Contacts of the helix formed by residues 602 - 613 (chain A) in PDB entry 5MJ6
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 ASP 602 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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594A ASN* 3.0 26.1 + - - -
599A GLN* 5.0 3.0 + - + +
600A THR 4.3 0.2 - - - -
601A LEU* 1.3 77.5 - - - +
603A VAL* 1.3 61.1 + - - +
604A LYS* 3.3 8.9 + - - +
605A ARG* 3.2 28.0 + - + +
606A MET* 3.1 18.7 + - - +
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Residues in contact with VAL 603 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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559A LEU* 4.3 12.8 - - + -
563A LEU* 4.6 11.0 - - + -
590A TRP* 3.8 27.6 - - + -
593A PHE* 4.0 19.5 - - + -
594A ASN* 2.8 15.7 + - - +
597A THR* 3.8 22.2 - - - +
601A LEU* 3.2 19.7 + - + +
602A ASP* 1.3 73.0 - - - +
604A LYS* 1.3 64.1 + - - +
606A MET* 3.2 7.6 + - + +
607A MET* 3.0 30.3 + - + +
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Residues in contact with LYS 604 (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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587A ASP* 4.0 38.1 + - - +
590A TRP* 3.8 22.1 - - + +
591A ASP* 2.9 31.9 + - - -
594A ASN* 3.8 10.7 + - - +
602A ASP* 3.2 11.8 + - - +
603A VAL* 1.3 80.0 - - - +
605A ARG* 1.3 68.4 + - + +
607A MET* 3.4 1.7 + - - +
608A LYS* 3.2 21.0 + - - +
2K NAG 4.2 5.5 + - - -
3K BMA 3.4 23.3 + - - +
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Residues in contact with ARG 605 (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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602A ASP* 3.2 27.5 + - + +
604A LYS* 1.3 84.1 + - + +
606A MET* 1.3 64.1 + - - +
607A MET 3.4 0.4 + - - -
608A LYS* 2.9 62.3 + - - +
609A THR* 5.1 0.5 + - - -
653A HIS* 3.7 21.8 + - + -
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Residues in contact with MET 606 (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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558A MET* 5.5 3.4 - - + -
559A LEU* 3.9 29.6 - - + -
562A TYR* 4.4 7.2 - - + -
601A LEU* 4.0 33.7 - - + -
602A ASP 3.1 12.9 + - - +
603A VAL* 3.2 12.5 + - - +
605A ARG* 1.3 80.3 - - - +
607A MET* 1.3 65.0 + - - +
608A LYS 3.7 0.2 + - - -
609A THR* 4.7 2.4 + - - -
610A TRP* 3.5 16.6 - - - +
653A HIS* 3.7 37.0 + - + +
655A PRO* 3.7 34.8 - - + -
673A LEU* 4.6 8.1 - - + -
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Residues in contact with MET 607 (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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555A LEU* 4.1 25.4 - - + +
558A MET* 4.6 5.4 - - + -
559A LEU* 3.7 26.5 - - + -
590A TRP* 3.6 51.8 - - + +
603A VAL* 3.0 24.7 + - + +
604A LYS 3.9 0.9 - - - +
606A MET* 1.3 89.4 - - - +
608A LYS* 1.3 64.9 + - - +
609A THR 3.3 2.5 - - - -
610A TRP* 3.2 32.6 + - + +
611A THR* 3.1 25.2 + - - +
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Residues in contact with LYS 608 (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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590A TRP* 6.0 0.4 - - - +
604A LYS 3.2 11.4 + - - +
605A ARG* 2.9 59.3 - - - +
606A MET 3.4 1.0 - - - -
607A MET* 1.3 78.1 - - - +
609A THR* 1.3 73.1 + - - +
611A THR* 3.2 6.4 + - - -
612A LEU* 3.0 44.6 + - + +
650A TYR* 5.8 15.3 - - - -
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Residues in contact with THR 609 (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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605A ARG 5.1 0.4 + - - -
606A MET 4.7 3.1 + - - -
607A MET 3.3 0.2 - - - -
608A LYS* 1.3 88.9 - - - +
610A TRP* 1.3 64.6 + - - +
612A LEU* 4.5 1.1 - - - +
613A GLN* 3.0 62.1 + - + +
650A TYR* 4.3 9.9 - - + +
651A LEU 2.7 28.3 + - - +
652A TRP* 3.6 22.0 + - + +
653A HIS* 5.3 4.5 - - - -
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Residues in contact with TRP 610 (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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530A ILE* 4.0 1.9 - - - +
551A LYS* 3.8 28.7 + - - -
555A LEU* 3.9 21.0 - - + +
558A MET* 3.4 26.3 - - + +
606A MET* 3.5 23.0 - - + +
607A MET* 3.2 34.9 + - + +
609A THR* 1.3 80.1 - - - +
611A THR* 1.3 58.2 + - - +
613A GLN 4.2 1.2 - - - +
615A GLY 5.1 0.2 - - - -
616A PHE* 4.3 1.6 - - + -
617A PRO* 3.5 22.0 - - + -
652A TRP* 3.3 33.4 - + + +
653A HIS 2.8 27.7 + - - +
654A ILE* 4.2 11.2 - - + -
655A PRO* 4.8 0.4 - - - +
699A TYR* 3.2 44.2 - + + -
700A TYR* 4.7 2.5 - + + -
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Residues in contact with THR 611 (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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484A TRP* 4.1 10.5 - - + -
530A ILE* 3.5 15.3 + - + +
531A SER* 3.2 32.0 + - - +
555A LEU* 4.0 14.6 - - + -
586A SER* 5.2 4.8 + - - -
590A TRP* 3.6 34.5 + - + +
607A MET* 3.1 17.6 + - + +
608A LYS* 3.2 6.1 + - - -
610A TRP* 1.3 79.4 - - - +
612A LEU* 1.3 75.4 + - - +
613A GLN 3.7 0.9 - - - -
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Residues in contact with LEU 612 (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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529A PRO* 3.1 20.9 - - - +
531A SER* 3.9 20.6 - - - +
586A SER* 6.5 0.7 - - - -
608A LYS* 3.0 38.3 + - + +
609A THR* 5.2 0.9 - - - -
611A THR* 1.3 91.6 - - - +
613A GLN* 1.3 61.7 + - - +
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Residues in contact with GLN 613 (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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529A PRO* 4.0 7.3 - - - +
551A LYS* 3.9 13.0 + - - -
609A THR* 3.0 36.8 + - + +
610A TRP 4.2 2.9 - - - +
611A THR 4.8 0.2 - - - -
612A LEU* 1.3 79.1 - - - +
614A LYS* 1.3 74.8 + - + +
615A GLY 4.3 1.4 - - - +
634A ARG* 5.3 4.3 - - - +
649A SER* 3.5 12.0 + - - -
650A TYR* 3.1 53.0 + - + +
652A TRP* 3.3 32.4 + - + -
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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