Contacts of the strand formed by residues 407 - 411 (chain A) in PDB entry 4FWF
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 LYS 407 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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381A HIS 4.9 1.3 + - - +
383A LYS 3.3 12.5 + - - +
384A SER* 3.5 15.8 - - - -
385A VAL* 2.8 28.5 + - - +
405A GLY 3.9 1.4 + - - -
406A ILE* 1.3 77.3 - - - +
408A VAL* 1.3 64.0 + - - +
409A THR* 4.9 16.2 - - + -
591A ASP* 5.7 3.1 + - - -
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Residues in contact with VAL 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A VAL* 3.5 18.6 - - + +
387A ILE* 3.5 34.8 - - + -
398A ALA* 3.9 11.0 - - + +
401A LEU* 3.6 12.6 - - + -
402A HIS* 3.5 41.7 - - + +
406A ILE 3.5 10.0 + - - +
407A LYS* 1.3 77.6 - - - +
409A THR* 1.3 65.3 + - - +
410A VAL* 5.2 1.6 - - + -
590A LEU* 5.9 1.1 - - + -
591A ASP* 3.6 19.1 + - - +
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Residues in contact with THR 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A SER* 6.6 0.4 - - - -
385A VAL 3.1 13.8 + - - +
386A ILE* 3.2 18.5 - - + +
387A ILE* 2.9 24.1 + - - +
407A LYS* 4.9 16.8 - - + +
408A VAL* 1.3 76.9 - - - +
410A VAL* 1.3 61.9 + - - +
411A LEU* 4.3 15.1 - - - +
591A ASP* 3.2 27.8 + - - +
593A GLN* 4.6 4.2 - - - +
618A TYR* 4.6 13.4 - - + -
619A SER 6.1 0.9 - - - +
620A ALA* 6.0 1.6 - - + -
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Residues in contact with VAL 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A ILE* 3.3 18.8 - - + +
389A GLY 4.0 9.9 - - - +
390A ALA* 3.8 29.6 - - + -
394A GLY 5.4 0.7 - - - +
395A LEU* 5.3 2.7 - - + -
398A ALA* 3.8 28.9 - - + -
408A VAL* 5.2 2.7 - - + -
409A THR* 1.3 77.3 + - - +
411A LEU* 1.3 62.3 + - - +
590A LEU* 5.3 3.1 - - + -
591A ASP 2.8 17.3 + - - +
592A ILE* 4.0 19.7 - - + -
593A GLN* 2.8 34.5 + - - +
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Residues in contact with LEU 411 (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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386A ILE* 4.2 14.4 - - + -
387A ILE 2.8 13.2 + - - +
388A ILE* 3.6 2.0 - - + -
389A GLY 2.9 25.0 + - - -
409A THR* 4.3 7.0 - - - +
410A VAL* 1.3 73.4 - - - +
412A GLU* 1.3 60.0 + - - +
593A GLN* 3.6 28.5 - - + -
596A SER* 4.1 14.6 - - - +
598A VAL* 3.8 24.2 - - + -
610A VAL* 4.1 12.1 - - + -
611A THR 6.4 0.2 - - - -
612A THR* 5.1 3.1 - - - +
618A TYR* 3.6 48.7 - - + -
904A FAD 3.2 8.6 - - - -
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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