Contacts of the helix formed by residues 1024 - 1035 (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 THR1024 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1019A GLU 4.2 2.0 - - - +
1020A ASN* 3.0 40.4 - - - +
1021A TYR* 2.8 18.9 + - - +
1022A LEU 2.6 5.7 + - - +
1023A LEU* 1.3 79.6 - - - +
1025A ASP* 1.3 65.3 + - - +
1026A GLU* 3.6 5.3 + - - +
1027A GLY 2.8 12.5 + - - -
1028A LEU* 3.1 23.6 + - - +
1042A LEU* 3.6 7.3 - - - +
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Residues in contact with ASP1025 (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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1024A THR* 1.3 75.5 - - - +
1026A GLU* 1.3 60.8 + - + +
1029A GLU* 3.0 28.6 + - - +
1042A LEU* 4.0 3.9 - - - +
1044A SER* 3.3 25.4 + - - -
1045A TYR* 3.1 39.6 + - + +
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Residues in contact with GLU1026 (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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764A LYS* 6.0 3.6 - - - +
1024A THR* 3.3 4.3 + - - +
1025A ASP* 1.3 78.6 - - + +
1027A GLY* 1.3 60.6 + - - +
1029A GLU* 3.6 6.2 - - - +
1030A ALA* 2.9 32.8 + - - +
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Residues in contact with GLY1027 (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* 3.3 28.9 - - - +
1021A TYR 3.2 23.8 - - - -
1022A LEU* 3.4 9.4 - - - +
1024A THR* 2.8 10.5 + - - -
1026A GLU* 1.3 78.7 - - - +
1028A LEU* 1.3 58.4 + - - +
1030A ALA* 4.6 0.2 - - - -
1031A VAL* 3.4 14.0 + - - +
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Residues in contact with LEU1028 (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* 4.1 13.5 - - + +
1022A LEU* 3.4 35.7 - - + +
1023A LEU* 4.3 11.9 - - + -
1024A THR 3.1 8.5 + - - +
1027A GLY* 1.3 72.0 - - - +
1029A GLU* 1.3 58.9 + - - +
1030A ALA 3.0 1.7 + - - -
1031A VAL* 3.1 1.7 + - + +
1032A ASN* 2.7 39.4 + - - +
1037A LEU* 3.8 23.5 - - + +
1040A VAL* 4.2 16.4 - - + -
1042A LEU* 3.8 36.6 - - + +
1045A TYR* 3.8 16.4 - - + -
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Residues in contact with GLU1029 (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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1025A ASP 3.0 19.6 + - - +
1026A GLU* 3.6 8.2 - - - +
1028A LEU* 1.3 78.2 - - - +
1030A ALA* 1.3 61.0 + - - +
1032A ASN* 3.5 3.6 + - - +
1033A LYS* 3.0 34.6 + - - +
1045A TYR* 3.1 31.9 + - + +
1048A GLU* 5.4 2.0 - - - +
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Residues in contact with ALA1030 (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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757A GLY* 3.9 21.1 - - - +
760A GLU* 4.7 16.2 - - + +
761A VAL* 4.2 7.0 - - + -
1026A GLU 2.9 16.6 + - - +
1027A GLY* 3.8 6.5 - - - +
1029A GLU* 1.3 80.4 + - - +
1031A VAL* 1.3 63.6 + - - +
1033A LYS* 3.2 23.0 + - - +
1034A ASP 3.5 4.5 + - - -
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Residues in contact with VAL1031 (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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749A ILE* 6.0 4.5 - - + -
753A LYS* 6.2 0.2 - - + -
754A GLY* 4.1 19.9 - - - +
757A GLY* 4.2 7.0 - - - -
758A LEU* 3.7 35.2 - - + -
761A VAL* 3.8 8.1 - - + -
1022A LEU* 3.9 8.3 - - + -
1027A GLY 3.4 15.6 + - - +
1028A LEU* 3.1 5.9 + - - +
1030A ALA* 1.3 75.9 - - - +
1032A ASN* 1.3 62.4 + - - +
1033A LYS 3.3 0.5 + - - -
1034A ASP* 3.3 10.7 + - - +
1035A LYS 3.3 13.3 + - - +
1037A LEU* 3.6 30.3 - - + -
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Residues in contact with ASN1032 (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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1028A LEU 2.7 22.2 + - - +
1029A GLU* 3.6 6.8 + - - +
1031A VAL* 1.3 75.3 - - - +
1033A LYS* 1.3 61.6 + - - +
1035A LYS 4.0 4.3 - - - -
1036A PRO* 3.3 29.1 - - - +
1037A LEU* 3.1 32.4 + - + +
1038A GLY 4.4 1.0 + - - +
1040A VAL* 5.8 0.2 - - - -
1045A TYR* 3.4 22.1 + - + +
1049A LEU* 4.2 26.1 - - - +
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Residues in contact with LYS1033 (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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760A GLU* 4.0 22.8 + - - +
971A SER* 4.2 3.3 + - - -
1029A GLU* 3.0 23.2 + - - +
1030A ALA* 3.3 12.3 + - - +
1032A ASN* 1.3 77.4 - - - +
1034A ASP* 1.3 87.8 + - - +
1036A PRO* 5.2 1.0 - - - +
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Residues in contact with ASP1034 (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 4.5 0.5 - - - +
754A GLY* 3.0 25.7 - - - -
755A TYR 3.6 0.2 + - - -
756A ASN* 3.0 22.9 + - - +
757A GLY* 3.0 33.9 + - - +
971A SER* 2.4 30.3 + - - -
1030A ALA 3.5 2.4 + - - -
1031A VAL 3.3 6.1 + - - +
1033A LYS* 1.3 92.4 + - - +
1035A LYS* 1.3 67.7 + - - +
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Residues in contact with LYS1035 (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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751A GLY 5.4 2.2 - - - -
752A ASP* 3.6 24.7 - - - +
753A LYS* 4.2 7.9 - - - -
754A GLY* 3.9 20.1 + - - +
755A TYR* 5.9 3.1 - - - -
968A TRP* 3.6 22.7 - - + +
971A SER* 3.9 13.5 + - - -
972A ASN* 3.9 28.0 + - - +
1031A VAL 3.3 12.7 + - - +
1032A ASN* 3.4 3.5 - - - -
1034A ASP* 1.3 94.9 + - - +
1036A PRO* 1.3 73.1 - - - +
1037A LEU* 3.4 6.6 + - - +
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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