Contacts of the helix formed by residues 804 - 811 (chain A) in PDB entry 3MP1
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 804 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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782A GLU* 3.8 31.9 + - - +
783A GLU* 6.0 3.0 - - - +
800A TRP* 3.4 27.9 - - + +
801A ALA 3.4 1.0 + - - -
802A HIS 3.2 0.8 - - - -
803A ASP* 1.3 82.7 + - - +
805A PHE* 1.3 66.2 + - + +
806A GLY 3.3 2.0 + - - -
807A GLY* 3.5 8.9 + - - -
808A TYR* 3.4 36.5 + - + +
1074A MET* 5.5 0.7 - - + -
1075A SER* 3.0 38.3 + - - +
1078A TRP* 3.8 20.7 - - + +
1079A TYR* 5.7 6.5 - - - -
2B GLC 2.9 39.3 + - - +
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Residues in contact with PHE 805 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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798A ILE* 3.4 28.5 - - + -
800A TRP* 3.9 26.9 - - + -
801A ALA 4.1 4.7 - - - -
802A HIS* 3.1 17.3 + - + +
804A ARG* 1.3 77.8 - - - +
806A GLY* 1.3 59.5 + - - +
807A GLY 3.3 0.2 - - - -
808A TYR* 3.4 18.9 + + - -
809A ALA* 2.9 30.1 + - - +
814A LEU* 3.6 9.3 - - + +
835A VAL* 5.0 3.4 - - + -
842A ILE* 3.5 14.5 - - + +
843A ALA* 3.3 35.2 - - + -
1001A SER* 3.2 36.8 - - - -
1003A GLY* 3.6 9.2 - - - -
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Residues in contact with GLY 806 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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802A HIS 4.0 4.6 + - - -
803A ASP 4.3 1.0 + - - -
804A ARG 3.3 0.8 - - - -
805A PHE* 1.3 74.2 - - - +
807A GLY* 1.3 60.1 + - - +
809A ALA* 4.5 0.2 - - - -
810A GLN* 2.8 31.2 + - - +
837A TYR* 3.7 20.6 - - - -
842A ILE* 4.1 6.0 - - - +
1070A ASN* 3.0 28.5 + - - +
1072A PRO* 4.8 1.8 - - - -
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Residues in contact with GLY 807 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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803A ASP 5.1 1.0 + - - -
804A ARG 3.5 7.4 + - - -
805A PHE 3.3 0.2 - - - -
806A GLY* 1.3 72.9 - - - +
808A TYR* 1.3 68.1 + - - +
810A GLN* 3.3 4.2 + - - +
811A SER* 3.0 27.2 + - - -
1070A ASN 4.1 2.8 + - - -
1071A ILE 4.6 1.2 + - - -
1072A PRO* 4.0 24.4 - - - +
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Residues in contact with TYR 808 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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782A GLU* 2.9 31.3 + - - +
785A PHE* 4.0 17.7 - + - -
786A PRO* 3.5 27.9 - - + +
798A ILE* 4.0 19.4 - - + +
800A TRP* 5.4 2.3 - - + -
804A ARG* 3.4 36.8 + - + +
805A PHE* 3.4 27.6 + + - +
806A GLY 3.3 0.4 - - - -
807A GLY* 1.3 78.4 - - - +
809A ALA* 1.3 61.5 + - - +
811A SER* 3.2 2.5 + - - -
812A GLY 3.1 4.3 + - - -
813A LEU* 2.8 41.5 + - + +
814A LEU* 3.4 23.3 - - + -
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Residues in contact with ALA 809 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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805A PHE 2.9 18.1 + - - +
806A GLY 3.9 2.9 - - - +
808A TYR* 1.3 76.3 - - - +
810A GLN* 1.3 63.3 + - - +
812A GLY* 3.0 13.7 + - - -
814A LEU* 4.1 17.7 - - + +
837A TYR* 4.0 10.3 - - + -
842A ILE* 3.7 36.3 - - + -
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Residues in contact with GLN 810 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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806A GLY 2.8 19.5 + - - +
807A GLY 3.6 4.7 - - - +
809A ALA* 1.3 80.1 - - - +
811A SER* 1.3 59.9 + - - +
812A GLY* 3.1 3.5 + - - -
837A TYR* 2.8 39.7 + - - +
838A ASN* 5.5 3.4 + - - +
1072A PRO* 3.8 18.8 - - + +
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Residues in contact with SER 811 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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807A GLY 3.0 17.9 + - - -
808A TYR* 3.2 3.3 + - - -
810A GLN* 1.3 78.9 - - - +
812A GLY* 1.3 61.1 + - - +
813A LEU* 3.4 22.8 - - - +
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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