Contacts of the helix formed by residues 57 - 71 (chain G) in PDB entry 1ZWS
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 SER 57 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47G ARG* 2.9 32.4 - - - +
55G GLY 4.1 0.4 + - - -
56G VAL* 1.3 72.9 - - - +
58G ARG* 1.3 63.6 + - - +
59G GLU* 2.9 19.1 + - - +
60G GLU* 2.9 36.6 + - - +
61G ILE* 2.9 26.3 + - - +
221H THR* 4.4 5.6 - - - +
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Residues in contact with ARG 58 (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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3G PRO* 6.2 0.6 - - - +
4G PHE* 3.3 31.8 - - - -
46G LYS* 6.0 5.2 - - - +
56G VAL 3.6 1.2 + - - -
57G SER* 1.3 69.3 + - - +
59G GLU* 1.3 61.3 + - - +
61G ILE* 3.1 12.1 - - - +
62G GLU* 2.8 101.7 + - - +
84G GLU* 3.4 19.4 + - - -
89G VAL* 6.2 2.4 - - - +
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Residues in contact with GLU 59 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57G SER* 2.9 10.0 + - - +
58G ARG* 1.3 78.5 - - - +
60G GLU* 1.3 57.1 + - + +
61G ILE 2.7 1.4 + - - -
62G GLU* 2.9 9.9 + - - -
63G ARG* 2.5 71.2 + - + +
166G HIS* 5.2 1.2 + - - -
221H THR* 5.1 10.5 - - + +
223H GLN* 4.4 7.9 + - - +
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Residues in contact with GLU 60 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47G ARG* 4.0 3.3 + - - -
56G VAL* 3.1 30.3 - - + +
57G SER* 2.9 30.0 + - - +
59G GLU* 1.3 78.6 - - + +
61G ILE* 1.3 62.9 + - - +
63G ARG* 3.1 34.4 + - - +
64G GLU* 3.1 21.3 + - - +
163G GLY* 5.2 4.3 - - - +
220H ASP 4.5 0.5 - - - +
221H THR* 3.5 21.4 - - + +
222H LYS 5.4 0.3 + - - -
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Residues in contact with ILE 61 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4G PHE* 4.4 14.8 - - + -
44G ILE* 3.1 44.6 - - + +
46G LYS* 5.3 3.4 - - + -
56G VAL* 3.7 14.8 - - + +
57G SER 2.9 25.9 + - - +
58G ARG* 3.1 15.9 - - - +
59G GLU 2.7 3.6 + - - -
60G GLU* 1.3 69.8 - - - +
62G GLU* 1.3 60.5 + - + +
64G GLU* 2.7 29.0 + - - +
65G VAL* 3.0 24.6 + - + +
89G VAL* 4.2 25.1 - - + -
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Residues in contact with GLU 62 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4G PHE* 4.5 6.7 - - + -
58G ARG* 2.8 64.1 + - - +
59G GLU* 3.6 5.9 + - - +
61G ILE* 1.3 78.9 - - - +
63G ARG* 1.3 56.8 - - - +
65G VAL* 3.1 7.7 + - - -
66G SER* 2.6 39.1 + - - -
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Residues in contact with ARG 63 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59G GLU* 2.5 49.8 + - + +
60G GLU* 3.1 37.7 + - - +
62G GLU* 1.3 74.0 - - - +
64G GLU* 1.3 52.8 + - - +
66G SER* 4.1 4.2 - - - -
67G ILE* 2.6 41.8 + - + +
165G ALA 4.3 13.8 + - - +
166G HIS* 3.5 40.4 + - - -
167G GLU* 5.4 1.8 - - + +
221H THR* 5.6 2.4 - - - +
223H GLN* 3.3 24.2 - - - +
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Residues in contact with GLU 64 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42G LYS* 2.8 32.5 + - - +
44G ILE* 4.0 15.6 - - + +
60G GLU 3.1 14.5 + - - +
61G ILE* 2.7 16.3 + - - +
63G ARG* 1.3 71.5 - - - +
65G VAL* 1.3 58.4 + - + +
67G ILE* 3.2 6.3 - - - +
68G LEU* 2.9 43.7 + - + +
91G LEU* 4.1 6.0 - - + +
93G LEU* 5.7 0.3 - - - +
162G PHE* 3.0 40.0 + - + +
163G GLY* 3.6 13.0 - - - +
