Contacts of the helix formed by residues 1009 - 1027 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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519A LEU* 4.4 20.0 - - + +
523A TYR* 3.7 44.2 - - + -
530A VAL* 6.0 4.7 - - + -
606A VAL* 4.4 17.5 - - + -
607A THR 2.8 19.4 + - - +
608A ILE* 4.6 9.4 - - + -
614A ALA* 4.5 11.4 - - + -
618A VAL* 4.2 11.2 - - + -
1007A MET 3.8 0.2 + - - -
1008A SER* 1.3 73.9 + - - +
1010A GLU* 1.3 63.3 + - - +
1012A ILE* 4.6 3.1 - - - +
1013A MET* 3.1 44.0 + - + +
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Residues in contact with GLU1010 (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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613A ARG* 4.4 20.6 - - + +
614A ALA* 4.6 10.6 - - + +
617A ARG* 3.0 47.6 + - + +
1008A SER* 3.2 10.2 + - - +
1009A LEU* 1.3 78.8 - - - +
1011A ASP* 1.3 59.0 + - - +
1014A GLY 3.2 11.1 + - - -
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Residues in contact with ASP1011 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617A ARG* 5.6 1.0 + - - +
1007A MET* 5.0 5.6 - - + -
1008A SER* 3.1 32.0 + - - +
1010A GLU* 1.3 77.0 - - - +
1012A ILE* 1.3 68.4 + - - +
1014A GLY* 2.8 12.7 + - - -
1015A GLU* 3.0 15.3 + - - +
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Residues in contact with ILE1012 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519A LEU* 4.1 22.7 - - + -
537A ILE* 5.0 9.6 - - + -
604A ILE* 5.9 2.0 - - + -
606A VAL* 5.2 6.3 - - + -
1007A MET* 4.9 13.1 - - + +
1008A SER 2.8 19.7 + - - +
1009A LEU* 4.3 3.1 - - - +
1011A ASP* 1.3 71.6 - - - +
1013A MET* 1.3 57.7 + - - +
1015A GLU* 3.6 1.5 + - - -
1016A ARG* 2.9 49.4 + - - +
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Residues in contact with MET1013 (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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516A THR* 3.7 30.3 - - + +
519A LEU* 4.2 15.3 - - + -
520A THR* 3.6 17.9 - - + -
617A ARG* 4.2 15.3 - - + +
618A VAL* 3.6 30.3 - - + -
621A LEU* 3.4 10.7 - - + +
622A MET* 3.9 16.4 - - + -
1009A LEU* 3.1 36.4 + - + +
1012A ILE* 1.3 72.2 - - - +
1014A GLY* 1.3 60.0 + - - +
1016A ARG* 4.5 3.8 - - - -
1017A PHE* 3.1 32.8 + - + +
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Residues in contact with GLY1014 (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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617A ARG* 4.2 15.8 - - - +
632A TRP* 4.0 16.0 - - - -
1010A GLU 3.2 12.9 + - - -
1011A ASP* 2.8 8.4 + - - -
1013A MET* 1.3 74.5 - - - +
1015A GLU* 1.3 63.8 + - - +
1018A GLY* 3.1 22.9 + - - -
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Residues in contact with GLU1015 (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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1011A ASP 3.0 15.2 + - - +
1012A ILE* 4.2 2.5 - - - +
1014A GLY* 1.3 70.4 - - - -
1016A ARG* 1.3 79.0 + - - +
1019A ARG* 3.0 26.7 + - - +
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Residues in contact with ARG1016 (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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512A ALA* 3.7 32.9 - - - +
513A HIS* 5.9 0.2 - - - -
515A GLN* 3.2 38.4 + - + +
516A THR* 3.6 17.0 - - - +
519A LEU* 6.1 2.7 - - + -
537A ILE* 4.5 15.2 - - + +
539A LEU* 5.4 4.4 - - - +
604A ILE* 4.5 18.9 - - - +
1012A ILE* 2.9 34.4 + - + +
1013A MET* 4.3 0.4 - - - +
1015A GLU* 1.3 90.6 - - - +
1017A PHE* 1.3 61.6 + - - +
1019A ARG* 3.6 3.7 - - - +
1020A TYR* 3.2 19.1 + - - +
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Residues in contact with PHE1017 (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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513A HIS* 4.9 10.5 - + - +
516A THR* 4.1 14.6 - - + +
621A LEU* 3.6 53.8 - - + -
622A MET* 3.9 23.6 - - + -
629A ARG* 4.2 22.2 - - + -
632A TRP* 4.8 3.4 - + - -
633A ILE* 4.6 5.6 - - + -
1013A MET* 3.1 21.2 + - + +
1016A ARG* 1.3 74.7 - - - +
1018A GLY* 1.3 56.7 + - - +
1020A TYR* 3.7 16.1 - + + +
1021A SER* 2.7 51.4 + - - -
1172A ALA* 4.6 12.1 - - + -
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Residues in contact with GLY1018 (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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632A TRP* 4.5 8.0 - - - -
637A VAL* 4.0 20.9 - - - +
1014A GLY 3.1 16.8 + - - -
1015A GLU 4.0 0.4 - - - -
1017A PHE* 1.3 74.5 - - - +
