Contacts of the strand formed by residues 341 - 345 (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 GLN 341 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313G ARG* 3.3 24.0 - - - +
314G PRO* 4.7 2.3 - - - +
338G ARG* 3.5 36.9 + - + +
339G PRO 3.7 0.4 - - - -
340G ARG* 1.3 79.9 - - - +
342G ALA* 1.3 66.9 + - - +
343G TRP* 4.0 31.1 - - + -
431G PRO* 4.9 8.8 - - - +
432G CYS 3.8 6.0 + - - +
433G HIS* 3.8 22.0 - - - +
434G ILE* 5.3 0.4 - - - -
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Residues in contact with ALA 342 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312G LYS 3.3 17.9 - - - +
313G ARG* 4.2 5.4 - - + -
341G GLN* 1.3 80.9 + - - +
343G TRP* 1.3 68.3 + - - +
401G LEU* 4.5 19.7 - - + -
431G PRO* 3.5 2.9 - - - +
432G CYS* 2.5 54.8 + - + +
434G ILE* 5.1 5.2 - - + -
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Residues in contact with TRP 343 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310G HIS 4.1 0.2 - - - +
311G CYS* 3.0 3.6 - - - +
312G LYS* 2.9 38.9 + - + +
314G PRO* 4.3 22.7 - - + -
337G ARG* 5.8 7.4 - - - -
341G GLN* 4.0 25.8 - - + -
342G ALA* 1.3 87.7 - - - +
344G CYS* 1.3 65.5 + - - +
345G TRP* 3.4 31.5 - + + -
407G TRP* 5.3 3.4 - - - -
429G TYR* 3.9 23.6 - + + -
430G VAL 3.2 18.8 - - - -
431G PRO* 3.9 17.3 - - + +
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Residues in contact with CYS 344 (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* 4.1 8.5 - - + -
310G HIS 3.4 3.6 - - - -
311G CYS* 2.0 48.0 - - - -
343G TRP* 1.3 75.9 - - - +
345G TRP* 1.3 64.2 + - - +
346G PHE* 4.0 5.2 + - + -
392G MET* 5.7 2.5 - - + -
394G THR* 5.7 1.6 - - - -
401G LEU* 4.5 5.2 - - - -
403G CYS* 4.2 4.5 - - - -
405G MET* 6.1 0.2 - - + -
429G TYR* 3.2 2.1 - - - -
430G VAL* 3.0 43.9 + - + +
432G CYS* 3.6 19.1 - - - -
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Residues in contact with TRP 345 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309G VAL* 3.3 4.7 - - - +
310G HIS* 2.7 50.6 + - + +
312G LYS* 3.6 45.1 - - + -
343G TRP* 3.4 32.1 - + + -
344G CYS* 1.3 77.4 - - - +
346G PHE* 1.3 60.8 + - - +
347G LYS* 3.5 29.1 + - + -
428G ASN* 3.7 18.4 - - - -
429G TYR* 3.8 31.5 - + + +
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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