165G ALA 5.6 1.1 - - - -
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Residues in contact with VAL 65 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4G PHE* 3.9 25.1 - - + -
44G ILE* 6.0 0.7 - - + -
61G ILE* 3.0 24.0 + - + +
62G GLU* 3.6 5.2 - - - +
64G GLU* 1.3 73.6 - - + +
66G SER* 1.3 69.8 + - - +
67G ILE 2.9 1.0 + - - -
68G LEU* 3.1 9.6 + - - +
69G ARG* 3.0 53.9 + - + +
79G LEU* 4.4 2.5 - - + -
82G VAL* 4.2 11.9 - - + -
89G VAL* 5.6 0.2 - - + -
91G LEU* 4.0 25.1 - - + -
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Residues in contact with SER 66 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62G GLU* 2.6 22.9 + - - -
63G ARG* 4.1 5.2 - - - -
65G VAL* 1.3 75.0 - - - +
67G ILE* 1.3 66.2 + - - +
69G ARG* 3.4 13.2 + - - +
70G GLN* 3.2 32.6 + - - +
167G GLU* 5.3 1.2 + - - -
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Residues in contact with ILE 67 (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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63G ARG* 2.6 25.6 - - + +
64G GLU* 3.2 10.3 - - - +
65G VAL 2.9 0.8 + - - -
66G SER* 1.3 74.5 - - - +
68G LEU* 1.3 56.9 + - - +
69G ARG 2.9 3.8 - - - -
70G GLN* 2.7 36.5 + - - +
71G VAL* 3.2 11.5 + - + +
135G ILE* 4.2 28.9 - - + -
162G PHE* 4.0 27.8 - - + -
165G ALA* 4.2 13.9 - - + +
166G HIS* 4.3 4.7 - - - +
167G GLU* 4.0 34.8 - - + +
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Residues in contact with LEU 68 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64G GLU* 2.9 41.9 + - + +
65G VAL* 3.1 4.7 + - - +
67G ILE* 1.3 72.4 - - - +
69G ARG* 1.3 59.0 + - - +
71G VAL* 3.0 29.4 - - + +
77G ILE* 4.3 14.5 - - + +
79G LEU* 4.2 28.1 + - + +
91G LEU* 4.4 9.6 - - + -
93G LEU* 4.1 29.4 - - + -
162G PHE* 3.4 44.2 - - + +
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Residues in contact with ARG 69 (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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2G GLU* 3.3 45.8 + - - +
3G PRO 3.9 7.3 + - - -
4G PHE* 4.1 15.8 - - - +
65G VAL* 3.0 33.0 + - - +
66G SER* 3.4 13.0 - - - +
67G ILE 2.8 5.1 + - - -
68G LEU* 1.3 73.3 - - - +
70G GLN* 1.3 64.0 + - + +
71G VAL 3.4 5.0 + - - +
72G LEU* 5.3 1.6 - - - +
79G LEU* 3.8 18.6 - - + +
82G VAL* 4.3 11.1 - - - +
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Residues in contact with GLN 70 (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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66G SER* 3.2 26.8 + - - +
67G ILE* 2.7 18.3 + - - +
69G ARG* 1.3 75.0 - - + +
71G VAL* 1.3 59.7 + - - +
72G LEU* 4.6 1.7 - - - +
129G TYR* 3.6 6.8 + - - -
133G LYS* 3.5 47.7 + - + +
135G ILE* 4.4 18.7 - - + +
167G GLU* 3.5 24.6 + - - +
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Residues in contact with VAL 71 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67G ILE* 4.2 6.7 - - + +
68G LEU* 3.0 49.5 - - + +
69G ARG 3.7 3.5 - - - +
70G GLN* 1.3 76.5 - - - +
72G LEU* 1.3 67.3 + - - +
73G HIS 4.0 0.4 - - - -
76G VAL* 4.3 21.8 - - + -
77G ILE 4.6 3.8 - - - +
78G THR* 5.0 4.9 - - - +
79G LEU 5.9 0.2 + - - -
129G TYR* 3.6 12.8 - - + -
130G LEU* 3.4 33.0 - - + -
133G LYS* 5.8 1.1 - - + -
135G ILE* 4.4 14.1 - - + -
162G PHE* 4.7 5.6 - - + -
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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