Contacts of the helix formed by residues 572 - 580 (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 THR 572 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148A ASN* 3.7 10.5 - - - +
414A PRO* 3.7 13.7 - - + -
416A ALA* 3.4 7.8 - - - +
563A TYR* 4.9 0.2 + - - -
569A THR 3.6 22.4 - - - +
570A MET* 2.8 11.9 + - - -
571A ASP* 1.3 74.1 - - - +
573A TYR* 1.3 59.5 + - - +
574A LYS* 3.5 9.5 + - - +
575A GLU* 3.1 23.6 + - - +
576A LEU* 2.9 28.4 + - - +
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Residues in contact with TYR 573 (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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141A THR* 3.5 33.2 + - - -
144A ILE* 3.7 22.4 - - + +
145A LYS* 3.8 42.6 + - + +
148A ASN* 3.0 30.2 + - + +
416A ALA* 3.4 11.1 - - + +
572A THR* 1.3 71.6 - - - +
574A LYS* 1.3 66.2 + - + +
576A LEU* 3.0 4.3 + - - +
577A ILE* 2.6 62.2 + - + +
583A LEU* 4.1 20.9 - - + -
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Residues in contact with LYS 574 (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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145A LYS* 6.3 2.9 - - - +
148A ASN* 5.5 2.0 - - - +
572A THR* 3.2 8.8 + - - +
573A TYR* 1.3 85.6 - - + +
575A GLU* 1.3 63.7 + - - +
577A ILE* 3.2 12.6 - - + +
578A GLU* 3.1 25.8 + - - +
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Residues in contact with GLU 575 (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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563A TYR* 4.0 3.8 - - - +
565A TYR* 3.5 44.9 + - + -
570A MET* 3.4 34.0 - - + +
572A THR* 3.1 14.0 + - - +
574A LYS* 1.3 77.9 - - - +
576A LEU* 1.3 62.4 + - - +
578A GLU* 3.1 30.1 + - - +
579A ARG* 3.1 28.9 + - - +
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Residues in contact with LEU 576 (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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144A ILE* 4.2 12.8 - - + -
416A ALA* 4.4 11.2 - - + -
417A ALA* 4.4 7.0 - - + +
421A VAL* 3.8 28.0 - - + -
488A VAL 4.4 11.2 - - - +
563A TYR* 3.5 25.7 + - + +
572A THR 2.9 13.9 + - - +
573A TYR 3.3 7.6 - - - +
575A GLU* 1.3 77.8 - - - +
577A ILE* 1.3 60.6 + - - +
578A GLU 3.0 0.4 + - - -
579A ARG* 3.4 0.6 + - - -
580A ILE* 3.0 53.2 + - + +
583A LEU* 3.8 25.1 - - + -
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Residues in contact with ILE 577 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A THR* 4.3 7.4 - - + -
573A TYR* 2.6 51.7 + - + +
574A LYS* 3.2 23.6 - - + +
576A LEU* 1.3 73.1 - - - +
578A GLU* 1.3 57.6 + - + +
580A ILE 3.8 6.1 - - - +
581A PRO* 3.3 34.4 - - + +
583A LEU* 3.7 29.8 - - + -
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Residues in contact with GLU 578 (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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574A LYS 3.1 18.0 + - - +
575A GLU* 3.1 24.8 + - - +
576A LEU 3.0 0.6 - - - -
577A ILE* 1.3 79.0 - - + +
579A ARG* 1.3 66.7 + - + +
580A ILE 3.2 1.7 + - - -
581A PRO* 4.1 10.6 - - - +
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Residues in contact with ARG 579 (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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289A PRO* 6.1 2.8 - - - +
489A LEU 4.2 7.7 + - - -
490A GLY* 5.8 0.4 - - - -
559A GLU* 5.2 5.1 + - - -
561A THR* 5.4 6.1 - - - +
563A TYR* 3.4 43.0 - - + -
564A PRO* 3.8 22.4 - - - +
565A TYR* 3.7 25.0 + - - -
575A GLU* 3.1 20.7 + - - +
576A LEU 4.3 0.4 - - - +
578A GLU* 1.3 79.8 - - + +
580A ILE* 1.3 68.8 + - + +
581A PRO* 3.7 6.6 - - - +
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Residues in contact with ILE 580 (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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488A VAL* 4.1 11.7 - - + -
489A LEU 3.7 7.4 - - - +
490A GLY* 3.7 33.2 - - - +
491A THR* 4.6 7.0 - - - +
563A TYR* 5.0 2.0 - - + -
576A LEU* 3.0 36.5 + - + +
577A ILE* 3.4 7.7 - - - +
579A ARG* 1.3 91.2 - - + +
581A PRO* 1.3 65.4 - - - +
582A GLU* 3.3 15.0 - - - +
583A LEU* 3.1 36.3 + - + +
586A VAL* 4.2 14.6 - - + -
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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