1019A ARG* 1.3 65.7 + - - +
1021A SER* 3.7 1.5 - - - -
1022A LYS* 3.0 27.9 + - - +
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Residues in contact with ARG1019 (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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509A THR* 4.5 9.8 - - + +
512A ALA* 4.6 9.2 - - + -
1015A GLU 3.0 20.6 + - - +
1016A ARG* 3.6 5.8 - - - +
1018A GLY* 1.3 78.2 - - - +
1020A TYR* 1.3 62.0 + - - +
1022A LYS* 3.9 3.8 - - - +
1023A TYR* 3.3 22.2 + - - +
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Residues in contact with TYR1020 (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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458A LYS* 3.5 26.7 + - - -
509A THR* 3.6 30.5 - - - +
510A ASP* 3.8 9.4 - - - -
512A ALA* 4.8 0.4 - - - +
513A HIS* 3.2 53.7 + + + +
1016A ARG 3.2 12.7 + - - +
1017A PHE* 3.9 15.7 - + - +
1019A ARG* 1.3 75.5 - - - +
1021A SER* 1.3 69.3 + - - +
1023A TYR* 3.3 0.5 + - - +
1024A ILE* 2.9 60.4 + - + +
1028A ARG* 5.3 2.1 + - - -
1172A ALA* 5.2 7.2 - - + -
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Residues in contact with SER1021 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632A TRP* 5.9 0.2 - - - -
633A ILE* 4.2 23.1 - - - -
637A VAL* 4.4 3.6 - - - -
1017A PHE* 2.7 41.6 + - - -
1018A GLY* 3.7 6.7 - - - -
1020A TYR* 1.3 77.0 - - - +
1022A LYS* 1.3 65.5 + - - +
1024A ILE* 3.0 1.8 + - - +
1025A ILE* 2.9 29.5 + - - +
1172A ALA* 4.6 10.5 - - - -
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Residues in contact with LYS1022 (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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637A VAL* 3.9 12.5 - - + +
638A LYS 2.6 29.7 + - - +
639A PHE* 3.8 26.3 - - + +
640A THR* 3.8 7.9 - - - +
1018A GLY 3.0 17.8 + - - +
1019A ARG* 3.9 4.0 - - - +
1021A SER* 1.3 75.4 - - - +
1023A TYR* 1.3 54.3 + - - +
1025A ILE* 3.3 1.6 + - - +
1026A GLN* 2.7 71.6 + - - +
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Residues in contact with TYR1023 (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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509A THR* 3.4 39.9 - - + -
1019A ARG 3.3 15.2 + - - +
1020A TYR 3.8 2.5 - - - +
1021A SER 3.2 0.6 - - - -
1022A LYS* 1.3 75.7 - - - +
1024A ILE* 1.3 71.5 + - + +
1026A GLN* 5.0 0.4 - - - -
1027A ASP* 2.6 75.7 + - + +
1028A ARG* 3.7 22.9 - - - -
1043A ARG* 5.2 5.7 + - - -
1074A HIS* 5.9 0.2 - - - -
1075A PRO* 5.0 3.8 - - - +
1076A HIS* 3.1 26.4 + + - -
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Residues in contact with ILE1024 (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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1020A TYR* 2.9 52.1 + - + +
1021A SER* 3.7 2.0 - - - +
1023A TYR* 1.3 81.7 - - + +
1025A ILE* 1.3 57.1 + - - +
1028A ARG* 2.9 55.1 + - + +
1029A ALA* 3.3 29.3 + - + +
1170A ILE 5.1 0.9 - - - +
1171A SER* 3.5 27.7 + - - +
1172A ALA* 3.8 16.4 - - + +
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Residues in contact with ILE1025 (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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633A ILE* 4.1 15.9 - - + -
639A PHE* 4.0 23.3 - - + -
1021A SER 2.9 27.0 + - - +
1022A LYS 3.7 2.7 - - - +
1024A ILE* 1.3 78.4 - - - +
1026A GLN* 1.3 66.0 + - - +
1030A LEU* 3.8 25.7 + - + +
1171A SER* 3.2 21.1 - - - +
1172A ALA 3.6 18.2 - - - +
1174A TYR* 4.1 8.5 - - + -
1332A ILE* 3.5 16.2 - - + +
1337A PRO* 3.8 31.2 - - + -
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Residues in contact with GLN1026 (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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639A PHE* 3.4 41.0 + - + +
1022A LYS* 2.7 42.9 + - - +
1023A TYR* 5.0 0.3 - - - -
1025A ILE* 1.3 76.1 - - - +
1027A ASP* 1.3 76.0 + - - +
1028A ARG 3.7 1.5 + - - -
1030A LEU 4.5 5.0 - - - +
1039A PRO* 4.4 5.5 - - - +
1332A ILE* 4.5 16.6 - - + +
1335A PHE* 2.9 45.0 + - + +
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Residues in contact with ASP1027 (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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1023A TYR* 2.6 60.2 + - + +
1026A GLN* 1.3 88.4 - - - +
1028A ARG* 1.3 63.3 + - - +
1039A PRO* 3.7 23.4 - - + +
1043A ARG* 5.9 2.4 + - - +
1074A HIS* 5.9 3.1 - - - -
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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