.5 - - + +
320A ASP* 1.3 81.8 - - - +
322A LEU* 1.3 62.9 + - - +
323A THR 3.2 0.9 - - - -
324A VAL* 3.9 13.4 - - - +
329A ARG* 3.7 7.6 + - - -
345A LYS* 4.8 1.7 + - - -
348A GLN* 4.7 0.3 - - - +
439A 2PG 5.4 0.3 + - - -
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Residues in contact with LEU 322 (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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296A ASP* 4.1 2.4 + - - -
299A ALA 4.2 0.2 - - - +
300A GLU* 3.6 29.1 - - - +
301A ASP 4.7 0.2 - - - +
302A ASP 4.9 0.2 - - - +
303A TRP* 3.7 44.3 - - + -
306A TRP* 3.3 58.6 - - + +
319A ALA* 4.0 19.7 - - + -
320A ASP 3.3 1.2 - - - -
321A ASP* 1.3 77.5 - - - +
323A THR* 1.3 56.6 + - + +
329A ARG* 2.9 30.5 + - - +
333A ALA* 4.2 6.5 - - + -
338A ALA* 4.0 10.5 - - + -
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Residues in contact with THR 323 (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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319A ALA* 3.2 37.6 + - + -
320A ASP 3.5 1.0 + - - -
322A LEU* 1.3 81.9 - - + +
324A VAL* 1.3 71.7 + - - +
325A THR 2.8 3.1 + - - -
326A ASN* 2.9 21.3 + - - +
329A ARG* 3.6 9.3 - - - +
330A ILE* 4.0 26.5 - - + -
333A ALA* 3.8 28.9 - - + -
342A LEU* 3.7 10.5 - - - +
343A LEU 5.1 0.3 + - - -
367A TRP* 4.6 5.8 - - + -
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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