Contacts of the strand formed by residues 428 - 432 (chain C) in PDB entry 3KSA
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 GLU 428 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426C LYS* 5.6 0.7 - - + -
427C ASN* 1.3 78.1 - - - +
429C LEU* 1.3 60.2 + - - +
430C TYR* 3.2 16.5 + - + -
449C PHE* 3.3 27.3 + - + +
450C GLN* 3.2 14.7 - - - +
451C ALA* 2.8 30.0 + - - +
498C TYR* 3.7 3.4 - - - -
500C LYS* 3.5 30.7 + - + +
502C ILE* 4.0 16.4 - - + -
598C PRO* 5.0 0.9 - - - +
601C ARG* 2.7 44.2 + - - -
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Residues in contact with LEU 429 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416C LEU* 4.5 3.6 - - + -
428C GLU* 1.3 72.9 - - - +
430C TYR* 1.3 70.1 + - - +
431C LEU* 3.7 21.3 + - + -
451C ALA* 3.8 15.7 - - + +
453C LEU* 3.7 24.9 - - + -
479C MET* 6.1 0.2 - - + -
482C THR* 4.0 18.4 - - - +
483C ILE* 4.1 20.9 - - + -
498C TYR* 3.6 31.8 - - + +
500C LYS 2.9 11.2 + - - +
501C ILE* 3.6 9.3 - - + +
502C ILE* 2.8 28.5 + - - +
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Residues in contact with TYR 430 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428C GLU* 3.2 12.5 + - + -
429C LEU* 1.3 75.8 - - - +
431C LEU* 1.3 62.7 + - - +
432C VAL* 3.8 4.6 + - + +
450C GLN* 3.4 34.6 + - + -
451C ALA 2.8 20.2 + - - +
452C ILE* 3.5 9.6 - - + -
453C LEU 2.9 27.9 + - - +
502C ILE* 3.5 37.2 - - + +
504C MET* 3.3 35.7 - - + -
538C ALA* 4.8 3.8 - - + -
595C THR 4.6 1.5 + - - -
596C MET* 3.7 28.7 + - + -
601C ARG* 3.0 29.5 + - - -
603C LEU* 5.1 1.3 - - + +
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Residues in contact with LEU 431 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429C LEU* 4.0 17.0 - - + -
430C TYR* 1.3 73.6 - - - +
432C VAL* 1.3 61.3 + - - +
453C LEU* 3.5 40.2 - - + +
455C LEU* 4.6 8.5 - - + -
479C MET* 4.0 26.2 - - + -
483C ILE* 5.5 0.7 - - + -
501C ILE* 3.8 24.9 - - + -
502C ILE 2.8 12.8 + - - +
503C ILE* 4.0 11.4 - - + +
504C MET* 2.9 30.0 + - - +
505C THR* 5.5 0.7 - - - +
518C LEU* 4.9 7.0 - - + -
522C PHE* 4.0 19.5 - - + -
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Residues in contact with VAL 432 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430C TYR 4.3 6.1 - - - +
431C LEU* 1.3 80.2 - - - +
433C GLU* 1.3 63.0 + - - +
434C GLY 3.3 24.7 - - - +
437C ALA* 3.5 19.3 - - + -
438C GLY* 3.7 8.7 - - - +
441C ALA* 4.5 13.5 - - + -
452C ILE* 4.9 3.4 - - + -
453C LEU 3.1 12.2 + - - +
454C PRO* 4.6 3.8 - - + -
455C LEU* 2.9 33.4 + - - +
504C MET* 3.6 36.3 - - + +
505C THR* 5.8 1.6 - - - -
583C LEU* 5.2 2.2 - - + -
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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