Contacts of the strand formed by residues 844 - 849 (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 844 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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817A ILE* 3.7 34.6 - - + +
818A THR 4.3 5.0 + - - -
819A PRO* 4.3 7.6 - - + +
823A PHE* 3.8 21.3 - + - -
832A TRP* 4.6 6.3 - + - -
843A ALA* 1.3 71.4 - - - +
845A PRO* 1.3 67.5 - - - +
846A ILE* 3.6 4.8 - - + +
1001A SER* 3.3 1.5 - - - -
1002A ALA* 2.9 41.6 + - + +
1004A ILE* 4.2 11.6 - - + +
1015A LYS* 3.5 15.8 - - + +
1018A LEU* 3.4 36.1 - - + -
1019A GLU* 2.6 44.5 + - + -
1023A LEU* 3.9 18.6 - - + -
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Residues in contact with PRO 845 (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* 3.6 16.6 - - + +
831A THR* 3.3 45.8 - - - +
832A TRP* 3.4 21.8 - - + -
835A VAL* 3.7 4.3 - - + -
843A ALA 3.4 10.5 - - - +
844A TYR* 1.3 83.9 - - - +
846A ILE* 1.3 68.7 + - - +
999A VAL* 3.7 14.6 - - + -
1001A SER* 3.8 11.0 - - - +
1023A LEU* 3.5 14.0 - - - +
1041A ALA* 4.0 2.1 - - - +
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Residues in contact with ILE 846 (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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799A PHE* 4.3 13.2 - - + -
844A TYR* 3.6 14.1 - - + +
845A PRO* 1.3 87.8 - - - +
847A ALA* 1.3 55.5 + - + +
999A VAL* 4.3 0.2 - - - +
1000A LEU* 2.8 33.1 + - + +
1001A SER* 4.0 6.7 - - - +
1002A ALA* 4.3 6.1 - - + +
1018A LEU* 5.5 0.4 - - + -
1022A LEU* 4.2 20.0 - - + -
1023A LEU* 4.0 21.0 - - + +
1028A LEU* 4.1 25.1 - - + +
1037A LEU* 4.4 13.7 - - + -
1040A VAL* 3.5 5.4 - - - +
1041A ALA* 2.7 31.3 + - - +
1042A LEU 4.5 0.7 + - - -
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Residues in contact with ALA 847 (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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846A ILE* 1.3 85.8 - - + +
848A VAL* 1.3 64.8 + - - +
849A GLU* 3.8 1.3 + - - +
998A GLY 3.7 0.2 - - - +
999A VAL* 3.2 8.6 - - - +
1000A LEU* 2.9 33.2 + - + +
1037A LEU* 3.5 36.6 - - + +
1039A ALA 3.1 16.8 - - - +
1040A VAL* 3.9 4.0 - - + +
1041A ALA* 4.0 2.0 - - - +
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Residues in contact with VAL 848 (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* 6.4 0.4 - - + -
830A PHE* 4.3 24.9 - - + -
831A THR* 4.4 13.0 - - + -
847A ALA* 1.3 75.3 - - - +
849A GLU* 1.3 64.0 + - - +
997A VAL* 3.7 26.0 - - + -
998A GLY 3.7 3.1 - - - +
999A VAL* 4.6 10.8 - - + +
1038A GLY* 3.8 1.7 - - - -
1039A ALA* 2.4 55.1 + - + +
1040A VAL 5.6 0.7 - - - -
1041A ALA 5.6 0.9 - - - +
1058A THR* 4.7 3.9 - - + +
1059A MET* 4.3 21.8 - - + -
1062A ALA* 5.0 2.9 - - + -
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Residues in contact with GLU 849 (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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753A LYS* 3.7 12.9 + - - -
801A ALA* 4.7 6.1 - - - +
847A ALA 4.3 5.8 - - - +
848A VAL* 1.3 76.8 - - - +
850A ALA* 1.3 63.8 + - - +
893A TYR* 4.3 7.5 + - - +
967A PRO* 4.2 11.0 - - + -
968A TRP* 3.2 31.9 - - + -
997A VAL* 4.0 3.3 - - - +
998A GLY* 3.1 39.3 + - - +
1000A LEU* 4.6 16.8 + - + +
1037A LEU 4.3 13.9 - - - +
1058A THR* 4.6 1.1 - - - -
1B GLC 2.5 34.2 + - - -
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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