Contacts of the helix formed by residues 574 - 579 (chain A) in PDB entry 4A3K
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 GLY 574 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534A LEU* 3.2 40.1 - - - +
535A THR* 4.2 6.1 - - - -
536A LEU 5.3 1.0 + - - -
539A THR* 3.2 12.6 + - - -
541A ILE* 3.9 6.1 - - - +
573A SER* 1.3 69.7 - - - +
575A LYS* 1.4 63.6 + - - +
577A ILE* 3.0 6.9 + - - +
578A LEU* 2.9 23.4 + - - +
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Residues in contact with LYS 575 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535A THR* 3.1 37.9 + - - +
536A LEU 4.1 2.8 + - - +
537A ARG* 4.0 18.4 - - - +
573A SER* 3.9 9.0 - - - +
574A GLY* 1.4 72.9 - - - +
576A GLN* 1.3 58.7 + - - +
578A LEU* 3.2 2.6 + - - +
579A SER* 2.7 34.0 + - - -
602A ASP* 2.7 35.5 + - - -
612A ILE* 3.6 32.2 - - + +
613A ILE 4.6 9.2 - - - +
614A PHE* 4.2 1.3 - - - +
615A GLY 3.2 29.4 - - - +
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Residues in contact with GLN 576 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561A PRO* 4.8 10.9 - - + +
562A THR 2.6 30.8 + - - +
563A PRO 3.9 0.2 - - - -
564A ALA* 3.1 31.1 + - - +
572A TRP* 3.4 17.1 - - + -
573A SER* 3.2 32.1 + - - +
575A LYS* 1.3 79.4 - - - +
577A ILE* 1.3 64.1 + - + +
579A SER* 3.4 17.7 + - - -
580A VAL* 3.8 8.8 + - - +
611A GLN* 4.5 8.6 + - - +
612A ILE 5.5 1.1 + - - -
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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
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534A LEU* 5.1 3.6 - - + -
541A ILE* 3.8 21.5 - - + -
546A VAL* 4.2 14.8 - - + -
549A MET* 3.4 46.7 - - + +
550A LEU* 5.3 4.0 - - + +
553A VAL* 5.6 0.5 - - - +
561A PRO* 5.1 4.9 - - + -
572A TRP* 3.8 32.1 - - + -
573A SER 3.2 9.2 + - - +
574A GLY* 3.0 7.1 + - - +
576A GLN* 1.3 77.2 - - + +
578A LEU* 1.3 67.5 + - - +
580A VAL* 3.4 25.0 + - + +
581A ALA 4.4 0.5 + - - -
652A VAL* 3.8 18.1 - - + +
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Residues in contact with LEU 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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531A ILE* 3.7 29.4 - - + -
534A LEU* 4.2 11.2 - - + -
535A THR* 3.6 20.6 - - + -
574A GLY 2.9 15.2 + - - +
575A LYS 3.7 2.7 - - - +
577A ILE* 1.3 78.7 - - - +
579A SER* 1.4 53.3 + - - +
581A ALA* 2.8 37.7 + - + +
582A ILE* 3.7 9.3 + - + +
612A ILE* 3.5 25.6 - - + -
617A VAL* 3.8 12.1 - - + -
649A ILE* 4.4 18.8 - - + -
652A VAL* 5.2 7.2 - - + -
653A VAL* 4.3 12.3 - - + -
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Residues in contact with SER 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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575A LYS 2.7 17.5 + - - -
576A GLN* 3.4 14.1 - - - -
577A ILE 3.2 0.2 - - - -
578A LEU* 1.4 73.1 - - - +
580A VAL* 1.4 56.8 + - - +
581A ALA 3.2 0.4 - - - -
582A ILE* 3.0 36.0 + - - +
610A GLY 3.0 8.3 - - - +
611A GLN* 3.4 34.8 - - - +
612A ILE* 3.0 28.4 + - - +
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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