Contacts of the helix formed by residues 78 - 90 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74H LEU* 3.0 36.0 + - + +
75H LEU 3.5 3.8 - - - -
76H GLU 3.3 0.2 - - - -
77H GLN* 1.3 84.5 + - + +
79H ALA* 1.3 62.5 + - - +
80H ASP 3.4 2.7 - - - -
81H GLU* 3.4 20.2 + - - +
82H ILE* 3.1 27.4 + - + +
183H TYR* 2.8 37.3 + + + +
187H LEU* 3.6 24.2 - - + +
190H GLU* 4.7 6.9 + - - -
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Residues in contact with ALA 79 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75H LEU 3.3 8.8 + - - +
76H GLU* 3.3 18.4 - - - +
77H GLN 3.3 4.6 + - - -
78H HIS* 1.3 76.9 - - - +
80H ASP* 1.3 60.3 + - - +
82H ILE* 3.5 0.7 + - - +
83H CYS* 2.9 37.3 + - - -
98H MET* 4.0 17.9 - - + -
101H LEU* 3.7 21.3 - - + -
105H ILE* 6.2 0.2 - - + -
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Residues in contact with ASP 80 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77H GLN 4.9 1.0 + - - +
78H HIS 3.4 0.4 - - - -
79H ALA* 1.3 81.1 - - - +
81H GLU* 1.3 65.9 + - + +
83H CYS* 3.6 5.2 + - - +
84H ARG* 3.0 28.7 + - - +
98H MET* 5.4 4.2 - - - +
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Residues in contact with GLU 81 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77H GLN 4.1 4.9 - - - +
78H HIS* 3.4 40.2 + - - +
79H ALA 3.3 0.2 - - - -
80H ASP* 1.3 82.9 + - + +
82H ILE* 1.3 60.4 + - - +
84H ARG* 3.5 17.7 + - - +
85H LEU* 3.0 35.1 + - + +
183H TYR* 3.9 22.6 + - + +
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Residues in contact with ILE 82 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75H LEU* 3.8 31.2 - - + +
78H HIS* 3.1 25.7 + - + +
79H ALA 3.8 3.1 - - - +
81H GLU* 1.3 74.3 - - - +
83H CYS* 1.3 59.5 - - - +
85H LEU* 3.4 8.4 + - - +
86H ILE* 3.0 33.1 + - + +
101H LEU* 4.1 19.5 - - + -
152H VAL* 4.1 25.1 - - + -
180H SER* 4.2 3.3 - - - +
183H TYR* 3.6 22.7 - - + -
184H ILE* 3.9 20.4 - - + -
187H LEU* 4.4 1.1 - - + -
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Residues in contact with CYS 83 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79H ALA 2.9 22.4 + - - +
80H ASP* 3.9 5.4 - - - +
82H ILE* 1.3 76.3 - - - +
84H ARG* 1.3 57.7 + - - +
86H ILE* 3.8 2.3 - - - +
87H GLY* 2.8 26.0 + - - -
94H ALA* 4.7 10.5 - - + +
97H ALA* 3.7 23.0 - - + +
98H MET* 3.5 49.1 - - + -
101H LEU* 4.2 8.1 - - - -
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Residues in contact with ARG 84 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80H ASP 3.0 19.5 + - - +
81H GLU* 3.5 22.1 + - - +
82H ILE 3.2 0.2 - - - -
83H CYS* 1.3 77.1 - - - +
85H LEU* 1.3 94.2 + - - +
87H GLY* 3.4 1.5 + - - -
88H GLU* 3.1 52.4 + - - +
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Residues in contact with LEU 85 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32H LYS* 5.1 6.1 - - - +
81H GLU* 3.0 23.5 + - + +
82H ILE* 3.4 5.4 + - - +
84H ARG* 1.3 100.4 - - - +
86H ILE* 1.3 64.3 + - - +
88H GLU* 3.6 12.1 + - - +
89H GLU* 3.6 29.3 + - - +
179H SER* 4.1 21.1 - - - +
180H SER* 3.9 15.7 - - - +
183H TYR* 3.7 46.0 - - + -
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Residues in contact with ILE 86 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82H ILE* 3.0 29.7 + - + +
83H CYS* 3.8 4.0 - - - +
85H LEU* 1.3 74.6 - - - +
87H GLY* 1.3 65.7 + - - +
88H GLU 3.2 0.2 + - - -
89H GLU* 3.3 0.6 + - - -
90H HIS* 2.9 34.5 + - + +
92H LYS* 3.6 33.2 - - + -
97H ALA* 4.1 19.7 - - + +
100H GLU* 3.9 17.9 - - + +
101H LEU* 5.5 0.9 - - + -
151H PRO* 4.2 7.6 - - + -
152H VAL* 3.6 23.6 - - + -
177H ASP* 6.1 0.9 - - - -
180H SER* 3.4 21.8 - - - +
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Residues in contact with GLY 87 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24H ASN* 5.2 0.9 - - - +
83H CYS 2.8 18.1 + - - -
84H ARG* 3.8 2.7 - - - -
86H ILE* 1.3 77.1 - - - +
88H GLU* 1.3 56.8 + - - +
91H GLY* 2.9 28.2 + - - -
92H LYS 3.4 22.4 + - - -
313H SER* 3.3 18.8 + - - -
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Residues in contact with GLU 88 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23H PHE 3.9 0.3 - - - +
24H ASN* 3.4 44.2 - - + +
25H PRO* 3.6 2.6 - - - +
32H LYS* 4.3 21.2 + - - +
84H ARG* 3.1 42.6 + - - +
85H LEU* 3.8 14.0 - - - +
86H ILE 3.2 0.2 - - - -
87H GLY* 1.3 78.6 - - - +
89H GLU* 1.3 65.6 + - + +
313H SER* 5.0 0.9 - - - -
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Residues in contact with GLU 89 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4H ILE* 4.2 1.0 - - - +
22H VAL* 3.9 10.8 - - + +
23H PHE 3.9 12.6 - - - +
25H PRO* 3.4 14.5 - - - +
32H LYS* 3.5 17.3 - - + +
85H LEU 3.6 13.8 + - - +
86H ILE 3.3 2.0 + - - +
88H GLU* 1.3 90.6 - - + +
90H HIS* 1.3 62.5 + - - +
176H ARG 4.0 8.9 - - - +
177H ASP* 3.3 24.2 - - + +
178H PRO* 4.1 5.8 - - - -
179H SER* 2.8 52.4 + - - -
180H SER* 4.0 1.2 + - - -
324H ILE* 3.6 13.7 - - - +
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Residues in contact with HIS 90 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25H PRO* 3.6 10.3 - - - +
86H ILE* 2.9 23.8 + - + +
89H GLU* 1.3 77.7 - - - +
91H GLY* 1.3 58.0 + - - +
92H LYS* 3.3 36.7 + - + +
148H PHE* 3.5 29.4 - + - -
149H ASN* 3.5 26.7 + - - +
151H PRO* 4.7 1.6 - - + -
177H ASP* 3.7 11.3 - - + +
275H SER* 4.5 12.1 - - - -
276H SER* 5.2 1.6 - - - -
278H GLU* 3.3 28.7 + - - +
322H PRO 3.7 12.6 - - - +
323H VAL 4.6 0.7 - - - +
324H ILE* 3.9 12.1 - - + +
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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