Contacts of the strand formed by residues 328 - 334 (chain A) in PDB entry 4ORA
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 ALA 328 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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295A ALA 4.1 0.3 - - - +
296A GLY* 3.9 2.2 - - - -
315A PHE 3.5 5.4 - - - -
316A SER 3.7 11.2 - - - -
317A ALA 3.9 0.2 - - - +
318A PRO* 3.6 28.9 - - + +
326A ASN* 4.7 0.2 - - - +
327A LYS* 1.3 75.2 - - - +
329A ALA* 1.3 66.4 + - - +
342A GLN* 3.3 7.8 - - - +
343A PHE* 2.8 55.9 + - + +
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Residues in contact with ALA 329 (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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295A ALA 4.2 3.6 - - - +
296A GLY* 3.3 21.5 - - - +
314A ILE* 3.3 11.5 - - + +
315A PHE 3.0 8.7 + - - +
316A SER* 2.9 23.0 + - - -
328A ALA* 1.3 78.1 - - - +
330A VAL* 1.3 64.1 + - - +
340A ILE* 3.7 23.3 - - + -
341A ARG 3.2 12.3 - - - +
342A GLN* 4.3 1.6 - - + -
343A PHE* 4.3 3.6 - - - -
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Residues in contact with VAL 330 (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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95A THR* 3.8 20.2 - - + -
96A VAL 3.5 10.5 - - - +
97A CYS* 4.0 11.2 - - - -
110A LEU* 3.7 37.2 - - + +
113A VAL* 4.7 9.4 - - + -
114A GLY* 4.8 3.6 - - - -
314A ILE* 3.6 4.9 - - - -
316A SER* 4.1 1.3 - - - +
329A ALA* 1.3 79.4 - - - +
331A LEU* 1.3 59.3 + - - +
332A LYS* 4.2 7.9 - - + -
340A ILE* 3.5 4.2 - - - +
341A ARG* 2.9 51.0 + - + +
343A PHE* 4.1 5.8 - - + -
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Residues in contact with LEU 331 (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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94A ILE 3.6 1.2 - - - +
95A THR* 3.3 3.4 - - - -
96A VAL* 2.9 55.7 + - + +
200A LEU* 5.8 1.1 - - + -
287A ILE* 4.8 15.3 - - + -
312A ILE* 4.2 21.8 - - + -
314A ILE* 3.7 11.4 - - + +
330A VAL* 1.3 72.7 - - - +
332A LYS* 1.3 64.1 + - - +
333A TYR* 4.3 14.6 - - + -
338A MET* 3.6 44.9 - - + -
339A ASN 3.7 3.1 - - - +
340A ILE* 3.8 20.9 - - + -
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Residues in contact with LYS 332 (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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94A ILE 3.8 5.2 - - - -
95A THR* 2.9 21.8 + - - +
113A VAL 4.8 2.0 - - - +
114A GLY* 2.5 43.0 + - - +
120A THR* 3.9 7.3 + - - +
330A VAL* 4.2 7.6 - - + -
331A LEU* 1.3 76.8 - - - +
333A TYR* 1.3 57.7 + - - +
334A GLU* 3.7 25.9 + - - +
337A VAL 3.3 4.0 - - - +
338A MET* 3.4 0.3 - - - -
339A ASN* 2.6 51.5 + - + +
341A ARG* 3.9 31.4 - - + +
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Residues in contact with TYR 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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92A ALA* 3.8 26.6 - - + +
93A PRO* 3.1 25.6 - - - +
94A ILE* 2.9 22.8 + - + +
200A LEU* 4.3 19.5 - - + -
201A ASN* 3.7 17.1 + - + -
203A GLN* 2.7 24.5 + - - -
204A PHE* 3.8 20.8 - + - -
331A LEU* 3.8 13.9 + - + -
332A LYS* 1.3 71.6 - - - +
334A GLU* 1.3 59.8 + - - +
336A ASN* 4.0 34.3 + - - -
337A VAL 3.5 10.5 - - - -
338A MET* 3.7 21.8 - - + +
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Residues in contact with GLU 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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92A ALA* 5.4 2.2 - - - -
93A PRO* 3.4 26.1 - - + +
94A ILE 4.8 1.3 - - - +
332A LYS* 3.7 28.4 + - + +
333A TYR* 1.3 83.3 - - - +
335A ASN* 1.3 74.7 + - - +
336A ASN 3.2 3.4 - - - -
337A VAL* 2.8 34.8 + - - +
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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