Contacts of the strand formed by residues 428 - 432 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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426D LYS* 6.4 0.2 - - + -
427D ASN* 1.3 79.4 - - - +
429D LEU* 1.3 60.8 + - - +
430D TYR* 3.2 15.3 + - + -
449D PHE* 3.3 28.0 + - + +
450D GLN* 3.3 14.7 - - - +
451D ALA* 2.8 30.3 + - - +
498D TYR* 3.7 3.7 - - - -
500D LYS* 3.5 30.4 + - + +
502D ILE* 4.0 16.2 - - + -
598D PRO* 5.0 0.5 - - - +
601D ARG* 2.7 44.6 + - - -
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Residues in contact with LEU 429 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416D LEU* 4.5 2.9 - - + -
428D GLU* 1.3 72.5 - - - +
430D TYR* 1.3 68.4 + - - +
431D LEU* 3.7 22.5 + - + -
451D ALA* 3.7 17.3 - - + +
452D ILE 4.3 0.2 - - - +
453D LEU* 3.7 25.1 - - + -
482D THR* 4.0 18.2 - - - +
483D ILE* 4.1 21.1 - - + -
498D TYR* 3.6 31.8 - - + +
500D LYS 2.9 11.4 + - - +
501D ILE* 3.6 9.7 - - + +
502D ILE* 2.8 28.6 + - - +
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Residues in contact with TYR 430 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428D GLU* 3.2 13.2 + - + -
429D LEU* 1.3 75.9 - - - +
431D LEU* 1.3 60.6 + - - +
432D VAL* 3.8 1.9 + - + +
450D GLN* 3.4 33.6 + - + -
451D ALA 2.8 20.5 + - - +
452D ILE* 3.5 12.0 - - + +
453D LEU 2.9 27.2 + - - +
502D ILE* 3.5 38.7 - - + +
504D MET* 3.3 35.7 - - + -
538D ALA* 4.8 3.8 - - + -
595D THR 4.6 2.2 + - - -
596D MET* 3.6 29.0 + - + -
601D ARG* 3.0 29.3 + - - -
603D LEU* 5.1 1.3 - - + +
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Residues in contact with LEU 431 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429D LEU* 4.0 16.4 - - + -
430D TYR* 1.3 72.8 - - - +
432D VAL* 1.3 61.4 + - - +
453D LEU* 3.5 40.8 - - + +
455D LEU* 4.5 8.3 - - + -
479D MET* 4.0 26.0 - - + -
483D ILE* 5.5 0.7 - - + -
501D ILE* 3.8 25.8 - - + -
502D ILE 2.8 12.8 + - - +
503D ILE* 4.0 11.2 - - + +
504D MET* 2.9 29.6 + - - +
505D THR* 5.5 0.3 - - - +
518D LEU* 4.9 7.2 - - + -
522D PHE* 3.9 20.6 - - + -
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Residues in contact with VAL 432 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430D TYR 4.3 6.3 - - - +
431D LEU* 1.3 78.1 - - - +
433D GLU* 1.3 63.0 + - - +
434D GLY 3.3 24.9 - - - +
437D ALA* 3.5 19.5 - - + +
438D GLY* 3.7 9.0 - - - +
441D ALA* 4.5 14.1 - - + -
452D ILE* 4.9 2.9 - - + -
453D LEU 3.1 12.5 + - - +
454D PRO* 4.6 3.4 - - + -
455D LEU* 2.9 33.6 + - - +
504D MET* 3.5 36.1 - - + +
505D THR* 5.8 1.6 - - - -
583D LEU* 5.2 2.5 - - + -
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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