Contacts of the helix formed by residues 797 - 802 (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 THR 797 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1273C MET* 6.0 6.1 - - - -
429D LEU* 5.7 4.7 - - - -
793D SER 5.2 3.3 + - - -
794D GLY* 4.3 15.4 - - - -
795D TYR 3.1 1.6 - - - +
796D LEU* 1.3 78.3 - - - +
798D ARG* 1.3 58.8 + - - -
800D LEU* 3.2 5.2 + - - +
801D VAL* 3.0 31.1 + - - +
920D ALA* 4.8 6.4 - - - +
921D GLN* 5.3 12.1 - - - +
924D GLY* 4.7 11.3 - - - -
16J A 6.0 0.2 + - - -
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Residues in contact with ARG 798 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
794D GLY 3.3 19.4 + - - +
795D TYR* 3.1 11.5 + - + -
797D THR* 1.3 78.6 - - - +
799D ARG* 1.3 57.7 + - - +
801D VAL* 3.3 3.6 + - - -
802D ASP* 3.0 33.3 + - - +
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Residues in contact with ARG 799 (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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795D TYR 2.8 19.8 + - - +
796D LEU* 5.2 2.0 - - - +
798D ARG* 1.3 72.9 - - - +
800D LEU* 1.3 58.0 + - - +
802D ASP* 4.4 9.3 + - - +
803D VAL* 4.6 3.3 - - - +
1309D ILE* 3.9 28.3 - - + +
1310D THR* 6.4 2.0 - - - -
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Residues in contact with LEU 800 (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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796D LEU 3.7 17.4 + - - +
797D THR 3.2 2.3 + - - +
798D ARG 3.1 0.8 - - - -
799D ARG* 1.3 78.5 - - - +
801D VAL* 1.3 60.8 + - - +
802D ASP 3.4 1.3 - - - -
803D VAL* 4.0 10.1 + - - +
804D ALA* 4.1 10.9 + - - +
920D ALA* 3.4 30.6 - - + +
923D ILE* 5.9 2.9 - - + -
1145D PHE* 6.3 2.9 - - + -
1256D ILE* 5.1 6.7 - - + +
1309D ILE* 5.6 2.2 - - - -
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Residues in contact with VAL 801 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1276C TRP* 6.0 4.9 - - + -
797D THR* 3.0 17.1 + - - +
798D ARG* 3.3 3.5 + - - +
800D LEU* 1.3 75.1 - - - +
802D ASP* 1.3 60.3 + - - +
803D VAL 3.1 6.5 + - - -
804D ALA 4.2 1.1 - - - +
805D GLN* 3.5 24.9 + - - +
916D GLY 5.1 3.1 - - - -
917D VAL* 4.7 19.0 - - + +
920D ALA* 4.3 9.9 - - + -
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Residues in contact with ASP 802 (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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798D ARG 3.0 17.0 + - - +
799D ARG* 4.7 7.6 - - - +
800D LEU 3.4 0.6 - - - -
801D VAL* 1.3 77.4 - - - +
803D VAL* 1.3 56.8 + - - +
805D GLN* 4.8 6.0 + - - +
1313D SER* 3.3 23.0 - - - +
1321D SER* 4.4 18.1 - - - +
1324D SER* 5.2 13.0 - - - -
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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