Contacts of the helix formed by residues 581 - 593 (chain D) in PDB entry 5MKE
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 ARG 581 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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579D PHE 5.0 0.2 - - - +
580D ASN* 1.3 133.8 + - + +
582D THR* 1.3 64.2 + - + +
583D MET* 3.0 22.4 - - + +
584D SER* 2.7 26.2 + - - -
585D GLN* 3.3 5.2 + - - +
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Residues in contact with THR 582 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581D ARG* 1.3 76.7 - - + +
583D MET* 1.3 67.7 + - - +
585D GLN* 3.0 9.7 + - - +
586D LEU* 3.0 43.9 + - - +
691D LEU* 6.2 4.0 - - + -
694D GLN* 3.9 24.9 - - - +
695D LYS* 6.1 2.2 - - - +
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Residues in contact with MET 583 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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595A LYS* 6.5 0.9 - - - -
599A GLY* 4.2 28.7 - - - +
600A PHE* 4.2 15.1 - - + -
578D ASN* 4.7 4.5 + - + -
580D ASN* 3.3 36.3 - - + +
581D ARG* 3.7 18.2 - - + -
582D THR* 1.3 82.1 + - - +
584D SER* 1.3 60.8 + - - +
586D LEU* 3.5 13.1 + - - +
587D SER* 3.7 10.2 + - - -
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Residues in contact with SER 584 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578D ASN* 3.0 34.9 + - - +
579D PHE* 3.0 12.0 - - - -
580D ASN* 2.6 34.8 + - - -
581D ARG 2.7 16.1 + - - -
583D MET* 1.3 74.7 - - - +
585D GLN* 1.3 60.7 + - - -
586D LEU 3.6 0.3 + - - -
587D SER* 4.1 6.4 + - - -
588D THR* 3.7 11.6 + - - -
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Residues in contact with GLN 585 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581D ARG 3.3 5.5 + - - +
582D THR* 3.0 13.2 + - - +
584D SER* 1.3 80.5 - - - +
586D LEU* 1.3 67.8 + - + +
587D SER 3.5 0.2 - - - -
588D THR* 3.3 30.4 + - - +
589D THR* 4.2 7.3 + - - +
694D GLN* 5.0 12.1 - - - +
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Residues in contact with LEU 586 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600A PHE* 4.7 13.5 - - + -
582D THR* 3.0 32.1 + - - +
583D MET* 4.2 6.5 - - - +
584D SER 3.4 0.4 - - - -
585D GLN* 1.3 81.0 - - + +
587D SER* 1.3 64.0 + - - +
588D THR 3.1 2.2 - - - -
589D THR* 2.4 32.0 + - + +
590D MET* 3.4 2.6 + - - +
684D TYR* 5.8 4.5 - - + +
687D VAL* 4.4 19.2 - - + +
690D ASP* 5.7 1.6 - - - +
691D LEU* 3.5 50.0 - - + -
694D GLN* 6.2 0.4 - - - +
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Residues in contact with SER 587 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600A PHE* 3.6 27.4 - - - -
603A MET* 5.3 0.7 - - - -
574D PHE* 4.6 15.1 - - - -
578D ASN* 4.8 10.1 - - - -
583D MET 3.7 8.2 + - - -
584D SER 4.1 4.0 + - - -
585D GLN 3.5 0.4 - - - -
586D LEU* 1.3 74.0 - - - +
588D THR* 1.3 66.3 + - - +
589D THR 3.2 0.2 - - - -
590D MET* 2.9 34.7 + - - +
591D SER* 3.8 3.6 + - - -
1008D PLM 5.3 0.9 + - - -
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Residues in contact with THR 588 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507D TRP* 4.8 26.9 - - + +
584D SER 3.7 10.6 + - - -
585D GLN* 3.3 32.1 + - - +
586D LEU 3.1 0.4 - - - -
587D SER* 1.3 78.7 - - - +
589D THR* 1.3 67.2 + - + +
591D SER* 4.1 0.9 + - - -
592D ARG* 3.1 33.8 + - + +
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Residues in contact with THR 589 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585D GLN* 4.6 9.4 - - - +
586D LEU* 2.4 24.7 + - + +
588D THR* 1.3 78.7 - - + +
590D MET* 1.3 56.0 + - - +
592D ARG* 2.7 14.9 + - + -
593D CYS* 2.5 41.4 + - - -
686D GLU* 6.0 0.4 - - - -
687D VAL* 3.3 26.7 - - + +
690D ASP* 3.9 20.4 - - - +
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Residues in contact with MET 590 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600A PHE* 4.8 5.4 - - + -
603A MET* 4.0 22.2 - - + +
671A ILE* 3.5 37.9 - - + -
675A MET* 4.3 29.2 - - + +
586D LEU 3.4 1.1 + - - +
587D SER* 2.9 34.7 + - - +
589D THR* 1.3 82.4 + - - +
591D SER* 1.3 58.8 + - - +
593D CYS* 3.6 9.7 - - - -
594D ALA* 3.1 20.1 + - - +
687D VAL* 5.8 1.3 - - - -
1008D PLM 3.6 20.2 - - - +
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Residues in contact with SER 591 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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587D SER 3.8 3.9 + - - -
588D THR 4.1 1.3 + - - -
590D MET* 1.3 79.9 - - - +
592D ARG* 1.3 60.1 + - - +
593D CYS 3.2 0.7 - - - -
594D ALA* 2.7 32.0 + - - +
595D LYS* 3.4 5.4 + - - +
598D PHE* 5.6 5.2 - - - -
1008D PLM 5.1 14.4 - - - -
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Residues in contact with ARG 592 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504D ARG* 4.9 25.1 - - - +
505D SER 4.5 8.5 + - - -
506D PHE* 5.7 5.6 - - - +
507D TRP* 4.0 22.0 - - - +
588D THR* 3.1 32.4 + - + +
589D THR* 2.7 18.6 + - + +
591D SER* 1.3 75.0 - - - +
593D CYS* 1.3 57.3 + - + +
595D LYS* 4.0 12.6 + - - +
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Residues in contact with CYS 593 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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589D THR* 2.5 40.9 + - - +
590D MET* 3.6 10.8 - - - -
592D ARG* 1.3 71.5 - - - +
594D ALA* 1.3 57.5 + - - +
595D LYS* 3.1 8.2 + - - +
596D ASP* 3.9 11.6 + - - +
679D ILE* 4.8 2.9 - - - +
683D THR* 3.2 54.5 + - + +
684D TYR* 5.6 0.4 - - - -
686D GLU* 5.1 4.0 - - - +
687D VAL* 4.7 4.0 - - - -
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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