Contacts of the helix formed by residues 59 - 71 (chain B) in PDB entry 2Z0E
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 ASN 59 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57B HIS 3.3 4.3 + - - +
58B VAL* 1.3 78.7 - - - +
60B MET* 1.3 65.7 - - - +
61B SER* 3.3 7.3 + - - -
62B GLU* 2.8 55.8 + - - +
63B LEU* 3.0 17.5 + - - +
91B VAL 3.4 13.7 + - - +
92B SER* 3.6 18.1 + - - +
93B THR 3.1 16.2 - - - +
94B PRO* 4.1 1.8 - - + -
95B ILE* 5.7 0.7 - - - -
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Residues in contact with MET 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B ASN* 1.3 74.3 - - - +
61B SER* 1.3 56.1 + - - +
63B LEU* 3.6 10.2 - - + +
64B ILE* 2.8 41.7 + - + +
81B LEU* 4.4 15.5 - - + +
83B VAL* 4.4 13.9 - - + -
88B MET* 4.0 25.4 - - + -
90B SER 3.9 11.0 - - - +
91B VAL* 3.4 17.4 + - + -
93B THR* 3.1 13.3 + - - +
95B ILE* 4.3 16.8 - - - -
98B VAL* 4.1 24.7 - - + -
111B MET* 4.2 22.4 - - - -
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Residues in contact with SER 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B ASN* 3.2 7.6 - - - -
60B MET* 1.3 74.3 - - - +
62B GLU* 1.3 62.4 + - - +
64B ILE* 3.6 8.0 + - - +
65B LYS* 3.2 44.4 + - - +
91B VAL* 2.8 42.2 + - - +
92B SER* 5.4 0.4 - - - -
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Residues in contact with GLU 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B HIS* 4.3 5.1 - - - +
58B VAL* 3.3 20.8 - - + +
59B ASN* 2.8 54.4 + - - +
61B SER* 1.3 75.5 - - - +
63B LEU* 1.3 66.3 + - - +
65B LYS* 3.2 10.1 + - + +
66B ILE* 3.0 25.3 + - - +
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Residues in contact with LEU 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B VAL* 5.4 0.7 - - + -
35B ILE* 4.2 12.1 - - + -
52B PHE* 6.2 0.9 - - + -
54B VAL* 4.7 21.3 - - + -
58B VAL* 4.1 9.5 - - + +
59B ASN 3.0 13.0 + - - +
60B MET* 3.6 19.7 - - - +
62B GLU* 1.3 76.9 - - - +
64B ILE* 1.3 61.9 + - - +
66B ILE* 3.0 29.6 - - + +
67B ILE* 3.1 26.4 + - + +
81B LEU* 3.8 13.2 - - + -
95B ILE* 4.3 7.4 - - + -
111B MET* 3.4 41.3 - - + -
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Residues in contact with ILE 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ASP* 3.3 42.6 - - + +
60B MET* 2.8 30.6 + - + +
61B SER* 3.7 7.2 - - - +
63B LEU* 1.3 74.6 - - - +
65B LYS* 1.3 65.5 + - + +
67B ILE* 4.0 0.4 - - - -
68B ARG* 3.1 27.6 + - - +
79B PHE* 3.9 22.0 - - + -
80B PHE* 6.4 0.4 - - - -
81B LEU* 4.3 28.3 - - + +
88B MET* 5.4 5.6 - - + -
91B VAL* 4.4 17.9 - - + -
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Residues in contact with LYS 65 (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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171A ASP* 6.1 0.7 - - - +
61B SER* 3.2 31.0 + - - +
62B GLU* 3.2 13.2 + - + +
64B ILE* 1.3 81.2 - - + +
66B ILE* 1.3 56.4 + - - +
68B ARG* 3.3 12.2 + - - +
69B ARG* 3.0 26.2 + - - +
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Residues in contact with ILE 66 (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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62B GLU 3.0 13.1 + - - +
63B LEU* 3.0 27.4 - - + +
65B LYS* 1.3 73.8 - - - +
67B ILE* 1.3 71.1 + - + +
69B ARG* 3.1 12.6 + - + +
70B ARG* 2.7 65.1 + - + +
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Residues in contact with ILE 67 (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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35B ILE* 3.8 35.2 - - + -
47B LEU* 4.6 11.0 - - + -
52B PHE* 4.2 22.9 - - + -
63B LEU* 3.1 29.0 + - + +
64B ILE 4.1 0.4 - - - +
66B ILE* 1.3 82.3 - - + +
68B ARG* 1.3 61.5 + - - +
70B ARG* 3.2 7.8 + - + +
71B LEU* 2.8 42.8 + - + +
79B PHE* 3.7 26.2 - - + -
81B LEU* 4.7 5.6 - - + -
113B TYR* 4.7 2.0 - - + -
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Residues in contact with ARG 68 (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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170A MET* 4.2 8.1 - - - +
171A ASP* 3.0 38.1 + - - +
64B ILE* 3.1 27.3 + - - +
65B LYS* 3.4 11.2 - - - +
67B ILE* 1.3 75.6 - - - +
69B ARG* 1.3 57.8 + - - +
71B LEU* 3.3 2.0 + - - -
72B GLN 3.0 7.8 + - - -
73B LEU* 2.9 49.3 + - + +
74B ASN 3.2 20.2 + - - -
75B ALA* 3.5 18.3 + - - +
77B GLN 2.9 28.4 + - - -
79B PHE* 3.5 36.5 + - + +
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Residues in contact with ARG 69 (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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65B LYS 3.0 13.7 + - - +
66B ILE* 3.1 20.2 + - + +
68B ARG* 1.3 75.3 - - - +
70B ARG* 1.3 57.8 + - - +
72B GLN* 2.8 29.4 + - - +
73B LEU 5.0 1.3 - - - +
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Residues in contact with ARG 70 (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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47B LEU* 3.8 24.6 - - + +
52B PHE* 5.0 15.1 - - + -
66B ILE* 2.7 56.9 + - + +
67B ILE* 3.5 16.4 - - + +
69B ARG* 1.3 74.2 - - - +
71B LEU* 1.3 61.2 + - - +
72B GLN* 3.4 9.9 + - - +
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Residues in contact with LEU 71 (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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44B LEU* 5.0 2.2 - - + -
45B PRO* 3.4 52.1 - - + +
46B VAL 4.5 1.3 - - - -
47B LEU* 3.3 26.2 - - + +
67B ILE* 2.8 24.4 + - + +
70B ARG* 1.3 73.7 - - - +
72B GLN* 1.3 71.9 + - - +
73B LEU* 3.2 19.7 + - + +
79B PHE* 3.6 34.3 - - + -
113B TYR* 3.5 22.2 - - + +
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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