Contacts of the strand formed by residues 341 - 346 (chain A) in PDB entry 5C5B
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 CYS 341 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297A TRP* 3.9 21.1 - - - -
332A ALA* 4.0 0.5 - - - +
333A VAL 3.0 36.3 + - - +
335A CYS 4.3 6.1 - - - +
338A ARG* 3.5 37.8 + - - +
340A TYR* 1.3 78.2 - - - +
342A PHE* 1.3 60.8 + - - +
354A ILE* 3.8 13.9 - - + -
355A LEU 3.2 4.0 - - - -
356A GLN* 4.0 13.9 - - - -
363A HIS* 3.0 13.6 + - - -
152B LYS* 5.8 1.6 - - - +
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Residues in contact with PHE 342 (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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284A LEU* 3.8 17.5 - - + -
309A LEU* 5.7 0.7 - - + -
330A VAL* 3.8 15.5 - - + -
331A MET 3.3 14.6 - - - +
333A VAL* 4.0 5.2 - - - +
340A TYR 4.4 1.6 - - - -
341A CYS* 1.3 75.5 - - - +
343A GLN* 1.3 66.1 + - - +
344A ILE* 4.6 2.0 - - + -
354A ILE* 3.7 1.5 - - - -
355A LEU* 2.7 77.5 + - + +
357A ALA* 4.9 3.4 - - + -
363A HIS* 3.9 22.7 - + - +
366A TRP* 3.7 35.0 - + + -
367A ILE* 4.1 13.5 - - + -
370A ILE* 3.9 21.1 - - + -
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Residues in contact with GLN 343 (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 VAL* 3.3 3.5 - - - +
331A MET* 2.9 38.0 + - + +
333A VAL* 3.7 22.7 - - + +
342A PHE* 1.3 76.7 - - - +
344A ILE* 1.3 69.9 + - - +
345A THR* 4.3 3.4 + - - +
351A LYS* 3.5 32.4 - - - +
352A SER* 2.9 32.4 + - - +
353A SER 4.0 4.7 - - - +
354A ILE* 3.9 23.2 - - + +
355A LEU* 5.8 0.2 - - - -
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Residues in contact with ILE 344 (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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309A LEU* 3.8 23.8 - - + -
323A MET* 3.8 19.3 - - + -
325A ILE* 3.9 13.0 - - + -
328A CYS* 3.8 22.4 - - + -
329A SER 3.3 12.8 - - - +
330A VAL* 4.2 5.4 - - + -
342A PHE* 4.6 6.5 - - + -
343A GLN* 1.3 77.6 - - - +
345A THR* 1.3 68.6 + - - +
346A SER 4.3 0.4 - - - -
351A LYS* 3.2 5.5 - - - +
352A SER* 2.8 49.9 + - - +
355A LEU* 4.8 1.8 - - + -
370A ILE* 3.7 31.6 - - + -
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Residues in contact with THR 345 (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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328A CYS* 3.4 2.6 - - - +
329A SER* 2.9 47.1 + - - -
330A VAL* 6.0 0.2 - - - -
331A MET* 6.2 0.3 - - - +
343A GLN* 4.9 4.0 + - - -
344A ILE* 1.3 76.9 + - - +
346A SER* 1.3 74.4 + - - +
349A GLY* 4.0 20.4 - - - +
350A LYS 3.4 2.0 - - - -
351A LYS* 3.9 23.5 - - + +
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Residues in contact with SER 346 (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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323A MET* 4.1 13.3 - - - +
324A ASP 5.1 4.5 + - - -
327A ASN 4.2 9.5 + - - -
328A CYS* 4.2 3.6 - - - -
345A THR* 1.3 80.8 - - - +
347A PHE* 1.3 68.6 + - - +
348A ASP* 2.9 25.0 + - - +
349A GLY* 2.8 18.4 + - - -
350A LYS* 2.6 35.0 + - - -
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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