Contacts of the helix formed by residues 540 - 547 (chain A) in PDB entry 3KAS
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 ALA 540 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453A TRP* 4.9 5.2 - - + -
460A SER* 3.5 25.2 + - - +
463A ALA* 4.8 8.7 - - + +
481A TYR* 4.0 8.1 - - - +
483A ASN* 3.4 22.3 + - - +
485A ASP* 4.1 10.4 + - - +
538A ASP 4.0 1.8 + - - -
539A ASN* 1.3 76.0 + - - +
541A ALA* 1.3 57.6 + - - +
542A PHE 3.1 0.2 - - - -
543A PRO* 3.0 17.1 - - - +
544A PHE* 3.4 17.5 - - - -
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Residues in contact with ALA 541 (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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481A TYR* 3.8 14.0 - - + -
483A ASN* 4.0 14.8 - - + -
535A LEU* 3.6 26.7 - - + +
539A ASN* 2.8 16.8 + - - +
540A ALA* 1.3 77.5 - - - +
542A PHE* 1.3 62.4 + - - +
543A PRO 3.6 0.2 - - - -
544A PHE* 3.5 2.4 + - - +
545A LEU 3.3 16.8 + - - -
552A ALA* 3.4 19.2 - - + +
553A VAL 4.5 3.4 - - - -
554A SER* 4.4 3.6 - - - -
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Residues in contact with PHE 542 (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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305A THR* 4.9 0.4 - - + -
535A LEU* 3.4 38.0 - - + +
536A THR* 3.2 19.3 - - - +
537A LEU* 4.0 22.0 - - + -
539A ASN* 2.9 17.8 + - - +
541A ALA* 1.3 75.3 - - - +
543A PRO* 1.3 64.2 - - + +
545A LEU* 3.2 3.0 + - + +
546A ALA* 2.8 38.9 + - + +
697A PHE* 3.4 48.9 - + + -
702A TRP* 3.4 26.9 - - + -
704A SER* 4.6 9.6 - - - -
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Residues in contact with PRO 543 (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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305A THR* 3.8 29.8 - - + +
460A SER* 4.3 6.7 - - - -
463A ALA* 5.6 0.9 - - + -
464A THR* 3.8 15.9 - - + +
467A LEU* 3.5 19.7 - - + -
539A ASN 3.3 6.5 - - - +
540A ALA 3.0 25.6 - - - +
542A PHE* 1.3 92.2 - - + +
544A PHE* 1.3 57.1 + - - +
547A TYR* 2.8 43.3 + - + +
548A SER* 3.0 4.3 + - - -
697A PHE* 4.5 1.8 - - + -
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Residues in contact with PHE 544 (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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404A VAL* 4.7 8.5 - - + -
453A TRP* 3.9 21.3 - + - -
463A ALA* 4.5 6.7 - - + -
466A TRP* 4.1 13.9 - + - -
467A LEU* 3.6 38.4 - - + -
474A LEU* 4.7 0.4 - - + -
478A ALA* 5.6 0.2 - - + -
481A TYR* 3.5 61.7 - + + -
540A ALA 3.4 20.9 - - - -
541A ALA 3.5 8.2 + - - +
542A PHE 3.2 0.6 - - - -
543A PRO* 1.3 79.9 - - - +
545A LEU* 1.3 57.8 + - - +
548A SER* 3.2 5.6 + - - -
549A GLY 2.9 24.3 + - - -
550A ILE* 3.0 31.0 + - + +
552A ALA* 4.2 0.9 - - + -
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Residues in contact with LEU 545 (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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498A ALA 4.8 1.3 - - - -
499A SER* 4.1 20.0 - - - +
535A LEU* 3.9 23.8 - - + +
541A ALA 3.3 11.3 + - - +
542A PHE* 3.2 4.7 + - + +
544A PHE* 1.3 78.9 - - - +
546A ALA* 1.3 60.4 + - + +
549A GLY* 3.1 24.1 + - - -
550A ILE 3.1 13.2 + - - +
552A ALA* 4.3 5.2 - - + +
682A GLU* 3.3 40.4 - - + +
686A LEU* 4.1 0.2 - - - +
699A HIS* 3.8 7.4 - - + -
702A TRP* 3.6 40.6 - - + +
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Residues in contact with ALA 546 (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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542A PHE* 2.8 34.9 + - + +
545A LEU* 1.3 75.7 - - + +
547A TYR* 1.3 56.1 + - - +
686A LEU* 3.9 3.4 - - - +
697A PHE* 4.1 7.2 - - + -
698A ARG 3.1 25.3 + - - -
699A HIS* 3.4 15.4 + - - +
702A TRP* 3.8 26.2 - - + +
703A GLY* 3.9 12.1 - - - -
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Residues in contact with TYR 547 (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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464A THR* 5.6 4.9 - - + -
467A LEU* 4.2 21.3 - - + -
468A GLU* 3.0 43.2 + - + +
471A LEU* 3.3 43.2 - - + +
543A PRO* 2.8 24.5 + - + +
546A ALA* 1.3 79.4 - - - +
548A SER* 1.3 71.9 + - - -
549A GLY 3.7 0.4 - - - -
686A LEU* 3.4 15.3 - - - +
692A PRO* 4.3 8.9 - - + +
696A PRO* 3.3 44.1 - - + +
697A PHE* 4.2 9.4 - + + -
698A ARG* 4.7 2.3 + - - -
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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