Contacts of the helix formed by residues 1009 - 1027 (chain B) in PDB entry 4Z4Q
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 LEU1009 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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519B LEU* 4.2 34.5 - - + +
523B TYR* 3.1 44.4 - - + -
530B VAL* 6.2 4.0 - - + -
606B VAL* 5.3 7.6 - - + -
607B THR 3.1 11.2 + - - +
608B ILE* 4.3 20.5 - - + +
614B ALA* 4.3 9.6 - - + -
618B VAL* 4.1 14.6 - - + -
1008B SER* 1.3 72.1 - - - +
1010B GLU* 1.3 63.0 + - - +
1012B ILE* 4.7 4.5 - - - -
1013B MET* 3.0 42.2 + - + +
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Residues in contact with GLU1010 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610B ASP 5.9 0.2 - - - +
613B ARG* 4.2 26.5 - - + +
614B ALA* 4.4 11.3 - - + +
617B ARG* 3.1 33.1 + - + +
618B VAL* 6.5 0.4 - - - -
1008B SER* 3.3 6.8 - - - +
1009B LEU* 1.3 76.9 - - - +
1011B ASP* 1.3 63.6 + - - +
1014B GLY 3.0 19.6 + - - -
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Residues in contact with ASP1011 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617B ARG* 4.7 3.8 - - - +
1007B MET* 5.6 5.2 - - + -
1008B SER* 2.8 27.9 + - - +
1010B GLU* 1.3 78.4 - - - +
1012B ILE* 1.3 62.0 + - + +
1014B GLY* 3.3 1.0 + - - -
1015B GLU* 3.0 23.5 + - - +
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Residues in contact with ILE1012 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519B LEU* 4.2 13.0 - - + -
537B ILE* 4.2 21.3 - - + -
604B ILE* 4.2 12.6 - - + -
606B VAL* 4.1 25.4 - - + -
1007B MET* 3.1 36.3 - - + +
1008B SER 2.8 26.4 + - - +
1009B LEU* 4.1 3.8 - - - +
1011B ASP* 1.3 71.2 - - - +
1013B MET* 1.3 66.3 + - - +
1015B GLU* 2.8 7.0 + - - +
1016B ARG* 2.8 51.5 + - + +
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Residues in contact with MET1013 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516B THR* 3.7 31.9 - - - +
519B LEU* 4.3 12.3 - - + -
520B THR* 3.3 26.7 - - + -
617B ARG* 4.4 6.7 - - + -
618B VAL* 3.7 24.5 - - + -
621B LEU* 4.0 13.5 - - + -
622B MET* 3.5 21.3 - - + -
1009B LEU* 3.0 38.0 + - + +
1010B GLU 4.0 1.8 - - - +
1012B ILE* 1.3 76.1 - - - +
1014B GLY* 1.3 64.7 + - - +
1016B ARG* 4.6 3.1 - - - +
1017B PHE* 3.0 30.5 + - - +
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Residues in contact with GLY1014 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617B ARG* 3.3 26.6 - - - +
621B LEU* 4.3 1.5 - - - +
632B TRP* 3.8 20.1 - - - -
1010B GLU 3.0 11.3 + - - -
1011B ASP 3.7 2.0 - - - -
1013B MET* 1.3 76.4 - - - +
1015B GLU* 1.3 55.4 + - - +
1018B GLY* 3.0 27.7 + - - -
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Residues in contact with GLU1015 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1011B ASP 3.0 14.5 + - - +
1012B ILE* 2.8 10.5 + - - +
1014B GLY* 1.3 69.6 - - - +
1016B ARG* 1.3 95.1 + - - +
1018B GLY* 4.0 0.7 - - - -
1019B ARG* 3.3 35.5 + - - +
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Residues in contact with ARG1016 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512B ALA* 3.7 39.3 - - - +
515B GLN* 3.1 38.2 + - + +
516B THR* 3.9 8.3 - - - +
519B LEU* 6.2 0.2 - - + -
537B ILE* 4.8 4.9 - - - +
539B LEU* 5.5 4.4 - - - +
604B ILE* 4.1 24.2 - - - +
1007B MET* 5.8 2.4 - - - +
1012B ILE* 2.8 41.3 + - + +
1013B MET* 4.4 1.1 - - - +
1015B GLU* 1.3 97.7 + - - +
1017B PHE* 1.3 66.4 + - - +
1019B ARG* 3.1 15.4 + - - +
1020B TYR* 3.2 10.9 + - - +
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Residues in contact with PHE1017 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464B LYS* 6.3 0.9 - - - -
512B ALA 6.0 0.2 - - - -
513B HIS* 4.6 13.0 - + - -
516B THR* 3.8 16.2 + - + +
621B LEU* 3.8 52.0 - - + -
622B MET* 4.0 19.5 - - + -
629B ARG* 4.1 17.9 - - - -
632B TRP* 4.9 2.7 - + - -
633B ILE* 4.5 8.5 - - + -
1013B MET 3.0 18.1 + - - +
1014B GLY 4.5 0.2 - - - +
1016B ARG* 1.3 77.9 - - - +
1018B GLY* 1.3 58.9 + - - +
1020B TYR* 4.4 16.4 - + - -
1021B SER* 2.8 46.7 + - - -
1172B ALA* 4.4 14.4 - - + -
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Residues in contact with GLY1018 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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632B TRP* 4.7 8.0 - - - -
