Contacts of the helix formed by residues 602 - 613 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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594B ASN* 3.1 19.1 + - - -
599B GLN 3.8 6.7 + - - +
600B THR 3.9 2.6 + - - -
601B LEU* 1.3 75.2 - - - +
603B VAL* 1.3 61.9 + - - +
604B LYS* 3.0 19.6 + - - +
605B ARG* 3.2 47.8 + - + +
606B MET* 3.1 21.3 + - - +
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Residues in contact with VAL 603 (chain B).
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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559B LEU* 4.2 15.7 - - + -
563B LEU* 4.7 13.0 - - + -
590B TRP* 3.8 24.9 - - + +
593B PHE* 3.8 34.5 - - + +
594B ASN* 3.0 13.2 + - - +
597B THR* 4.0 12.3 - - - +
601B LEU* 4.2 13.9 - - + +
602B ASP* 1.3 71.9 - - - +
604B LYS* 1.3 57.6 + - - +
606B MET* 3.2 8.5 + - + +
607B MET* 2.8 36.5 + - + +
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Residues in contact with LYS 604 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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587B ASP* 4.1 35.2 - - - +
590B TRP* 3.7 19.6 - - + +
591B ASP* 2.9 36.2 + - - +
594B ASN* 3.9 11.2 - - - +
602B ASP* 3.0 11.5 + - - +
603B VAL* 1.3 78.5 - - - +
605B ARG* 1.3 64.5 + - - +
607B MET* 3.3 2.4 + - - +
608B LYS* 3.2 22.9 + - - +
2N NAG 3.7 4.9 + - - -
3N BMA 2.9 28.3 + - - +
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Residues in contact with ARG 605 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602B ASP* 3.2 36.8 + - + +
604B LYS* 1.3 80.7 - - - +
606B MET* 1.3 63.5 + - - +
607B MET 3.4 0.2 + - - -
608B LYS* 3.5 25.0 + - + +
609B THR* 4.6 2.4 + - - -
653B HIS* 3.7 22.2 + - + -
3N BMA 4.7 12.1 + - - -
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Residues in contact with MET 606 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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558B MET* 5.1 2.5 - - + -
559B LEU* 4.0 27.1 - - + -
562B TYR* 4.4 17.9 - - + -
601B LEU* 4.8 11.0 - - + -
602B ASP 3.1 13.5 + - - +
603B VAL* 3.4 12.3 - - - +
605B ARG* 1.3 79.6 - - - +
607B MET* 1.3 71.5 + - - +
608B LYS 3.6 0.5 + - - -
609B THR* 4.4 3.6 + - - -
610B TRP* 3.4 15.6 - - - +
653B HIS* 3.6 33.0 + - + +
655B PRO* 3.5 36.8 - - + -
673B LEU* 4.4 16.2 - - + -
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Residues in contact with MET 607 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555B LEU* 3.9 32.5 - - + +
558B MET* 4.5 3.6 - - + -
559B LEU* 4.1 15.5 - - + -
590B TRP* 3.3 62.1 - - + +
603B VAL* 2.8 26.5 + - + +
604B LYS 3.3 0.8 + - - -
606B MET* 1.3 92.2 - - - +
608B LYS* 1.3 64.7 + - - +
609B THR 3.4 1.8 - - - -
610B TRP* 3.4 26.7 + - + +
611B THR* 2.9 27.4 + - - +
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Residues in contact with LYS 608 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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590B TRP* 5.8 0.7 - - - +
604B LYS* 3.2 11.7 + - + +
605B ARG* 3.6 22.7 - - + +
606B MET 3.3 1.0 - - - -
607B MET* 1.3 77.3 - - - +
609B THR* 1.3 69.8 + - - +
611B THR* 3.0 8.2 + - - -
612B LEU* 2.9 49.8 + - + +
649B SER* 5.5 6.3 + - - -
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Residues in contact with THR 609 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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605B ARG 4.6 2.4 + - - -
606B MET 4.4 4.0 + - - -
607B MET 3.4 0.2 - - - -
608B LYS* 1.3 82.6 + - - +
610B TRP* 1.3 61.7 + - - +
611B THR 3.3 0.7 + - - -
612B LEU* 4.6 1.6 - - - +
613B GLN* 3.3 47.3 + - + +
649B SER 5.8 1.1 - - - -
651B LEU 2.9 29.5 + - - +
652B TRP* 3.3 32.8 + - + +
653B HIS* 5.1 5.5 + - - -
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Residues in contact with TRP 610 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530B ILE* 3.9 9.7 + - - +
551B LYS* 4.0 21.8 + - - +
555B LEU* 3.8 25.0 - - + +
558B MET* 3.4 38.5 - - + +
606B MET* 3.4 22.8 - - - +
607B MET* 3.4 21.2 + - + +
608B LYS 3.3 0.6 - - - -
609B THR* 1.3 79.9 - - - +
611B THR* 1.3 58.5 + - - +
613B GLN 4.3 2.8 - - - +
615B GLY 5.2 0.7 - - - -
616B PHE* 4.4 1.1 - - + -
617B PRO* 3.5 29.4 - - + -
652B TRP* 3.5 28.7 - + + +
653B HIS 3.0 25.8 + - - +
654B ILE* 4.2 11.0 - - + -
655B PRO* 4.7 0.4 - - - +
699B TYR* 3.3 40.6 - + + -
700B TYR* 4.7 2.2 - + - -
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Residues in contact with THR 611 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484B TRP* 3.8 17.3 - - + -
530B ILE* 3.6 18.2 + - + +
531B SER* 3.2 37.8 + - - +
555B LEU* 4.0 7.2 - - + -
586B SER* 5.0 6.1 - - - +
590B TRP* 3.7 31.5 + - + +
607B MET 2.9 22.8 + - - +
608B LYS* 3.0 8.5 + - - -
610B TRP* 1.3 81.9 - - + +
612B LEU* 1.3 65.3 + - - +
613B GLN 3.6 1.3 - - - -
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Residues in contact with LEU 612 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529B PRO* 3.6 17.5 - - - +
531B SER* 4.3 20.4 - - - +
586B SER* 6.5 0.4 - - - -
608B LYS* 2.9 43.8 + - + +
609B THR* 4.2 1.1 - - - -
611B THR* 1.3 90.1 - - - +
613B GLN* 1.3 61.3 + - - +
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Residues in contact with GLN 613 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529B PRO* 4.0 8.8 - - - +
530B ILE 4.9 0.2 + - - -
551B LYS* 4.0 12.0 + - - -
609B THR* 3.3 32.8 + - + +
610B TRP 4.3 4.3 - - - +
611B THR 3.6 0.2 - - - -
612B LEU* 1.3 81.8 - - - +
614B LYS* 1.3 74.8 + - + +
615B GLY 4.0 1.4 + - - +
634B ARG* 4.6 11.1 - - - +
649B SER* 3.0 23.5 + - - +
650B TYR* 3.4 34.6 - - - +
652B TRP* 3.7 26.5 + - + -
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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