Contacts of the strand formed by residues 330 - 337 (chain A) in PDB entry 5C7Z
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 THR 330 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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326A THR* 3.8 1.2 - - - +
327A PRO* 2.6 45.0 + - - +
328A LEU 3.1 7.5 + - - +
329A ASN* 1.3 72.9 - - - +
331A SER* 1.3 60.7 + - - +
332A GLY 3.8 22.0 - - - +
333A VAL* 4.0 2.9 - - + -
344A TYR* 3.2 39.2 + - + +
349A ASN* 4.8 0.2 - - - -
370A ILE* 3.8 14.7 - - + +
371A GLU 3.5 3.6 - - - -
372A LEU* 4.3 0.8 - - - +
373A LEU* 4.5 5.6 - - - +
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Residues in contact with SER 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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329A ASN 3.4 4.4 + - - -
330A THR* 1.3 72.8 - - - +
332A GLY* 1.3 58.9 + - - -
344A TYR* 5.7 0.4 - - - -
371A GLU* 2.7 33.3 + - - +
372A LEU 4.2 4.5 - - - -
373A LEU* 3.9 29.2 - - - +
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Residues in contact with GLY 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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330A THR* 3.3 6.9 - - - +
331A SER* 1.3 85.0 + - - +
333A VAL* 1.3 69.4 + - - +
344A TYR* 4.9 6.7 - - - -
371A GLU* 2.9 35.3 + - - +
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Residues in contact with VAL 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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326A THR* 4.6 1.1 - - + -
330A THR* 4.0 15.3 - - + -
332A GLY* 1.3 80.4 - - - +
334A GLN* 1.3 77.2 + - - +
335A VAL* 3.6 26.9 + - + +
344A TYR* 3.9 35.1 - - + +
351A ILE* 3.9 18.2 - - + -
368A ALA* 4.9 0.4 - - + -
369A GLU 3.6 3.1 - - - +
370A ILE* 3.9 22.9 - - + -
371A GLU* 4.4 1.2 + - - -
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Residues in contact with GLN 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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333A VAL* 1.3 84.5 + - - +
335A VAL* 1.3 66.5 + - - +
368A ALA* 3.0 4.2 - - - +
369A GLU* 2.7 59.6 + - + +
371A GLU* 4.3 17.0 + - - +
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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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333A VAL* 3.6 21.9 + - + -
334A GLN* 1.3 85.9 + - - +
336A ILE* 1.3 69.3 + - - +
337A CYS* 5.3 2.5 - - - +
342A ALA* 4.1 31.0 - - + +
343A LYS* 5.8 0.4 - - - -
344A TYR 5.8 2.0 - - - +
351A ILE* 4.1 16.8 - - + -
366A ILE* 4.7 7.2 - - + -
367A SER 3.3 8.3 - - - +
368A ALA* 3.7 13.0 - - + -
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Residues in contact with ILE 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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335A VAL* 1.3 78.5 - - - +
337A CYS* 1.3 73.8 + - - +
338A MET* 4.8 10.8 - - + +
365A GLN 4.6 0.2 - - - +
366A ILE* 3.7 2.6 - - - -
367A SER* 2.9 41.3 + - - +
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Residues in contact with CYS 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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335A VAL* 4.4 3.1 + - - -
336A ILE* 1.3 82.4 - - - +
338A MET* 1.3 64.9 + - - +
339A LYS 3.3 19.4 - - - +
340A GLY 4.0 13.0 - - - +
341A LYS* 4.6 0.4 - - - -
342A ALA* 4.3 12.3 - - - -
353A TRP* 3.7 23.6 - - - +
365A GLN 4.0 11.9 - - - +
366A ILE* 4.0 16.6 - - + -
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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