Contacts of the strand formed by residues 412 - 417 (chain E) in PDB entry 4KRM
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 PHE 412 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380E PHE* 3.5 5.0 - - - +
407E LYS* 3.5 3.9 - - - -
408E GLN* 2.8 62.3 + - + +
409E HIS* 5.0 10.8 - + + -
411E GLN* 1.3 111.3 - - + +
413E SER* 1.3 60.0 + - - +
414E LEU 4.1 4.9 - - - +
415E ALA* 4.5 2.1 - - + +
436E ASP* 3.5 22.4 - - + +
437E VAL 4.7 1.3 - - - -
438E ILE* 3.7 54.7 - - + -
465E LYS* 4.8 9.4 - - + -
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Residues in contact with SER 413 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380E PHE* 3.1 13.1 - - - +
381E LEU 2.9 24.4 + - - -
402E ILE* 3.5 14.4 - - - +
404E GLY* 3.9 17.0 - - - -
406E THR 5.0 0.9 - - - -
407E LYS* 5.0 0.7 - - - -
411E GLN 3.9 1.4 + - - -
412E PHE* 1.3 73.0 - - - +
414E LEU* 1.3 61.7 + - - +
432E ILE* 3.3 15.9 - - - +
434E ASP 3.0 28.0 + - - -
435E GLY* 3.5 5.3 + - - -
436E ASP 2.9 12.3 + - - -
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Residues in contact with LEU 414 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381E LEU* 3.5 35.7 - - + +
402E ILE* 4.0 11.4 - - + -
412E PHE* 4.1 0.9 - - - +
413E SER* 1.3 83.5 + - - +
415E ALA* 1.3 67.7 - - - +
416E VAL* 4.3 20.2 - - + +
424E LEU* 6.1 0.2 - - + -
426E LEU* 4.2 22.0 - - + -
429E LEU* 4.3 14.8 - - + -
432E ILE* 4.3 9.0 - - + -
436E ASP 3.5 2.4 + - - +
437E VAL* 3.5 28.6 - - + -
438E ILE* 3.1 25.0 + - - +
439E ILE* 5.0 2.9 - - + -
453E TRP* 4.6 7.9 - - + -
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Residues in contact with ALA 415 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380E PHE* 6.3 0.2 - - + -
381E LEU 2.9 11.8 + - - +
382E LEU* 3.5 22.3 - - + +
383E ILE* 2.8 33.1 + - - +
408E GLN* 4.0 13.2 - - + +
412E PHE* 4.5 3.6 - - + +
414E LEU* 1.3 76.5 - - - +
416E VAL* 1.3 61.3 + - - +
417E VAL* 3.9 4.5 - - + -
438E ILE* 3.3 24.7 - - + -
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Residues in contact with VAL 416 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383E ILE* 3.6 8.3 - - + -
393E LEU* 4.2 13.2 - - + -
414E LEU* 4.3 19.7 - - + -
415E ALA* 1.3 74.2 - - - +
417E VAL* 1.3 59.5 + - - +
419E LEU* 3.4 28.3 - - + -
421E ILE* 4.3 4.3 - - + -
424E LEU* 3.8 33.4 - - + -
426E LEU* 5.5 0.9 - - + -
438E ILE 3.0 7.5 + - - -
439E ILE* 3.3 15.6 - - + -
440E SER 3.2 12.1 + - - -
442E ASN* 3.1 25.7 + - - +
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Residues in contact with VAL 417 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382E LEU* 5.1 4.3 - - + -
383E ILE 2.9 13.7 + - - +
384E GLN* 3.5 20.5 - - + +
415E ALA* 4.3 12.6 - - + +
416E VAL* 1.3 85.9 - - - +
418E SER* 1.3 87.7 + - - +
419E LEU* 3.2 15.6 - - - +
438E ILE* 4.5 15.5 - - + -
440E SER* 3.3 22.2 - - - +
441E GLY* 5.4 0.2 - - - -
442E ASN* 3.8 0.2 - - - -
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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