Contacts of the helix formed by residues 1020 - 1035 (chain G) in PDB entry 1WQ1
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 GLN1020 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1013G SER 3.1 23.1 + - - +
1014G ASN* 4.3 7.3 + - - +
1015G GLU 3.1 22.8 + - - +
1016G ARG* 3.3 27.1 - - - +
1017G GLY 2.8 19.0 + - - +
1019G GLN* 1.3 74.8 - - - +
1021G HIS* 1.3 52.9 + - - +
1023G LEU* 2.7 14.9 + - - +
1024G LYS* 2.7 62.3 + - - +
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Residues in contact with HIS1021 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
729G LEU* 6.2 0.9 - - + -
1017G GLY 4.4 0.8 + - - -
1018G ALA 4.5 3.3 + - - +
1019G GLN 3.6 0.4 - - - -
1020G GLN* 1.3 77.8 - - - +
1022G VAL* 1.3 69.6 + - + +
1024G LYS* 3.4 30.5 - - + +
1025G LYS* 3.1 49.1 + - + +
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Residues in contact with VAL1022 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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729G LEU* 4.1 19.3 - - + +
732G GLN* 6.2 4.7 - - + -
734G GLU* 5.0 6.3 - - - +
736G HIS* 3.7 34.8 - - + +
737G VAL* 3.9 25.6 - - + +
1018G ALA 4.1 7.4 - - - +
1019G GLN 3.1 8.7 - - - +
1020G GLN 2.8 1.0 + - - -
1021G HIS* 1.3 87.8 - - + +
1023G LEU* 1.3 60.7 + - + +
1025G LYS* 3.1 7.9 + - - +
1026G LEU* 2.9 26.3 + - - +
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Residues in contact with LEU1023 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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736G HIS 5.0 1.3 - - - +
737G VAL* 4.8 7.4 - - + +
740G ALA* 3.5 27.6 - - + -
1009G LEU* 4.6 7.9 - - + +
1012G LEU* 3.7 36.1 - - + +
1013G SER* 3.9 15.7 - - - +
1015G GLU 5.9 0.4 - - - +
1019G GLN* 2.7 41.9 + - + +
1020G GLN* 2.7 9.0 + - - +
1022G VAL* 1.3 71.2 - - + +
1024G LYS* 1.3 65.5 + - - +
1026G LEU* 3.4 33.9 + - + +
1027G LEU* 3.4 15.6 + - - +
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Residues in contact with LYS1024 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1013G SER* 4.4 9.8 - - - +
1020G GLN* 2.7 52.2 + - + +
1021G HIS* 3.4 36.7 - - + +
1023G LEU* 1.3 75.0 - - - +
1025G LYS* 1.3 63.3 + - - +
1026G LEU 3.1 1.2 + - - -
1027G LEU* 3.2 12.8 + - - +
1028G ALA* 3.3 12.5 + - - +
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Residues in contact with LYS1025 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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725G GLU* 5.7 2.0 + - - +
729G LEU* 4.2 21.9 - - + +
1021G HIS* 3.1 32.0 + - + +
1022G VAL* 3.1 10.2 + - - +
1024G LYS* 1.3 79.3 - - - +
1026G LEU* 1.3 57.5 + - - +
1028G ALA* 3.5 9.3 - - + +
1029G ILE* 2.9 48.5 + - + +
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Residues in contact with LEU1026 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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726G PHE* 3.9 24.2 - - + -
729G LEU* 3.8 17.7 - - + -
737G VAL* 3.8 31.4 - - + -
741G LEU* 5.6 0.7 - - + -
1002G CYS* 4.6 8.1 - - - -
1009G LEU* 4.4 24.0 - - + -
1022G VAL 2.9 12.4 + - - +
1023G LEU* 3.4 31.9 - - + +
1025G LYS* 1.3 75.3 - - - +
1027G LEU* 1.3 54.8 + - + +
1029G ILE* 2.9 7.2 + - - +
1030G THR* 2.7 47.8 + - - +
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Residues in contact with LEU1027 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1006G SER* 3.5 41.7 - - - +
1009G LEU* 3.9 18.4 - - + +
1010G ARG* 3.6 36.0 + - + +
