Contacts of the helix formed by residues 1010 - 1021 (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 ASN1010 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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741A GLU 2.7 33.7 + - - -
742A GLU* 3.6 6.9 - - - +
743A GLY* 3.1 20.3 + - - -
744A LYS 3.2 15.0 + - - +
745A LEU* 4.2 6.5 - - + +
796A ASP* 3.0 22.8 + - - +
1008A SER* 3.0 5.3 + - - -
1009A PRO* 1.3 86.3 - - - +
1011A LYS* 1.3 63.6 + - - +
1012A GLU 3.1 3.1 - - - +
1013A LEU* 3.2 18.3 + - + +
1014A ALA* 3.0 22.9 + - - +
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Residues in contact with LYS1011 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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815A ALA* 4.0 16.2 - - + -
1004A ILE* 3.9 23.2 - - + +
1005A ASN 3.5 12.3 - - - +
1006A ALA* 2.6 43.4 + - - +
1007A ALA 3.7 1.4 + - - -
1008A SER* 2.4 36.2 + - - +
1009A PRO 3.6 1.8 - - - -
1010A ASN* 1.3 76.7 - - - +
1012A GLU* 1.3 59.0 + - - +
1014A ALA* 3.5 3.7 + - - +
1015A LYS* 3.2 23.9 + - - +
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Residues in contact with GLU1012 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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818A THR* 5.2 2.3 + - - -
1010A ASN 3.1 1.0 - - - -
1011A LYS* 1.3 78.4 - - - +
1013A LEU* 1.3 62.4 + - - +
1014A ALA 3.3 0.2 - - - -
1015A LYS* 3.7 29.7 + - - +
1016A GLU* 3.4 28.3 + - + +
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Residues in contact with LEU1013 (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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743A GLY* 5.0 2.0 - - - -
744A LYS 4.9 6.3 - - - +
745A LEU* 4.0 8.4 - - + +
765A PHE* 3.7 28.4 - - + -
769A THR* 5.2 3.4 - - - +
771A ILE* 4.0 42.0 - - + -
1010A ASN* 3.2 31.3 + - + +
1012A GLU* 1.3 76.4 - - - +
1014A ALA* 1.3 65.8 + - - +
1015A LYS 3.2 0.4 - - - -
1016A GLU* 3.3 23.5 + - - +
1017A PHE* 3.1 21.8 + - - +
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Residues in contact with ALA1014 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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745A LEU* 4.3 12.3 - - + +
796A ASP* 4.8 2.9 - - + +
797A ILE* 4.0 24.4 - - + +
1004A ILE* 3.8 22.9 - - + -
1010A ASN 3.0 16.3 + - - +
1011A LYS 3.6 7.0 - - - +
1013A LEU* 1.3 78.5 - - - +
1015A LYS* 1.3 62.5 + - - +
1017A PHE* 3.5 1.7 + - - +
1018A LEU* 3.1 29.6 + - - +
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Residues in contact with LYS1015 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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818A THR* 3.1 37.1 + - - +
819A PRO* 5.0 0.4 - - - -
820A ASP 5.5 0.8 - - - +
844A TYR* 3.5 10.5 - - - +
1004A ILE* 4.2 8.4 - - + +
1011A LYS 3.2 15.5 + - - +
1012A GLU* 3.9 30.4 + - - +
1013A LEU 3.2 0.2 - - - -
1014A ALA* 1.3 75.0 - - - +
1016A GLU* 1.3 66.0 + - - +
1018A LEU* 3.2 2.4 + - - -
1019A GLU* 3.0 60.8 + - + +
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Residues in contact with GLU1016 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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765A PHE* 4.0 9.6 - - + -
769A THR* 4.6 11.6 - - - +
1012A GLU* 3.4 18.8 + - + +
1013A LEU* 3.3 32.8 + - - +
1014A ALA 3.3 0.2 - - - -
1015A LYS* 1.3 79.5 - - + +
1017A PHE* 1.3 64.3 + - - +
1020A ASN* 3.1 37.7 + - - +
1021A TYR* 3.3 15.5 + - + -
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Residues in contact with PHE1017 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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745A LEU* 4.1 15.0 - - + -
747A ILE* 3.6 26.0 - - + -
758A LEU* 4.3 16.4 - - + -
761A VAL* 3.9 28.9 - - + -
762A GLY* 3.8 26.2 - - - -
765A PHE* 3.7 32.7 - + + -
773A VAL* 4.8 2.7 - - + -
775A VAL* 6.4 0.2 - - + -
797A ILE* 4.0 9.4 - - + -
799A PHE* 5.0 1.3 - + - -
1013A LEU 3.1 11.0 + - - +
1014A ALA* 3.7 7.6 - - - +
1015A LYS 3.2 0.2 - - - -
1016A GLU* 1.3 79.3 - - - +
1018A LEU* 1.3 78.9 + - + +
1021A TYR* 3.2 8.3 + - + +
1022A LEU* 3.1 33.5 + - + -
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Residues in contact with LEU1018 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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797A ILE* 3.9 16.2 - - + -
799A PHE* 4.3 2.0 - - + -
844A TYR* 3.4 42.8 - - + -
846A ILE* 5.5 1.1 - - + -
1002A ALA* 3.8 26.7 - - + +
1004A ILE* 4.3 12.1 - - + -
1014A ALA 3.1 16.6 + - - +
1015A LYS 3.2 2.7 + - - +
1017A PHE* 1.3 97.9 - - + +
1019A GLU* 1.3 58.3 + - - +
1022A LEU* 3.9 22.8 - - + +
1023A LEU* 3.0 37.9 + - + +
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Residues in contact with GLU1019 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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819A PRO* 3.8 9.8 - - - +
820A ASP* 5.3 2.3 + - - +
823A PHE* 3.7 49.8 - - + +
844A TYR* 2.6 45.0 + - + +
1015A LYS* 3.0 45.1 + - - +
1018A LEU* 1.3 72.8 - - - +
1020A ASN* 1.3 70.6 + - - +
1023A LEU 4.0 8.5 - - - +
1024A THR* 4.2 2.9 - - - +
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Residues in contact with ASN1020 (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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1016A GLU* 3.1 32.0 + - - +
1019A GLU* 1.3 85.5 - - - +
1021A TYR* 1.3 78.9 + - + +
1024A THR* 3.0 20.3 - - - +
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Residues in contact with TYR1021 (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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761A VAL* 3.7 17.0 - - + +
764A LYS* 4.1 15.7 - - + -
765A PHE* 3.6 50.0 - + - -
768A ASP* 3.6 33.3 + - + +
769A THR* 4.4 6.3 - - + +
1016A GLU* 3.3 19.0 + - + -
1017A PHE* 3.2 12.6 + - + +
1019A GLU 3.7 0.4 - - - -
1020A ASN* 1.3 101.2 - - + +
1022A LEU* 1.3 62.6 + - - +
1024A THR* 2.8 21.1 + - - -
1027A GLY* 3.2 10.7 - - - -
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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