Contacts of the helix formed by residues 658 - 673 (chain B) in PDB entry 5MJA
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 SER 658 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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656B GLY 3.9 0.6 + - - -
657B TYR* 1.3 81.9 - - - +
659B GLU* 1.3 62.6 + - - +
660B LYS* 3.7 8.9 + - - +
661B GLN* 2.8 41.2 + - - +
662B ARG 3.1 17.7 + - - -
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Residues in contact with GLU 659 (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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657B TYR* 4.1 10.7 + - - +
658B SER* 1.3 73.5 - - - +
660B LYS* 1.3 56.1 + - - +
662B ARG* 3.4 30.0 + - - +
663B ARG* 3.0 29.7 + - - +
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Residues in contact with LYS 660 (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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658B SER* 3.2 8.2 - - - +
659B GLU* 1.3 75.7 - - - +
661B GLN* 1.4 58.6 + - + +
663B ARG* 3.3 18.1 + - + +
664B ASP* 2.9 55.1 + - - +
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Residues in contact with GLN 661 (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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629B GLU 5.9 0.4 + - - -
630B PHE* 3.6 34.2 - - + +
653B LEU* 4.4 3.6 - - + -
656B GLY 4.7 0.5 - - - +
657B TYR* 3.4 15.4 - - + -
658B SER* 2.8 48.7 + - - +
660B LYS* 1.4 76.1 - - - +
662B ARG* 1.4 51.9 + - - +
664B ASP* 3.4 2.3 + - - +
665B PHE* 2.9 35.7 + - - +
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Residues in contact with ARG 662 (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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653B LEU* 3.6 17.6 - - + +
657B TYR* 3.6 40.7 + - + -
658B SER 3.1 5.9 + - - +
659B GLU* 3.5 28.4 + - - +
661B GLN* 1.4 73.4 - - - +
663B ARG* 1.3 58.0 + - - +
665B PHE* 3.3 2.6 + - - +
666B LEU* 3.0 55.6 + - + +
688B THR* 2.8 33.7 + - - +
693B VAL* 3.7 16.2 - - + +
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Residues in contact with ARG 663 (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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659B GLU 3.0 13.8 + - - +
660B LYS* 3.3 25.1 + - + +
662B ARG* 1.3 75.3 - - - +
664B ASP* 1.4 61.4 + - - +
666B LEU* 3.5 4.6 + - - +
667B SER* 3.0 29.5 + - - -
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Residues in contact with ASP 664 (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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630B PHE* 3.6 25.0 - - + -
660B LYS* 2.9 42.4 + - - +
661B GLN* 3.7 3.3 - - - +
663B ARG* 1.4 73.8 - - - +
665B PHE* 1.4 65.7 + - - +
667B SER* 2.9 24.8 + - - -
668B GLU* 3.7 4.3 + - - +
764B GLY* 6.0 1.6 - - - -
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Residues in contact with PHE 665 (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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630B PHE* 3.9 36.9 - + + -
651B LYS* 3.4 41.7 - - + -
652B THR* 3.8 22.0 - - - -
653B LEU* 4.1 14.1 - - + -
661B GLN 2.9 17.7 + - - +
662B ARG 3.3 4.5 + - - +
664B ASP* 1.4 74.9 - - - +
666B LEU* 1.3 74.8 + - + +
668B GLU* 3.3 13.7 + - - +
693B VAL* 4.0 29.4 - - + -
694B MET 4.3 0.2 - - - -
695B ILE* 3.2 46.4 - - + +
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Residues in contact with LEU 666 (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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610B PHE* 4.1 14.5 - - + -
662B ARG* 3.0 55.8 + - + +
