Contacts of the strand formed by residues 412 - 417 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380I PHE* 3.4 4.2 - - - +
407I LYS* 3.1 7.6 - - - -
408I GLN* 2.7 64.0 + - + +
409I HIS* 4.7 12.1 - + + -
411I GLN* 1.3 115.7 - - + +
413I SER* 1.3 59.5 + - - +
414I LEU 4.4 3.4 - - - +
415I ALA* 4.5 2.9 - - + -
436I ASP* 3.4 24.7 - - + +
437I VAL 4.5 2.7 - - - -
438I ILE* 3.6 49.8 - - + -
465I LYS* 4.8 9.0 - - + -
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Residues in contact with SER 413 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380I PHE* 3.0 13.6 - - - -
381I LEU* 2.7 30.4 + - - +
402I ILE* 3.6 10.7 - - - +
404I GLY* 4.1 16.2 - - - -
407I LYS* 4.8 1.6 - - - -
412I PHE* 1.3 74.1 - - - +
414I LEU* 1.3 58.8 + - - +
432I ILE* 3.3 14.3 - - - +
434I ASP 2.8 29.4 + - - -
435I GLY* 3.2 8.5 + - - -
436I ASP 2.9 11.8 + - - +
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Residues in contact with LEU 414 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381I LEU* 3.5 32.5 - - + +
402I ILE* 4.0 14.4 - - + -
412I PHE* 4.4 0.2 - - - +
413I SER* 1.3 83.9 + - - +
415I ALA* 1.3 64.0 + - - +
416I VAL* 4.2 20.6 - - + -
426I LEU* 4.3 24.2 - - + -
429I LEU* 4.6 3.8 - - + -
432I ILE* 4.3 17.0 - - + -
436I ASP 3.5 2.1 + - - +
437I VAL* 3.4 30.1 - - + -
438I ILE* 2.9 26.9 + - - +
439I ILE* 5.0 2.0 - - + -
453I TRP* 4.3 9.6 - - + -
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Residues in contact with ALA 415 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380I PHE* 6.2 0.2 - - + -
381I LEU 2.8 12.8 + - - +
382I LEU* 3.5 25.7 - - + -
383I ILE* 2.9 27.9 + - - +
408I GLN* 3.7 13.7 - - + +
412I PHE* 4.5 3.8 - - + -
414I LEU* 1.3 75.4 - - - +
416I VAL* 1.3 65.7 + - - +
417I VAL* 4.0 4.3 - - + -
438I ILE* 3.4 22.2 - - + -
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Residues in contact with VAL 416 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383I ILE* 3.6 8.1 - - + -
393I LEU* 4.4 12.1 - - + -
414I LEU* 4.2 24.0 - - + -
415I ALA* 1.3 76.0 - - - +
417I VAL* 1.3 60.6 + - - +
419I LEU* 3.4 30.7 - - + -
421I ILE* 4.4 3.8 - - + -
424I LEU* 4.2 26.7 - - + -
426I LEU* 5.6 0.9 - - + -
438I ILE 2.9 10.7 + - - +
439I ILE* 3.4 14.7 - - + -
440I SER 3.2 22.3 + - - -
442I ASN* 3.3 15.8 + - - +
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Residues in contact with VAL 417 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382I LEU* 4.9 5.2 - - + -
383I ILE 2.9 12.2 + - - +
384I GLN* 3.3 27.2 - - + +
408I GLN* 6.0 0.2 - - - +
415I ALA* 4.5 12.8 - - + -
416I VAL* 1.3 85.2 - - - +
418I SER* 1.3 86.1 + - - +
419I LEU* 3.3 14.8 - - - +
438I ILE* 4.8 12.3 - - + +
440I SER* 3.4 19.1 - - - +
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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