Contacts of the helix formed by residues 78 - 90 (chain B) in PDB entry 4ZZ7
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 HIS 78 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74B LEU* 2.9 42.0 + - - +
75B LEU 3.7 2.7 - - - -
76B GLU 3.2 0.2 - - - -
77B GLN* 1.3 88.3 + - + +
79B ALA* 1.3 63.5 + - - +
80B ASP 3.3 2.5 - - - -
81B GLU* 3.2 22.0 + - - +
82B ILE* 3.1 33.4 + - + +
183B TYR* 2.8 29.5 + - + +
187B LEU* 3.7 26.6 - - + +
190B GLU* 4.8 5.5 + - - -
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Residues in contact with ALA 79 (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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75B LEU 3.2 8.4 + - - +
76B GLU* 3.2 19.8 + - - +
77B GLN 3.3 1.4 + - - -
78B HIS* 1.3 77.4 - - - +
80B ASP* 1.3 65.6 + - - +
82B ILE* 3.4 1.4 + - - +
83B CYS* 3.0 29.9 + - - -
98B MET* 4.0 18.6 - - + -
101B LEU* 3.6 22.0 - - + -
105B ILE* 6.2 0.2 - - + -
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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
----------------------------------------------------------
77B GLN 5.2 0.2 + - - -
78B HIS 3.3 0.6 - - - -
79B ALA* 1.3 80.5 - - - +
81B GLU* 1.3 66.9 + - + +
83B CYS* 3.4 6.4 + - - +
84B ARG* 3.0 28.7 + - - +
98B MET* 5.5 4.0 - - - +
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Residues in contact with GLU 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B GLN 4.0 5.7 - - - +
78B HIS* 3.2 42.6 + - - +
80B ASP* 1.3 83.1 - - + +
82B ILE* 1.3 60.7 + - - +
84B ARG* 3.3 23.5 + - - +
85B LEU* 3.0 35.5 + - + +
183B TYR* 3.6 19.6 + - + +
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Residues in contact with ILE 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B LEU* 3.7 28.7 - - + +
78B HIS* 3.1 26.1 + - + +
79B ALA* 3.8 3.8 - - - +
81B GLU* 1.3 77.4 - - - +
83B CYS* 1.3 57.3 - - - +
85B LEU* 3.3 9.3 + - - +
86B ILE* 3.0 33.0 + - + +
101B LEU* 4.3 19.7 - - + -
152B VAL* 3.8 27.1 - - + -
180B SER* 4.9 2.9 - - - +
183B TYR* 3.6 23.6 - - + -
184B ILE* 4.0 20.2 - - + -
187B LEU* 4.5 1.1 - - + -
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Residues in contact with CYS 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ALA 3.0 21.0 + - - +
80B ASP* 3.4 6.5 + - - +
82B ILE* 1.3 77.3 - - - +
84B ARG* 1.3 57.6 + - - +
86B ILE* 3.9 2.8 - - - +
87B GLY* 2.9 26.0 + - - -
92B LYS 4.8 0.5 - - - +
94B ALA* 4.6 11.6 + - + +
97B ALA* 3.6 21.2 - - + +
98B MET* 3.3 52.9 - - + -
101B LEU* 4.3 7.0 - - - -
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Residues in contact with ARG 84 (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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80B ASP 3.0 17.3 + - - +
81B GLU* 3.4 30.8 + - - +
82B ILE 3.2 0.2 - - - -
83B CYS* 1.3 76.5 - - - +
85B LEU* 1.3 81.5 + - - +
87B GLY* 3.4 1.7 + - - -
88B GLU* 2.9 49.7 + - + +
313B SER* 5.3 0.7 + - - -
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Residues in contact with LEU 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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32B LYS* 4.9 5.6 - - - +
81B GLU* 3.0 21.7 + - + +
82B ILE* 3.6 4.5 - - - +
84B ARG* 1.3 92.5 - - - +
86B ILE* 1.3 67.3 + - - +
88B GLU* 3.4 26.0 + - - +
89B GLU* 3.4 21.1 + - - +
179B SER* 3.6 27.1 - - - +
180B SER* 3.9 14.6 - - - +
183B TYR* 3.7 43.7 - - + -
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Residues in contact with ILE 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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82B ILE* 3.0 29.5 + - + +
83B CYS* 3.9 4.3 - - - +
85B LEU* 1.3 74.3 - - - +
87B GLY* 1.3 59.5 + - - +
89B GLU* 5.7 0.2 - - - -
90B HIS* 2.9 36.9 + - + +
92B LYS* 3.7 32.5 - - + -
97B ALA* 4.1 24.0 - - + +
100B GLU* 4.0 11.7 - - - +
101B LEU* 5.3 0.7 - - + -
151B PRO* 4.2 12.6 - - + -
152B VAL* 3.5 28.3 - - + -
177B ASP* 6.0 1.3 - - - -
180B SER* 3.6 22.2 - - - +
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Residues in contact with GLY 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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24B ASN* 5.2 1.7 - - - +
25B PRO* 5.2 0.3 - - - +
83B CYS 2.9 17.9 + - - -
84B ARG* 3.7 1.3 - - - -
86B ILE* 1.3 78.6 - - - +
88B GLU* 1.3 56.6 + - - +
91B GLY* 2.9 26.5 + - - -
92B LYS 3.3 26.7 + - - -
313B SER* 3.5 18.0 + - - -
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Residues in contact with GLU 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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23B PHE 3.8 0.9 - - - +
24B ASN* 3.6 30.5 - - + +
25B PRO* 3.6 14.6 - - - +
32B LYS* 4.6 17.5 + - - +
84B ARG* 2.9 36.3 + - - +
85B LEU* 3.7 22.1 - - - +
86B ILE 3.2 0.4 - - - -
87B GLY* 1.3 77.3 - - - +
89B GLU* 1.3 63.1 + - + +
313B SER* 4.3 1.5 + - - -
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Residues in contact with GLU 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ILE* 4.0 1.7 - - - +
22B VAL* 3.9 18.2 - - + +
23B PHE 3.8 8.7 - - - +
25B PRO* 3.4 13.5 - - - +
32B LYS* 3.6 15.3 - - + +
85B LEU 3.4 10.0 + - - +
86B ILE 3.3 1.8 + - - -
88B GLU* 1.3 85.8 - - + +
90B HIS* 1.3 65.8 + - - +
176B ARG 3.8 7.5 - - - +
177B ASP* 3.1 26.0 - - + +
178B PRO* 3.9 7.9 - - - -
179B SER* 2.6 53.1 + - - -
180B SER* 4.1 2.3 + - - -
324B ILE* 3.7 11.4 - - - +
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Residues in contact with HIS 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B PRO* 3.2 15.0 - - - +
86B ILE* 2.9 22.2 + - + +
89B GLU* 1.3 78.7 - - - +
91B GLY* 1.3 56.7 + - - +
92B LYS* 3.4 39.8 + - + +
148B PHE* 3.6 34.5 - + - -
149B ASN* 3.6 22.0 + - - +
151B PRO* 4.9 0.9 - - + -
177B ASP* 3.7 11.8 - - + +
275B SER* 4.5 10.7 - - - -
276B SER* 5.7 0.9 - - - -
278B GLU* 3.4 26.6 + - - +
322B PRO 4.0 12.8 - - - +
324B ILE* 3.9 14.2 - - + +
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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