Contacts of the helix formed by residues 79 - 90 (chain B) in PDB entry 4Z2C
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 GLY 79 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A ARG* 3.7 16.2 - - - +
72B MET* 3.6 2.2 - - - -
78B HIS* 1.3 83.8 - - - +
80B ASP* 1.3 67.9 + - - +
81B SER* 3.4 2.5 - - - -
82B SER* 3.7 8.6 + - - -
83B ILE* 3.5 21.5 + - - +
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Residues in contact with ASP 80 (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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65A ALA* 4.5 10.5 - - - +
80A ASP* 4.8 7.0 - - - +
118A GLN* 5.1 11.6 + - - +
119A ARG* 5.6 1.7 + - - +
68B THR* 3.6 19.0 - - - +
69B GLY* 5.1 1.0 + - - -
72B MET* 3.3 24.3 - - - +
79B GLY* 1.3 69.1 - - - -
81B SER* 1.3 66.8 + - - +
82B SER 3.2 0.5 + - - -
83B ILE* 3.2 4.3 + - - +
84B TYR* 2.9 24.8 + - - +
118B GLN* 3.8 23.8 + - - +
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Residues in contact with SER 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B GLY* 3.4 1.1 - - - -
80B ASP* 1.3 79.5 - - - +
82B SER* 1.3 56.1 + - - +
84B TYR* 4.1 6.2 - - - +
85B GLU* 2.9 31.9 + - - +
118B GLN* 5.2 0.4 - - - -
1F G 5.5 8.7 - - - -
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Residues in contact with SER 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B VAL* 4.7 3.7 - - - +
76B HIS* 5.5 4.5 - - - -
78B HIS* 5.3 5.8 - - - -
79B GLY* 3.7 15.1 + - - -
80B ASP 3.2 0.6 - - - -
81B SER* 1.3 76.9 - - - +
83B ILE* 1.3 61.0 + - - +
85B GLU* 3.2 6.8 + - - +
86B ALA* 2.9 29.0 + - - +
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Residues in contact with ILE 83 (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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42B VAL* 4.2 8.5 - - + -
46B ILE* 3.3 32.5 - - + +
68B THR* 4.1 20.4 - - + +
71B VAL* 4.0 22.4 - - + -
72B MET* 3.9 28.5 - - + +
76B HIS* 3.5 35.4 - - + +
78B HIS 4.8 0.4 - - - +
79B GLY 3.5 15.3 - - - +
80B ASP 3.2 5.3 + - - +
82B SER* 1.3 75.1 - - - +
84B TYR* 1.3 58.5 + - - +
86B ALA 3.2 1.9 + - - -
87B MET* 2.9 29.9 + - + +
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Residues in contact with TYR 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B SER* 3.5 31.6 - - - -
68B THR* 4.3 8.7 - - - +
80B ASP 2.9 10.1 + - - +
81B SER* 4.1 4.9 - - - +
83B ILE* 1.3 77.0 - - - +
85B GLU* 1.3 59.4 + - - +
87B MET* 3.3 10.8 + - - +
88B VAL* 2.9 55.9 + - + +
107B PHE* 4.7 4.4 - + - -
115B ALA* 3.8 11.1 - - + +
116B ALA 2.7 28.7 + - - -
117B ALA* 5.0 1.1 - - - -
118B GLN* 3.2 41.1 - - + +
121B THR* 2.7 22.4 + - - +
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Residues in contact with GLU 85 (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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81B SER 2.9 21.6 + - - +
82B SER* 3.2 6.9 + - - +
84B TYR* 1.3 78.9 - - - +
86B ALA* 1.3 55.9 + - - +
88B VAL* 3.3 7.5 + - - +
89B ARG* 2.9 35.6 + - + +
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Residues in contact with ALA 86 (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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42B VAL* 3.7 16.4 - - + -
43B HIS* 4.3 20.1 + - + +
46B ILE* 3.7 13.7 - - + -
82B SER 2.9 13.1 + - - +
83B ILE 3.2 8.7 + - - +
85B GLU* 1.3 75.7 - - - +
87B MET* 1.3 56.9 + - - +
89B ARG* 3.1 10.6 + - - +
90B MET* 2.9 34.0 + - - +
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Residues in contact with MET 87 (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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46B ILE* 3.7 24.1 - - + +
50B MET* 4.3 3.8 - - + -
64B SER* 4.5 14.8 - - - +
67B ILE* 3.5 41.5 - - + -
68B THR* 5.1 6.3 - - - +
83B ILE* 2.9 15.6 + - + +
84B TYR* 3.6 15.5 - - + +
86B ALA* 1.3 75.1 - - - +
88B VAL* 1.3 63.8 + - - +
90B MET* 3.1 23.9 + - + +
91B ALA* 3.4 11.3 + - - +
101B VAL* 4.0 18.3 - - + +
107B PHE* 4.9 5.2 - - + -
123B ALA* 4.1 21.5 - - + -
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Residues in contact with VAL 88 (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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84B TYR* 2.9 51.6 + - + +
85B GLU* 3.6 7.0 - - - +
87B MET* 1.3 75.1 - - - +
89B ARG* 1.3 60.6 + - + +
91B ALA* 3.0 18.2 + - - +
92B GLN* 3.2 36.3 + - - +
107B PHE* 3.5 28.2 - - + +
115B ALA* 3.7 20.0 - - + +
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Residues in contact with ARG 89 (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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43B HIS* 4.5 9.5 + - - +
85B GLU* 2.9 18.5 + - + +
86B ALA* 3.1 11.4 + - - +
88B VAL* 1.3 77.8 - - + +
90B MET* 1.3 58.7 + - + +
91B ALA 3.1 2.6 + - - -
92B GLN* 3.8 17.2 + - - +
95B SER* 3.6 42.8 + - - +
96B TYR* 3.9 38.4 + - - -
170B THR* 4.9 17.9 - - - +
263B TYR* 4.9 7.3 + - - -
264B MET* 6.2 2.4 - - - -
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Residues in contact with MET 90 (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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43B HIS* 3.4 36.8 - - + +
46B ILE* 3.5 41.3 - - + -
47B LEU* 4.8 5.4 - - + -
86B ALA 2.9 12.0 + - - +
87B MET* 3.1 16.7 + - - +
89B ARG* 1.3 75.3 - - - +
91B ALA* 1.3 54.2 + - - +
92B GLN 3.7 0.2 - - - -
96B TYR* 3.4 32.3 - - + -
99B MET* 3.9 2.6 - - - +
100B LEU* 3.2 22.5 + - + -
101B VAL* 2.7 50.3 + - + +
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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