Contacts of the helix formed by residues 1052 - 1065 (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 ASP1052 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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970A TRP* 5.7 0.2 - - - -
1048A GLU 4.6 1.2 + - - +
1049A LEU* 2.7 26.4 + - + +
1050A ALA 4.1 0.9 - - - +
1051A LYS* 1.3 71.7 - - - +
1053A PRO* 1.3 72.0 - - - +
1054A ARG* 2.7 68.6 + - - +
1055A ILE* 3.0 22.8 + - + +
1056A ALA* 3.1 11.0 + - - +
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Residues in contact with PRO1053 (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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982A VAL 4.7 2.5 - - - +
1051A LYS 3.2 8.5 - - - +
1052A ASP* 1.3 90.0 - - - +
1054A ARG* 1.3 62.0 + - + +
1056A ALA* 3.0 11.0 + - + +
1057A ALA* 2.9 23.0 + - - +
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Residues in contact with ARG1054 (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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970A TRP* 3.2 55.4 - - + +
974A ASP* 4.0 9.7 + - - -
980A TYR* 3.2 28.0 + - - -
982A VAL* 3.4 32.8 - - + +
1036A PRO* 5.0 4.2 - - - +
1052A ASP* 2.7 37.4 + - - +
1053A PRO* 1.3 74.4 - - + +
1055A ILE* 1.3 56.2 + - - +
1057A ALA* 3.2 4.3 + - - +
1058A THR* 2.9 30.7 + - - -
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Residues in contact with ILE1055 (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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970A TRP* 4.1 20.0 - - + -
1036A PRO* 6.5 0.2 - - + -
1038A GLY* 3.2 31.2 - - - +
1039A ALA* 4.4 14.8 - - + -
1046A GLU* 3.7 21.8 - - - +
1049A LEU* 3.5 31.6 - - + +
1050A ALA* 4.8 4.5 - - - +
1052A ASP* 3.0 18.3 + - + +
1054A ARG* 1.3 75.9 - - - +
1056A ALA* 1.3 57.7 + - - +
1058A THR* 3.2 7.5 + - - +
1059A MET* 2.9 35.7 + - + +
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Residues in contact with ALA1056 (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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1050A ALA 5.1 6.5 + - - +
1051A LYS 5.6 0.7 - - - +
1052A ASP 3.1 8.4 + - - +
1053A PRO* 3.0 21.4 + - + +
1055A ILE* 1.3 77.5 - - - +
1057A ALA* 1.3 59.8 + - - +
1059A MET* 3.4 5.3 + - - +
1060A GLU* 3.0 24.0 + - - +
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Residues in contact with ALA1057 (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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852A SER* 4.0 0.4 - - - +
982A VAL* 3.2 38.6 - - + +
983A THR* 3.8 13.2 - - - -
984A VAL 4.6 0.2 - - - +
1053A PRO 2.9 9.1 + - - +
1054A ARG 3.2 7.2 + - - +
1056A ALA* 1.3 76.0 - - - +
1058A THR* 1.3 63.5 + - - +
1060A GLU* 2.9 21.0 + - - +
1061A ASN* 3.0 21.6 + - - +
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Residues in contact with THR1058 (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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848A VAL* 4.7 8.1 - - + +
849A GLU 4.6 1.8 - - - -
850A ALA* 3.7 34.5 + - + +
852A SER* 3.5 14.6 + - - -
967A PRO* 4.1 11.1 - - + +
970A TRP* 3.5 22.2 - - - -
1038A GLY* 5.5 0.2 - - - -
1039A ALA* 5.4 4.5 - - + +
1054A ARG 2.9 15.6 + - - -
1055A ILE* 3.4 13.2 - - - -
1057A ALA* 1.3 77.3 - - - +
1059A MET* 1.3 62.7 + - + +
1061A ASN* 3.7 1.2 + - - +
1062A ALA* 3.1 24.3 + - - +
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Residues in contact with MET1059 (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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830A PHE* 5.8 8.7 - - + -
848A VAL* 4.3 16.6 - - + -
1039A ALA* 4.0 28.3 - - + -
1046A GLU* 5.9 0.2 - - - +
1055A ILE* 2.9 25.2 + - + +
1056A ALA* 3.9 4.9 - - - +
1058A THR* 1.3 79.5 - - - +
1060A GLU* 1.3 60.5 + - - +
1062A ALA* 3.5 15.8 - - + +
1063A GLN* 2.9 30.9 + - + +
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Residues in contact with GLU1060 (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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984A VAL* 3.5 29.3 + - + +
1056A ALA 3.0 13.7 + - - +
1057A ALA* 2.9 16.0 + - - +
1059A MET* 1.3 76.3 - - - +
1061A ASN* 1.3 65.8 + - - +
1063A GLN* 3.3 8.3 + - - +
1064A LYS* 3.3 48.4 + - - +
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Residues in contact with ASN1061 (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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850A ALA* 4.8 1.3 - - + -
851A LEU 3.7 19.5 - - - +
852A SER* 3.2 16.9 + - - +
983A THR 3.5 4.2 + - - -
984A VAL* 3.4 26.9 - - - +
985A LEU* 2.9 33.9 + - - +
993A SER 5.0 2.1 - - - +
995A PRO* 3.3 18.8 - - + +
1057A ALA 3.0 21.8 + - - +
1058A THR 4.0 3.6 - - - +
1060A GLU* 1.3 77.6 - - - +
1062A ALA* 1.3 65.5 + - - +
1064A LYS* 3.4 7.7 + - - +
1065A GLY 3.2 16.1 + - - -
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Residues in contact with ALA1062 (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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848A VAL* 5.0 1.6 - - + -
850A ALA* 3.9 9.0 - - + -
997A VAL* 3.5 37.0 - - + +
1058A THR 3.1 17.6 + - - +
1059A MET* 3.5 24.5 - - + +
1060A GLU 3.1 0.2 - - - -
1061A ASN* 1.3 82.1 - - - +
1063A GLN* 1.3 62.2 + - - +
1065A GLY 3.2 15.1 + - - +
1067A ILE* 5.1 4.0 - - - +
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Residues in contact with GLN1063 (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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1059A MET* 2.9 18.9 + - + +
1060A GLU* 3.7 8.0 - - - +
1061A ASN 3.3 0.2 - - - -
1062A ALA* 1.3 75.8 - - - +
1064A LYS* 1.3 66.0 + - + +
1065A GLY 3.6 5.0 + - - +
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Residues in contact with LYS1064 (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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984A VAL* 3.6 21.9 - - + +
987A THR* 6.3 0.8 - - - +
992A PRO* 3.9 33.6 - - + +
993A SER 4.4 5.4 - - - +
994A LYS* 3.3 22.1 - - - +
1060A GLU* 3.3 43.7 + - - +
1061A ASN* 3.9 6.7 - - - +
1062A ALA 3.1 1.0 - - - -
1063A GLN* 1.3 82.5 - - + +
1065A GLY* 1.3 61.0 + - - +
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Residues in contact with GLY1065 (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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994A LYS* 3.7 15.9 - - - -
995A PRO* 3.5 18.2 - - - -
1061A ASN 3.2 5.3 + - - -
1062A ALA 3.2 16.2 + - - +
1063A GLN 3.8 5.7 - - - +
1064A LYS* 1.3 82.5 - - - +
1066A GLU* 1.3 66.1 + - - +
1067A ILE* 4.9 2.3 - - - +
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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