Contacts of the strand formed by residues 402 - 406 (chain A) in PDB entry 3C7N
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 VAL 402 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398A HIS* 3.7 3.1 - - + -
400A TYR* 3.5 12.3 - - + +
401A SER* 1.3 80.1 + - - +
403A SER* 1.3 69.7 + - - +
404A TYR* 4.2 10.1 - - + -
417A GLU* 4.1 0.2 - - - -
418A VAL* 3.0 21.1 + - - +
419A PHE* 3.1 18.7 + - + +
443A ALA* 4.6 0.7 - - + -
444A SER 3.4 12.1 - - - +
445A TYR* 4.1 19.3 - - + -
446A THR* 3.6 1.8 - - - -
459A ILE* 4.0 12.3 - - + -
490A HIS* 3.5 43.1 - - + +
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Residues in contact with SER 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A VAL* 1.3 74.1 - - - +
404A TYR* 1.3 71.7 + - - +
415A HIS* 5.1 7.2 - - - -
416A MET 3.2 21.5 - - - -
417A GLU* 3.6 8.1 + - - +
444A SER* 2.8 35.7 + - - -
446A THR* 2.6 34.9 + - - +
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Residues in contact with TYR 404 (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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402A VAL* 4.2 7.0 - - + -
403A SER* 1.3 79.9 - - - +
405A SER* 1.3 59.8 + - - +
406A TRP* 3.4 7.0 - - + -
415A HIS* 3.0 4.5 - - - -
416A MET 2.9 31.3 + - - -
418A VAL* 3.7 24.5 - - + -
419A PHE* 3.7 29.9 - + - -
441A MET* 4.1 16.6 - - + -
442A ALA 3.4 5.4 - - - -
443A ALA* 3.6 19.3 - - + -
462A TRP* 3.8 12.3 - + - -
482A LEU* 3.8 22.2 - - + -
490A HIS* 3.6 10.0 - + - +
491A THR 2.9 31.0 + - - -
492A ILE* 3.6 25.6 - - + -
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Residues in contact with SER 405 (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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404A TYR* 1.3 74.6 - - - +
406A TRP* 1.3 67.6 + - - +
414A ASP 3.1 14.8 - - - -
415A HIS* 3.6 9.0 - - - +
441A MET* 3.2 7.6 - - - +
442A ALA* 2.8 48.3 + - - +
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Residues in contact with TRP 406 (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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404A TYR* 3.4 28.5 - - + -
405A SER* 1.3 81.4 - - - +
407A ASP* 1.3 80.7 + - - +
411A GLU* 3.8 6.3 - - + +
413A GLU* 3.0 25.9 + - + -
414A ASP* 2.8 30.6 + - - +
415A HIS 3.5 19.1 - - - -
416A MET* 3.5 37.0 - - + -
418A VAL* 5.6 0.2 - - + -
431A ILE* 4.5 11.4 - - + -
433A LEU* 3.2 42.1 - - + +
435A ARG* 3.9 4.5 - - - +
439A PHE* 4.7 0.4 - - + -
440A SER 3.4 6.5 - - - +
441A MET* 3.5 32.3 - - + +
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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