1013G SER* 3.6 23.8 - - - +
1023G LEU 3.8 12.3 - - - +
1024G LYS* 3.2 8.1 + - - +
1026G LEU* 1.3 77.2 - - + +
1028G ALA* 1.3 60.4 + - - +
1030G THR* 3.7 9.0 - - + +
1031G GLU* 2.8 33.3 + - - +
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Residues in contact with ALA1028 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1024G LYS 3.3 10.7 + - - +
1025G LYS* 3.5 13.9 - - + +
1027G LEU* 1.3 78.1 - - - +
1029G ILE* 1.3 53.3 + - + +
1031G GLU* 3.6 5.0 - - - +
1032G LEU* 2.7 38.2 + - - +
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Residues in contact with ILE1029 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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725G GLU* 3.5 38.8 - - + +
726G PHE* 3.4 40.8 - - + +
729G LEU* 3.8 19.5 - - + -
1025G LYS* 2.9 36.6 + - + +
1026G LEU* 3.4 7.9 - - - +
1028G ALA* 1.3 72.1 - - + +
1030G THR* 1.3 58.2 + - - +
1032G LEU* 3.2 10.7 + - + +
1033G LEU* 2.8 41.7 + - + +
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Residues in contact with THR1030 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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726G PHE* 4.8 2.0 - - - -
999G HIS* 3.0 29.8 - - + +
1002G CYS* 3.6 31.4 - - + +
1003G VAL* 3.9 16.6 - - + +
1006G SER* 5.4 5.4 - - - +
1009G LEU* 6.0 0.3 - - - +
1026G LEU* 2.7 39.0 + - - +
1027G LEU* 3.7 11.9 - - + +
1029G ILE* 1.3 74.7 - - - +
1031G GLU* 1.3 52.9 + - - +
1034G GLN* 2.8 33.6 + - + +
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Residues in contact with GLU1031 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1010G ARG* 4.1 24.3 + - - +
1027G LEU 2.8 21.6 + - - +
1028G ALA* 3.6 5.5 - - - +
1030G THR* 1.3 70.8 - - - +
1032G LEU* 1.3 60.7 + - - +
1034G GLN* 3.0 13.7 - - + +
1035G GLN* 2.9 49.4 + - - +
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Residues in contact with LEU1032 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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725G GLU* 5.6 10.1 - - + -
1028G ALA 2.7 22.0 + - - +
1029G ILE* 3.6 10.1 - - + +
1031G GLU* 1.3 73.3 - - - +
1033G LEU* 1.3 62.8 + - + +
1035G GLN* 3.7 20.2 + - - +
1036G LYS* 3.3 39.0 + - + +
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Residues in contact with LEU1033 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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718G MET* 3.7 28.3 - - + +
722G GLU* 3.6 23.8 - - + +
723G TYR* 4.4 10.5 - - + -
725G GLU* 3.8 8.7 - - + +
726G PHE* 3.7 38.6 - - + -
999G HIS* 3.4 30.0 + - + +
1029G ILE* 2.8 22.9 + - + +
1032G LEU* 1.3 78.9 - - + +
1034G GLN* 1.3 66.0 + - - +
1036G LYS* 4.4 7.6 - - + +
1037G GLN* 3.5 17.7 + - - +
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Residues in contact with GLN1034 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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999G HIS* 3.7 4.6 + - - -
1003G VAL* 4.0 39.0 - - + +
1030G THR* 2.8 19.1 + - + +
1031G GLU* 3.0 20.0 - - + +
1033G LEU* 1.3 77.8 - - - +
1035G GLN* 1.3 63.8 + - + +
1037G GLN* 3.3 21.2 + - - +
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Residues in contact with GLN1035 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1031G GLU* 2.9 35.4 + - - +
1032G LEU* 3.8 21.4 - - - +
1034G GLN* 1.3 77.2 - - + +
1036G LYS* 1.3 62.9 + - + +
1037G GLN 3.1 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