637B VAL* 4.3 14.9 - - - +
1014B GLY 3.0 20.8 + - - -
1015B GLU* 4.0 1.6 - - - -
1017B PHE* 1.3 76.4 - - - +
1019B ARG* 1.3 59.9 + - - +
1021B SER* 3.8 4.7 - - - -
1022B LYS* 3.1 26.2 + - - +
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Residues in contact with ARG1019 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509B THR* 3.9 15.8 - - + +
512B ALA* 4.4 8.5 - - + -
1015B GLU* 3.3 33.7 + - - +
1016B ARG* 3.1 11.0 + - - +
1018B GLY* 1.3 73.7 - - - +
1020B TYR* 1.3 65.8 + - - +
1022B LYS* 3.8 3.4 - - - +
1023B TYR* 3.0 25.5 + - - +
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Residues in contact with TYR1020 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458B LYS* 3.5 20.1 + - - -
509B THR* 3.7 26.8 + - - +
510B ASP* 3.7 8.7 - - - -
513B HIS* 3.1 65.1 + + + -
1016B ARG 3.2 9.1 + - - +
1017B PHE* 3.7 20.9 - + - +
1019B ARG* 1.3 79.9 - - - +
1021B SER* 1.3 57.6 + - - +
1023B TYR* 3.2 1.6 + - - +
1024B ILE* 2.9 72.8 + - + +
1028B ARG* 4.8 2.0 + - - -
1172B ALA* 4.9 3.1 - - + -
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Residues in contact with SER1021 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632B TRP* 6.0 0.2 - - - -
633B ILE* 4.3 25.4 - - - -
637B VAL* 4.6 1.6 - - - -
1017B PHE* 2.8 41.0 + - - -
1018B GLY* 3.8 5.6 - - - -
1020B TYR* 1.3 73.9 - - - +
1022B LYS* 1.3 65.9 + - - +
1024B ILE* 3.3 1.1 + - - +
1025B ILE* 3.0 31.0 + - - +
1172B ALA* 4.3 14.8 - - - -
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Residues in contact with LYS1022 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637B VAL* 3.7 26.6 - - + +
638B LYS 2.9 26.7 + - - +
639B PHE* 4.0 19.9 - - + +
640B THR* 4.4 5.3 - - - +
1018B GLY 3.1 17.0 + - - +
1019B ARG* 3.8 4.3 - - - +
1021B SER* 1.3 77.6 - - - +
1023B TYR* 1.3 58.5 + - - +
1025B ILE* 3.6 1.7 - - - +
1026B GLN* 2.9 65.0 + - - +
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Residues in contact with TYR1023 (chain B).
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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509B THR* 3.4 39.0 - - + +
1019B ARG 3.0 16.2 + - - +
1020B TYR 3.5 2.9 - - - +
1022B LYS* 1.3 81.0 - - - +
1024B ILE* 1.3 66.3 + - + +
1026B GLN* 4.8 3.4 - - - +
1027B ASP* 2.7 66.1 + - + +
1028B ARG* 3.7 25.1 - - - -
1043B ARG* 5.4 4.2 + - - -
1075B PRO* 5.3 2.8 - - - +
1076B HIS* 3.4 24.3 + + - -
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Residues in contact with ILE1024 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1020B TYR* 2.9 70.6 + - + +
1021B SER 3.8 3.6 - - - +
1023B TYR* 1.3 76.7 - - + +
1025B ILE* 1.3 62.3 + - - +
1028B ARG* 3.3 45.5 + - + +
1029B ALA* 3.1 27.3 + - + +
1170B ILE 5.6 0.2 - - - +
1171B SER* 3.5 22.0 + - - +
1172B ALA* 3.8 24.0 - - + +
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Residues in contact with ILE1025 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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633B ILE* 4.1 12.3 - - + -
639B PHE* 4.1 22.0 - - + -
1021B SER* 3.0 29.1 + - - +
1022B LYS 3.6 2.9 - - - +
1024B ILE* 1.3 80.2 - - - +
1026B GLN* 1.3 63.9 + - - +
1030B LEU* 3.8 28.8 + - + +
1171B SER* 3.1 19.3 - - - +
1172B ALA 3.5 20.0 - - - +
1174B TYR* 4.1 11.7 - - + -
1332B ILE* 3.5 15.4 - - + +
1337B PRO* 3.7 28.0 - - + -
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Residues in contact with GLN1026 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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639B PHE* 3.4 14.0 + - + +
1022B LYS* 2.9 59.2 + - - +
1023B TYR* 4.5 1.1 - - - +
1025B ILE* 1.3 76.6 - - + +
1027B ASP* 1.3 81.1 + - - +
1028B ARG 3.9 0.7 - - - -
1030B LEU 4.7 3.6 - - - +
1039B PRO* 4.3 5.2 - - - +
1332B ILE* 4.1 21.2 - - + +
1335B PHE* 2.9 37.2 - - + +
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Residues in contact with ASP1027 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1023B TYR* 2.7 53.0 + - + +
1026B GLN* 1.3 95.9 + - - +
1028B ARG* 1.3 62.0 + - - +
1039B PRO* 3.5 27.6 - - + +
1043B ARG* 5.8 1.2 + - - -
1074B HIS* 5.8 2.9 - - - -
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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