663B ARG* 4.1 3.8 - - - +
665B PHE* 1.3 92.9 - - + +
667B SER* 1.4 60.5 + - - +
668B GLU 3.1 2.0 - - - -
669B ALA* 3.1 9.7 + - + +
670B SER* 3.0 29.8 + - - -
686B VAL* 5.4 0.9 - - + -
687B VAL 4.8 4.9 - - - +
688B THR* 3.7 32.1 - - + -
693B VAL* 4.9 4.0 - - + -
694B MET 5.0 1.6 - - - +
695B ILE* 4.6 9.0 - - + -
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Residues in contact with SER 667 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663B ARG 3.0 16.1 + - - -
664B ASP* 2.9 18.7 + - - -
665B PHE 3.3 0.4 - - - -
666B LEU* 1.4 75.7 - - - +
668B GLU* 1.4 62.7 + - - +
670B SER* 3.3 9.8 + - - -
671B ILE* 3.1 34.2 + - - +
764B GLY* 5.2 6.9 + - - -
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Residues in contact with GLU 668 (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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651B LYS* 2.8 30.3 + - - +
664B ASP 3.7 2.6 + - - +
665B PHE* 3.3 13.2 + - - +
666B LEU 3.1 0.8 - - - -
667B SER* 1.4 81.0 + - - +
669B ALA* 1.4 55.3 + - - +
671B ILE* 3.3 9.7 + - - +
672B MET* 3.0 38.2 + - - +
695B ILE* 4.6 4.9 - - + +
762B ASP* 3.6 1.7 + - - -
763B PHE* 3.0 41.1 + - + +
764B GLY* 4.0 9.2 - - - +
901B 7O3 2.7 34.3 + - - -
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Residues in contact with ALA 669 (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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610B PHE* 4.0 10.0 - - + -
666B LEU* 3.1 15.2 + - + +
668B GLU* 1.4 75.5 - - - +
670B SER* 1.4 57.7 + - - +
672B MET* 4.3 9.0 - - - -
673B GLY* 2.9 28.1 + - - -
683B LEU* 3.7 7.5 - - - +
686B VAL* 3.7 29.2 - - + -
695B ILE* 3.7 23.9 - - + +
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Residues in contact with SER 670 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610B PHE* 3.4 21.9 - - - -
666B LEU* 3.0 16.0 + - - +
667B SER* 3.3 10.4 + - - -
669B ALA* 1.4 77.5 - - - +
671B ILE* 1.4 62.1 + - - +
673B GLY* 3.6 5.6 + - - -
674B GLN* 3.3 26.3 + - - +
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Residues in contact with ILE 671 (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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667B SER* 3.1 24.4 + - - +
668B GLU* 3.3 6.3 + - - +
670B SER* 1.4 73.8 - - - +
672B MET* 1.3 58.3 + - - +
674B GLN* 3.0 33.7 + - - +
675B PHE* 3.5 33.8 - - + -
740B TYR* 4.3 21.1 - - + +
763B PHE* 3.6 36.8 - - + +
764B GLY* 5.3 2.0 - - - +
766B SER* 3.8 22.4 - - - +
767B ARG* 5.3 1.3 - - - +
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Residues in contact with MET 672 (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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612B LYS* 5.7 0.2 + - - -
668B GLU* 3.0 40.1 + - + +
669B ALA* 3.7 4.7 - - - +
671B ILE* 1.3 74.8 - - - +
673B GLY* 1.3 58.2 + - - +
674B GLN 3.1 0.2 - - - -
675B PHE* 3.0 36.3 + - - +
681B ILE* 3.6 31.9 - - + +
683B LEU* 4.2 22.8 + - + +
695B ILE* 4.2 13.5 - - - -
697B THR* 3.2 30.7 - - + -
763B PHE* 3.7 22.2 - - + -
901B 7O3 4.1 10.5 - - - -
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Residues in contact with GLY 673 (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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876A ASN* 5.6 1.6 - - - +
612B LYS* 5.3 9.6 + - - +
669B ALA 2.9 17.3 + - - -
670B SER* 4.0 4.0 - - - -
671B ILE 3.2 0.6 - - - -
672B MET* 1.3 76.4 - - - +
674B GLN* 1.3 60.1 + - - +
675B PHE 3.3 3.8 + - - +
683B LEU* 3.8 18.1 - - - +
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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