Contacts of the strand formed by residues 308 - 313 (chain G) in PDB entry 5CAY
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 308 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306G ASN* 3.5 11.5 + - - +
307G LEU* 1.3 78.7 - - - +
309G VAL* 1.3 71.5 + - - +
310G HIS* 4.7 7.1 - - - -
346G PHE* 3.7 2.1 - - - -
347G LYS* 2.9 47.2 + - - +
350G TRP* 3.9 2.3 + - - -
461G SER 3.1 17.7 - - - +
462G THR* 4.2 9.2 - - - -
463G VAL* 3.7 6.0 - - - +
609G NAG 4.2 29.4 + - - +
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Residues in contact with VAL 309 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277G PHE* 3.9 20.0 - - + -
308G THR* 1.3 71.5 - - - +
310G HIS* 1.3 66.4 + - - +
311G CYS* 3.5 26.7 - - - -
344G CYS* 4.1 7.9 - - + -
345G TRP 3.3 6.7 - - - +
346G PHE* 3.3 37.2 - - + -
392G MET* 5.9 2.9 - - + -
459G CYS 3.9 0.7 - - - +
461G SER* 2.6 40.9 + - - +
463G VAL* 3.3 25.0 - - + +
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Residues in contact with HIS 310 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308G THR* 4.7 11.0 - - - -
309G VAL* 1.3 75.0 - - - +
311G CYS* 1.3 58.0 + - - +
344G CYS* 3.4 0.5 - - - -
345G TRP* 2.7 55.0 + - + +
347G LYS* 5.1 9.4 - - + -
458G THR* 4.3 11.0 + - - -
459G CYS 3.0 11.9 + - - -
460G ASN* 3.0 53.8 + - + +
461G SER 4.9 0.4 - - - -
609G NAG 4.8 14.3 + - - -
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Residues in contact with CYS 311 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309G VAL* 3.5 17.5 - - - -
310G HIS* 1.3 72.2 + - - +
312G LYS* 1.3 61.1 + - - +
343G TRP 3.0 5.4 - - - +
344G CYS* 2.0 46.9 - - - -
392G MET* 6.0 0.2 - - - -
394G THR* 5.4 7.6 - - - -
396G CYS* 4.2 10.1 - - + -
401G LEU* 4.4 16.8 - - + -
458G THR* 3.2 6.4 + - - -
459G CYS* 2.9 35.2 + - + +
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Residues in contact with LYS 312 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310G HIS 4.4 0.2 + - - -
311G CYS* 1.3 74.6 - - - +
313G ARG* 1.3 61.6 + - - +
314G PRO* 4.0 20.1 - - + +
342G ALA* 3.3 6.6 - - - -
343G TRP* 2.9 35.6 + - + -
345G TRP* 3.6 38.9 - - + -
396G CYS* 5.7 0.7 - - - -
401G LEU* 6.3 0.2 - - - -
456G GLN* 5.1 13.7 - - + +
457G LEU 3.2 14.4 - - - +
458G THR* 4.1 10.1 - - - +
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Residues in contact with ARG 313 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312G LYS* 1.3 72.9 - - - +
314G PRO* 1.3 88.0 + - + +
315G GLY 3.9 2.2 - - - +
337G ARG 5.3 1.4 + - - +
338G ARG 3.8 2.2 - - - +
339G PRO* 3.1 40.6 + - - +
341G GLN 3.3 21.5 - - - +
342G ALA* 4.2 5.8 - - + +
434G ILE* 4.1 11.0 - - + +
452G PRO* 4.6 0.8 - - - +
453G ARG 2.4 34.7 + - - -
454G GLU* 3.6 7.9 + - - +
455G GLY 2.9 29.6 + - - +
456G GLN* 3.6 2.1 - - - +
457G LEU* 3.1 65.1 + - + +
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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