Contacts of the helix formed by residues 965 - 979 (chain A) in PDB entry 1MWH
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 GLU 965 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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966A VAL* 1.3 64.1 + - - +
967A ARG* 2.7 19.5 + - - +
968A GLU* 3.0 35.4 + - - +
969A GLN* 3.2 32.1 + - + +
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Residues in contact with VAL 966 (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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480A PHE* 3.6 41.3 - - + +
481A LYS 4.1 14.4 - - - +
482A GLY 4.4 3.8 - - - +
483A LEU* 3.5 26.7 - - + +
965A GLU* 1.3 81.7 - - - +
967A ARG* 1.3 58.6 + - + +
969A GLN* 3.5 25.5 - - - +
970A PHE* 3.1 25.6 + - - +
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Residues in contact with ARG 967 (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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483A LEU* 4.2 9.4 - - + -
965A GLU 2.7 8.0 - - - +
966A VAL* 1.3 80.0 - - + +
968A GLU* 1.3 67.4 + - + +
970A PHE* 3.3 3.0 + - - +
971A THR* 3.1 31.4 + - - +
1014A HIS* 6.2 3.6 - - - -
1017A TYR* 3.2 49.9 + - + +
1018A GLN* 6.2 1.2 - - - +
1021A GLN* 5.4 1.2 + - - -
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Residues in contact with GLU 968 (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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965A GLU* 3.0 27.4 + - - +
967A ARG* 1.3 77.4 - - + +
969A GLN* 1.3 53.8 + - + +
971A THR* 3.8 3.7 - - - -
972A GLN* 2.8 39.5 + - + +
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Residues in contact with GLN 969 (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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480A PHE* 4.0 15.6 - - + -
965A GLU* 3.2 36.8 + - + +
966A VAL* 3.5 29.2 - - - +
967A ARG 3.1 0.2 - - - -
968A GLU* 1.3 79.9 - - + +
970A PHE* 1.3 55.6 + - - +
972A GLN* 3.6 5.8 + - - +
973A ALA* 3.0 27.0 + - - +
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Residues in contact with PHE 970 (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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480A PHE* 3.6 27.6 - + + -
483A LEU* 3.3 26.0 - - + -
485A VAL* 4.3 9.9 - - + -
491A ILE* 4.5 6.7 - - + -
492A PHE* 3.6 41.5 - + - -
495A ALA* 3.3 26.0 - - + -
966A VAL 3.1 6.0 + - - +
967A ARG 3.3 3.6 + - - +
969A GLN* 1.3 74.6 - - - +
971A THR* 1.3 59.1 + - - +
972A GLN 2.9 0.9 - - - -
973A ALA* 2.6 27.4 + - - +
974A LEU* 3.0 33.9 + - + +
1017A TYR* 3.5 33.9 - + + -
1020A ALA* 4.8 2.0 - - + -
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Residues in contact with THR 971 (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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967A ARG* 3.1 18.2 + - - +
968A GLU* 4.0 4.0 - - - -
970A PHE* 1.3 77.6 - - - +
972A GLN* 1.3 58.0 + - - +
974A LEU* 3.5 10.8 + - - -
975A SER* 2.9 27.0 + - - -
1013A PRO* 3.6 25.0 - - + +
1014A HIS* 3.8 30.6 - - + +
1017A TYR* 4.3 21.1 - - - +
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Residues in contact with GLN 972 (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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968A GLU 2.8 21.3 + - - +
969A GLN* 3.6 7.0 - - - +
971A THR* 1.3 75.6 - - - +
973A ALA* 1.3 61.2 + - - +
975A SER* 3.1 16.6 + - - -
976A ASP* 2.8 57.5 + - - +
985A LYS* 6.0 2.4 - - - +
