Contacts of the helix formed by residues 828 - 835 (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 TYR 828 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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827A LEU* 1.3 71.7 - - - +
829A PRO* 1.3 74.2 - - + +
830A PHE* 3.5 39.5 - + + -
831A THR* 2.9 29.9 + - + -
832A TRP* 3.4 5.1 + - - -
848A VAL* 6.4 0.4 - - + -
1040A VAL 3.4 20.2 - - - -
1041A ALA* 3.0 29.6 + - - -
1043A LYS* 3.7 42.4 + - + +
1046A GLU* 3.5 27.4 - - + +
1047A GLU 5.2 0.2 + - - -
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Residues in contact with PRO 829 (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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824A GLN 6.0 0.4 - - - +
827A LEU 3.3 8.0 - - - +
828A TYR* 1.3 86.9 - - + +
830A PHE* 1.3 63.3 + - + +
832A TRP* 3.3 20.7 + - + +
833A ASP* 2.8 23.0 + - - +
1043A LYS* 4.1 15.9 - - - +
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Residues in contact with PHE 830 (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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828A TYR* 3.5 38.1 - + + -
829A PRO* 1.3 81.1 - - + +
831A THR* 1.3 83.8 + - + +
832A TRP 3.2 0.2 - - - -
833A ASP* 3.2 28.1 + - + +
834A ALA* 3.4 7.4 + - - +
848A VAL* 4.3 16.2 - - + -
999A VAL* 5.6 0.8 - - + +
1059A MET* 5.8 8.3 - - + -
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Residues in contact with THR 831 (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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827A LEU* 4.1 2.6 - - - +
828A TYR* 2.9 37.4 + - + -
830A PHE* 1.3 91.3 - - + +
832A TRP* 1.3 63.9 + - - +
834A ALA* 3.5 17.7 + - - +
835A VAL* 3.8 2.9 + - - +
845A PRO* 3.3 39.0 - - - +
848A VAL* 4.4 11.7 - - + -
999A VAL* 4.5 8.5 - - + +
1041A ALA* 3.6 23.6 - - + +
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Residues in contact with TRP 832 (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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817A ILE* 3.9 21.1 - - + -
819A PRO* 4.3 11.9 - - + -
823A PHE* 4.2 16.6 - + - -
824A GLN* 2.8 49.2 + - + +
827A LEU* 3.4 34.2 - - + +
828A TYR 3.4 16.1 + - - -
829A PRO* 3.3 15.9 + - + +
830A PHE 3.2 0.4 - - - -
831A THR* 1.3 78.6 + - - +
833A ASP* 1.3 67.6 - - - +
834A ALA 3.1 0.4 - - - -
835A VAL* 3.2 22.8 + - + +
836A ARG* 3.5 23.6 + - - +
841A LEU* 4.0 23.2 - - + +
843A ALA 4.0 0.2 - - - -
844A TYR* 4.6 4.9 - + - -
845A PRO* 3.4 24.7 - - + -
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Residues in contact with ASP 833 (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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829A PRO 2.8 18.6 - - - +
830A PHE* 3.2 19.0 - - + +
832A TRP* 1.3 78.8 - - - +
834A ALA* 1.3 59.6 + - - +
836A ARG* 3.1 40.4 + - - +
1070A ASN* 5.2 1.2 + - - -
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Residues in contact with ALA 834 (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* 3.5 29.6 - - + +
830A PHE 3.4 6.9 + - - +
831A THR 3.6 10.8 - - - +
832A TRP 3.1 0.8 - - - -
833A ASP* 1.3 80.9 - - - +
835A VAL* 1.3 58.6 + - + +
836A ARG 3.3 0.4 - - - -
999A VAL* 3.7 32.8 - - + -
1067A ILE* 5.4 7.6 - - + -
1070A ASN* 3.5 20.4 + - - -
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Residues in contact with VAL 835 (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* 4.5 7.4 - - + -
805A PHE* 5.0 2.5 - - + -
831A THR 3.8 4.3 - - - +
832A TRP* 3.4 20.2 - - + +
834A ALA* 1.3 78.5 - - + +
836A ARG* 1.3 57.7 + - - +
841A LEU* 3.8 3.8 - - + -
842A ILE* 2.9 35.6 + - + +
843A ALA* 3.0 36.6 - - + +
845A PRO* 3.7 21.8 - - + -
999A VAL* 5.2 0.2 - - + -
1001A SER* 3.3 34.3 - - - +
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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