Contacts of the helix formed by residues 720 - 728 (chain D) in PDB entry 5MS0
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 ASN 720 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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643D ASP* 5.1 12.8 - - + +
701D LEU* 5.1 2.9 - - + -
717D VAL* 3.6 21.1 - - + +
718D SER 3.2 3.5 - - - +
719D PHE* 1.3 77.0 - - - +
721D SER* 1.3 59.9 + - - +
722D ILE 3.5 0.9 - - - +
723D TYR* 3.8 18.2 - - + +
724D MET* 3.0 30.5 + - - +
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Residues in contact with SER 721 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637D ALA* 4.0 27.9 - - - +
638D SER 3.3 32.8 - - - -
639D VAL* 4.2 4.7 - - - -
643D ASP* 4.9 8.2 - - - +
719D PHE 4.1 1.4 + - - -
720D ASN* 1.3 72.5 - - - +
722D ILE* 1.3 59.1 + - - +
724D MET* 3.2 4.4 + - - +
725D MET* 2.9 32.4 + - - +
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Residues in contact with ILE 722 (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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1104C PRO* 5.7 5.2 - - + +
639D VAL* 4.8 13.7 - - + +
640D GLY 6.0 0.2 - - - +
643D ASP* 4.5 26.2 - - + +
644D MET* 5.0 5.4 - - + +
720D ASN* 3.5 0.8 - - - +
721D SER* 1.3 78.8 - - - +
723D TYR* 1.3 59.9 + - - +
725D MET* 4.1 5.4 - - - +
726D ALA* 3.7 20.8 + - - +
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Residues in contact with TYR 723 (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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643D ASP 5.9 0.2 + - - -
701D LEU* 4.5 17.3 - - + -
717D VAL 5.2 0.9 - - - +
718D SER 5.6 2.0 - - - +
720D ASN* 3.5 23.7 + - + +
721D SER 3.2 0.6 - - - -
722D ILE* 1.3 79.4 - - - +
724D MET* 1.3 59.9 + - - +
726D ALA* 4.1 1.2 - - - +
727D ASP* 2.9 34.0 + - - +
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Residues in contact with MET 724 (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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511D TYR* 5.8 0.6 - - + +
512D TYR* 6.2 4.9 - - + -
637D ALA* 6.3 2.2 - - + -
718D SER 5.1 6.9 + - - +
719D PHE* 6.3 0.2 - - - -
720D ASN 3.0 18.1 + - - +
721D SER* 4.0 3.6 - - - +
723D TYR* 1.3 75.9 - - - +
725D MET* 1.3 59.8 + - - +
726D ALA 3.2 0.9 - - - -
727D ASP* 4.3 5.8 - - - -
728D SER* 3.2 31.0 + - - -
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Residues in contact with MET 725 (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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1100C PRO 5.8 1.8 - - - +
1101C LEU* 5.8 11.0 - - + -
1104C PRO* 5.1 11.0 - - + -
637D ALA* 6.2 2.9 - - + +
721D SER 2.9 17.5 + - - +
722D ILE* 4.0 5.1 + - - +
724D MET* 1.3 76.4 - - - +
726D ALA* 1.3 56.9 + - - +
728D SER 4.5 2.7 - - - +
730D ALA* 4.1 12.1 - - + +
731D ARG 3.2 28.9 + - - +
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Residues in contact with ALA 726 (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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1104C PRO* 5.3 6.7 - - + -
722D ILE 3.7 14.3 + - - +
723D TYR* 3.6 2.3 + - - +
724D MET 3.2 0.2 - - - -
725D MET* 1.3 79.8 - - - +
727D ASP* 1.3 63.4 + - - +
728D SER 3.3 9.1 - - - +
731D ARG 4.9 0.7 - - - +
732D GLY* 4.1 27.0 - - - -
733D SER 5.0 7.0 - - - +
737D ILE* 5.2 11.2 - - + -
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Residues in contact with ASP 727 (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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598D LYS* 4.9 4.2 - - - +
723D TYR 2.9 21.4 + - - +
724D MET* 4.3 4.5 - - - -
726D ALA* 1.3 77.5 - - - +
728D SER* 1.3 60.8 + - - +
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Residues in contact with SER 728 (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 VAL* 5.0 5.2 - - - -
508D LEU* 6.2 0.9 - - - -
511D TYR* 4.2 24.7 - - - -
598D LYS* 4.2 13.9 - - - -
724D MET 3.2 19.8 + - - -
725D MET 4.5 0.5 - - - +
726D ALA* 3.3 14.1 - - - +
727D ASP* 1.3 83.3 - - - +
729D GLY* 1.3 60.1 + - - +
730D ALA* 3.2 15.8 + - - -
731D ARG 5.0 0.7 + - - -
732D GLY* 5.0 2.9 + - - +
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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