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Residues in contact with ALA 973 (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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480A PHE* 4.0 7.6 - - + -
495A ALA* 3.2 33.9 - - + +
498A ALA* 3.0 18.1 - - + +
499A ASN* 4.6 6.7 - - - +
969A GLN 3.0 13.5 + - - +
970A PHE 2.6 15.2 + - - +
972A GLN* 1.3 70.0 - - - +
974A LEU* 1.3 62.0 + - - +
976A ASP* 3.1 8.2 + - - +
977A TYR 3.0 17.7 + - - -
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Residues in contact with LEU 974 (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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491A ILE* 3.4 31.0 - - + +
494A ALA* 4.1 5.8 - - + -
495A ALA* 3.8 17.0 - - + +
970A PHE* 3.0 42.2 + - + +
971A THR* 3.6 8.1 - - - +
973A ALA* 1.3 75.3 - - - +
975A SER* 1.3 64.7 + - - +
977A TYR* 3.0 17.1 + - - +
978A LEU* 3.1 14.0 + - - +
1013A PRO* 3.8 26.5 - - + +
1016A TRP* 4.0 35.3 - - + -
1017A TYR* 4.2 2.7 - - - +
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Residues in contact with SER 975 (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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971A THR* 2.9 16.3 + - - -
972A GLN* 3.3 22.9 + - - -
974A LEU* 1.3 77.3 - - - +
976A ASP* 1.3 57.3 + - - +
978A LEU* 3.4 1.2 + - - +
979A MET* 2.8 46.2 + - - +
1010A PHE* 5.7 3.3 - - - -
1013A PRO* 3.7 21.0 - - - +
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Residues in contact with ASP 976 (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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498A ALA* 4.5 6.6 - - + +
499A ASN* 2.9 37.6 + - - +
972A GLN* 2.8 44.5 + - - +
973A ALA 3.1 6.5 + - - +
975A SER* 1.3 69.9 - - - +
977A TYR* 1.3 67.6 + - - +
979A MET* 4.8 3.5 - - - +
980A GLN* 2.9 29.4 + - - +
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Residues in contact with TYR 977 (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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452A ARG* 2.7 88.8 + - + +
455A TYR* 3.2 24.4 + - - -
456A VAL* 3.4 15.3 - - + -
494A ALA* 4.1 24.2 - - + +
497A LEU* 5.5 4.0 - - + -
498A ALA* 4.1 17.9 - - + +
533A VAL* 3.7 16.9 - - + +
537A GLN* 5.7 0.5 - - - +
973A ALA 3.0 10.9 + - - +
974A LEU* 3.0 13.8 + - - +
976A ASP* 1.3 78.8 - - - +
978A LEU* 1.3 65.0 + - + +
980A GLN* 3.4 7.2 - - - +
1016A TRP* 4.1 17.9 - + + -
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Residues in contact with LEU 978 (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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449A ALA* 4.2 24.9 - - + +
452A ARG* 5.3 3.5 + - + +
453A SER* 4.5 1.6 - - - -
974A LEU 3.1 10.5 + - - +
975A SER* 4.0 3.8 - - - +
977A TYR* 1.3 81.0 - - + +
979A MET* 1.3 71.5 + - + +
980A GLN* 3.0 10.6 + - - +
981A ASN 4.6 1.4 + - - -
984A LEU* 3.9 15.1 - - + +
1009A LEU* 3.8 15.7 - - + +
1012A VAL* 3.5 36.3 - - + -
1013A PRO* 4.6 5.2 - - + -
1016A TRP* 4.1 17.3 - - + -
1116A VAL* 4.0 29.2 - - + -
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Residues in contact with MET 979 (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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975A SER* 2.8 33.1 + - - +
976A ASP* 3.5 5.6 - - - -
978A LEU* 1.3 78.0 - - + +
980A GLN* 1.3 66.3 + - - +
981A ASN 3.2 12.4 + - - +
982A PRO* 4.9 1.2 - - - +
984A LEU* 4.2 11.4 - - - -
985A LYS* 4.1 44.5 - - + +
988A VAL* 4.1 2.9 - - + -
1009A LEU* 3.3 44.6 - - + +
1010A PHE* 3.8 27.8 - - + -
1013A PRO* 6.3 0.7 - - + -
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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