Contacts of the helix formed by residues 693 - 705 (chain B) in PDB entry 4MS0
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 TYR 693 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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771A THR* 4.8 7.7 + - - -
772A ALA* 3.6 37.3 + - + -
774A TRP* 4.2 3.8 - + - -
689B ALA 4.1 7.2 - - - -
690B ASN 3.1 8.8 + - - +
692B ILE* 1.3 98.2 - - + +
694B ALA* 1.3 63.2 + - - +
695B GLU 3.2 3.4 + - - -
696B PHE* 3.2 10.1 + + - +
697B TRP* 3.0 62.4 + + + -
713B MET 4.9 3.6 - - - -
718B LYS 5.9 1.6 - - - -
721B GLU 3.2 13.6 + - - -
722B VAL* 3.8 36.1 - - + -
725B GLY* 3.1 25.5 - - - -
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Residues in contact with ALA 694 (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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523B PRO* 4.7 15.9 - - + +
524B TYR* 4.3 20.9 - - + +
525B HIS* 5.3 2.7 - - + +
569B GLY 4.2 2.9 - - - +
690B ASN 3.3 7.8 + - - +
691B ASP* 3.0 17.4 + - - +
692B ILE 3.4 0.6 - - - -
693B TYR* 1.3 77.8 - - - +
695B GLU* 1.3 61.0 + - + +
697B TRP* 3.9 7.8 - - - +
698B ALA* 3.0 28.2 + - - +
716B ARG* 4.8 3.4 + - - +
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Residues in contact with GLU 695 (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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525B HIS* 3.5 32.1 + - + -
567B HIS* 3.8 4.9 + - - -
569B GLY 3.6 19.2 - - - +
570B PHE* 3.6 8.1 - - - +
571B SER* 3.5 44.9 + - - +
574B TYR* 5.8 0.7 - - - +
691B ASP 6.0 0.2 - - - +
692B ILE 4.8 2.5 + - - +
693B TYR 3.3 0.8 - - - -
694B ALA* 1.3 75.0 - - + +
696B PHE* 1.3 69.1 + - + +
698B ALA* 4.0 0.9 - - - +
699B GLU* 3.1 23.4 + - - +
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Residues in contact with PHE 696 (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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772A ALA* 3.8 18.2 - - + -
773A THR 5.3 5.4 - - - -
774A TRP* 3.6 30.7 - + - -
692B ILE 4.0 14.4 - - - -
693B TYR* 3.2 9.8 + - + +
695B GLU* 1.3 79.2 - - + +
697B TRP* 1.3 62.6 + - + +
699B GLU* 3.3 5.9 + - - +
700B GLY 3.0 22.3 + - - -
713B MET* 3.5 42.6 - - - +
714B MET* 3.5 32.2 - - + +
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Residues in contact with TRP 697 (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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690B ASN* 3.7 44.9 - - + -
693B TYR* 3.0 51.7 + + + +
694B ALA* 4.1 4.3 - - - +
696B PHE* 1.3 74.4 - - + +
698B ALA* 1.3 58.3 + - - +
700B GLY* 3.3 1.0 + - - -
701B ASP* 2.9 34.0 + - - +
712B PRO 5.0 0.4 + - - -
713B MET 3.9 13.4 + - - -
714B MET 3.6 15.5 - - - +
715B ASP 3.5 9.7 + - - -
716B ARG* 3.6 61.7 - - + +
718B LYS 4.2 12.8 + - - -
719B LYS* 4.0 15.7 - - + -
722B VAL* 3.9 16.2 - - + -
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Residues in contact with ALA 698 (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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568B ARG 5.8 0.2 - - - +
569B GLY* 3.7 22.9 - - - +
570B PHE* 3.7 18.1 - - + -
694B ALA 3.0 18.6 + - - +
695B GLU 4.0 2.0 - - - +
696B PHE 3.4 0.2 - - - -
697B TRP* 1.3 72.6 - - - +
699B GLU* 1.3 64.2 + - - +
701B ASP* 3.6 12.1 + - - +
702B GLU* 3.3 26.7 + - - +
716B ARG* 3.9 4.2 - - - +
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Residues in contact with GLU 699 (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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570B PHE* 4.6 1.4 - - + -
571B SER* 4.8 2.9 + - - -
573B SER* 5.3 0.9 - - - -
574B TYR* 3.7 48.5 + - + +
578B PHE* 3.7 18.7 - - + -
695B GLU 3.1 13.7 + - - +
696B PHE* 3.5 9.3 - - - +
698B ALA* 1.3 72.3 - - - +
700B GLY* 1.3 65.9 + - - +
702B GLU* 3.1 5.7 + - - +
703B MET* 3.1 29.5 + - + +
714B MET* 3.5 31.7 - - - +
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Residues in contact with GLY 700 (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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696B PHE 3.0 10.9 + - - -
697B TRP 3.3 0.6 + - - -
699B GLU* 1.3 77.3 - - - +
701B ASP* 1.3 56.6 + - - +
703B MET* 3.2 6.7 + - - +
704B LYS* 2.9 33.0 + - - +
710B PRO* 3.8 11.0 - - - +
714B MET* 3.1 33.6 - - - +
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Residues in contact with ASP 701 (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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697B TRP 2.9 19.2 + - - +
698B ALA* 3.7 8.9 - - - +
699B GLU 3.3 0.2 - - - -
700B GLY* 1.3 72.0 - - - +
702B GLU* 1.3 59.6 + - - +
704B LYS* 3.3 18.9 + - - +
705B LYS* 3.1 41.4 + - - +
716B ARG* 2.9 47.2 + - - +
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Residues in contact with GLU 702 (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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570B PHE* 3.8 22.5 - - + -
574B TYR* 3.7 22.5 + - + +
698B ALA 3.3 14.7 + - - +
699B GLU 3.1 9.0 + - - +
701B ASP* 1.3 76.5 - - - +
703B MET* 1.3 76.2 + - + +
705B LYS* 3.1 47.6 + - - +
706B LEU* 3.4 17.0 + - - +
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Residues in contact with MET 703 (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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574B TYR* 4.6 2.0 - - + +
578B PHE* 3.6 40.2 - - + -
699B GLU* 3.1 27.5 + - + +
700B GLY* 3.4 9.0 - - - +
702B GLU* 1.3 86.6 - - + +
704B LYS* 1.3 66.0 + - - +
706B LEU* 3.0 25.9 + - + +
708B ILE* 3.0 46.2 + - + +
710B PRO* 4.2 12.8 - - + -
714B MET* 5.9 2.0 - - + -
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Residues in contact with LYS 704 (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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700B GLY 2.9 17.8 + - - +
701B ASP* 3.5 25.7 + - - +
702B GLU 3.3 0.2 - - - -
703B MET* 1.3 75.0 - - - +
705B LYS* 1.3 58.8 + - + +
707B GLY* 2.8 23.1 + - - -
708B ILE 3.4 7.4 - - - +
709B GLN* 4.6 8.7 - - - +
710B PRO* 3.6 24.3 - - + +
714B MET 4.5 2.0 + - - -
715B ASP* 3.0 40.1 + - - +
716B ARG* 4.0 9.9 - - - +
717B ASP* 4.4 10.5 + - - -
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Residues in contact with LYS 705 (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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701B ASP* 3.1 21.7 + - - +
702B GLU* 3.1 43.6 + - - +
703B MET 3.2 0.6 - - - -
704B LYS* 1.3 76.7 - - + +
706B LEU* 1.3 60.2 + - + +
707B GLY 3.2 1.5 + - - -
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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