Contacts of the helix formed by residues 574 - 581 (chain J) in PDB entry 6C6S
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 VAL 574 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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527J LEU* 5.5 4.3 - - + -
533J ALA* 3.8 31.6 - - + +
536J LEU* 5.6 0.7 - - + -
537J TYR* 4.5 7.0 - - + -
542J ALA* 4.6 13.5 - - + -
543J SER 3.7 24.7 - - - +
544J LEU* 3.8 4.0 + - - +
546J ALA* 3.5 18.1 + - + +
548J VAL* 4.1 18.6 - - + -
550J VAL* 5.9 0.9 - - - -
573J THR* 1.3 74.3 - - - +
575J GLY* 1.3 65.9 + - - +
577J ALA* 3.1 8.0 + - - +
578J ILE* 3.0 31.1 + - + +
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Residues in contact with GLY 575 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513J MET* 3.9 21.4 - - - +
514J THR* 4.9 1.1 - - - -
544J LEU* 3.0 37.7 + - - -
573J THR* 3.9 1.2 + - - -
574J VAL* 1.3 75.2 - - - +
576J ARG* 1.3 56.7 + - - +
578J ILE* 3.3 4.6 + - - +
579J LEU* 2.9 30.3 + - - +
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Residues in contact with ARG 576 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514J THR* 3.2 25.6 + - - +
515J ARG* 3.7 14.8 + - - +
516J ASP* 4.5 8.5 + - - +
572J THR* 3.2 28.7 - - - +
573J THR* 3.0 43.5 + - - +
574J VAL 3.2 0.4 - - - -
575J GLY* 1.3 78.0 - - - +
577J ALA* 1.3 55.3 + - - +
579J LEU* 3.4 6.0 + - - +
580J TRP* 2.9 26.3 + - - +
589J TYR* 3.5 7.8 + - + +
592J VAL* 3.3 19.1 - - - +
593J ASN* 2.6 33.7 + - - +
594J GLN* 2.9 25.5 + - - +
595J ALA* 3.8 6.9 - - - +
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Residues in contact with ALA 577 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530J PRO* 3.3 35.5 - - + +
533J ALA* 4.1 9.2 - - + -
550J VAL* 4.4 18.8 - - + -
552J ILE* 5.3 0.4 - - + -
573J THR 3.4 9.4 + - - +
574J VAL 3.1 9.4 + - - +
576J ARG* 1.3 75.5 - - - +
578J ILE* 1.3 62.2 + - - +
580J TRP* 2.9 23.7 + - - +
581J MET 3.1 9.9 + - - -
589J TYR* 3.9 4.4 + - - +
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Residues in contact with ILE 578 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513J MET* 4.6 4.3 - - - -
530J PRO 4.9 0.4 - - - +
533J ALA* 4.4 2.2 - - + -
534J GLU* 4.1 31.2 - - + +
537J TYR* 3.9 33.0 - - + -
544J LEU* 4.0 18.8 - - + -
574J VAL* 3.0 19.3 + - + +
575J GLY* 3.3 7.6 + - - +
577J ALA* 1.3 74.3 - - - +
579J LEU* 1.3 62.4 + - - +
581J MET* 3.3 24.7 + - - +
582J ILE* 4.1 9.8 - - + +
627J THR* 5.3 1.1 - - - +
631J TYR* 3.4 32.8 - - + +
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Residues in contact with LEU 579 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510J LEU* 3.8 18.6 - - + -
513J MET* 3.7 24.2 - - + -
514J THR* 4.3 8.1 - - + -
575J GLY 2.9 16.3 + - - +
576J ARG* 3.8 5.2 - - - +
578J ILE* 1.3 74.8 - - - +
580J TRP* 1.3 64.3 + - - +
582J ILE* 3.2 21.5 + - + +
583J VAL* 3.5 12.7 + - + +
592J VAL* 4.5 15.3 - - + -
596J LEU* 3.6 31.6 - - + -
604J MET* 5.3 3.8 - - + -
620J PHE* 6.0 1.1 - - + -
624J ILE* 5.4 5.4 - - + -
627J THR* 4.2 19.7 - - + -
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Residues in contact with TRP 580 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530J PRO* 3.9 22.0 - - + -
552J ILE* 4.5 7.0 - - + -
553J THR* 3.6 33.5 + - - +
554J GLU* 3.9 17.9 - - + -
555J TYR 5.2 0.2 - - - -
576J ARG 2.9 15.6 + - - +
577J ALA* 2.9 11.4 + - - +
579J LEU* 1.3 73.0 - - - +
581J MET* 1.3 56.5 + - - +
582J ILE 3.0 10.9 + - - -
583J VAL* 3.5 46.0 + - + +
584J PRO 4.6 7.4 - - - -
585J LYS* 5.0 2.7 - - - -
587J LEU 3.4 23.6 - - - -
588J PRO 4.0 2.5 - - - -
589J TYR* 3.5 43.1 - + + -
591J ILE* 5.3 0.4 - - + -
592J VAL* 4.3 6.7 - - + +
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Residues in contact with MET 581 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182H ARG* 3.4 38.6 - - - +
530J PRO* 3.6 41.1 - - + +
531J LYS* 3.8 24.5 - - + -
534J GLU* 3.6 20.2 - - - +
577J ALA 3.1 4.7 + - - +
578J ILE* 3.6 12.8 - - - +
579J LEU 3.1 1.8 - - - -
580J TRP* 1.3 77.4 - - - +
582J ILE* 1.3 61.5 + - + +
583J VAL 4.6 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