Contacts of the helix formed by residues 78 - 90 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74C LEU* 3.1 36.7 + - - +
75C LEU 3.7 3.4 - - - -
77C GLN* 1.3 89.1 + - + +
79C ALA* 1.3 63.7 + - - +
80C ASP 3.3 2.9 + - - -
81C GLU* 3.3 20.7 + - - +
82C ILE* 2.9 27.0 + - + +
183C TYR* 2.9 35.8 + - + +
187C LEU* 3.3 24.5 - - + +
190C GLU* 4.5 7.3 + - - -
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Residues in contact with ALA 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C LEU 3.3 8.5 + - - +
76C GLU* 3.4 17.3 - - - +
77C GLN 3.2 4.2 + - - -
78C HIS* 1.3 75.9 - - - +
80C ASP* 1.3 63.3 + - - +
82C ILE* 3.2 3.1 + - - +
83C CYS* 2.8 34.5 + - - -
98C MET* 4.0 17.9 - - + -
101C LEU* 3.7 20.9 - - + -
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Residues in contact with ASP 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C GLN 5.0 1.0 + - - +
78C HIS 3.3 0.6 - - - -
79C ALA* 1.3 81.0 - - - +
81C GLU* 1.3 64.9 + - + +
83C CYS* 3.5 5.9 + - - +
84C ARG* 2.9 29.2 + - - +
98C MET* 5.2 5.5 - - - +
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Residues in contact with GLU 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C GLN 4.0 5.6 - - - +
78C HIS* 3.4 42.3 + - - +
80C ASP* 1.3 78.7 + - + +
82C ILE* 1.3 67.3 + - - +
84C ARG* 3.2 20.2 + - - +
85C LEU* 3.0 30.2 + - + +
183C TYR* 4.0 21.0 + - + +
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Residues in contact with ILE 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C LEU* 3.7 30.3 - - + +
78C HIS* 2.9 25.5 + - + +
79C ALA 3.4 6.1 - - - +
81C GLU* 1.3 76.1 - - - +
83C CYS* 1.3 59.1 + - - +
85C LEU* 3.2 10.2 + - - +
86C ILE* 2.9 45.1 + - + +
101C LEU* 4.0 21.5 - - + -
152C VAL* 4.1 15.5 - - + -
180C SER* 4.3 3.7 - - - +
183C TYR* 3.7 20.0 - - + -
184C ILE* 3.8 20.9 - - + -
187C LEU* 4.3 3.4 - - + -
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Residues in contact with CYS 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C ALA 2.8 22.3 + - - +
80C ASP* 3.8 6.7 - - - +
82C ILE* 1.3 73.6 - - - +
84C ARG* 1.3 57.2 + - - +
86C ILE* 3.3 3.9 + - - +
87C GLY* 2.8 26.7 + - - -
92C LYS 5.0 0.2 - - - +
94C ALA* 4.8 10.2 - - + +
97C ALA* 3.7 22.5 - - + +
98C MET* 3.5 51.8 - - + -
101C LEU* 4.4 7.0 - - - -
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Residues in contact with ARG 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C ASP 2.9 18.6 + - - +
81C GLU* 3.2 25.1 + - - +
83C CYS* 1.3 77.9 - - - +
85C LEU* 1.3 86.0 + - - +
87C GLY* 3.5 1.5 + - - -
88C GLU* 2.9 51.9 + - - +
313C SER* 5.5 0.2 + - - -
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Residues in contact with LEU 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C LYS* 5.5 4.3 - - - +
81C GLU* 3.0 20.2 + - + +
82C ILE* 3.7 6.1 - - - +
84C ARG* 1.3 101.5 - - - +
86C ILE* 1.3 66.6 + - - +
88C GLU* 3.9 12.3 - - - +
89C GLU* 3.8 24.1 + - - +
179C SER* 4.1 19.1 - - - +
180C SER* 3.9 19.4 + - - +
183C TYR* 3.7 45.5 - - + -
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Residues in contact with ILE 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C ILE* 2.9 26.1 + - + +
83C CYS* 3.6 7.2 - - - +
84C ARG 3.3 0.2 - - - -
85C LEU* 1.3 77.8 - - - +
87C GLY* 1.3 57.4 + - - +
89C GLU 3.3 1.2 + - - -
90C HIS* 2.9 39.6 + - + +
92C LYS* 3.4 36.8 - - + -
97C ALA* 4.1 20.6 - - + +
100C GLU* 3.9 19.1 - - + +
101C LEU 5.4 0.4 - - - +
151C PRO* 4.2 7.6 - - + -
152C VAL* 3.6 25.1 - - + -
177C ASP* 5.4 1.0 - - - +
180C SER* 3.6 21.3 - - - +
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Residues in contact with GLY 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C ASN* 5.2 1.6 - - - +
83C CYS 2.8 16.5 + - - -
84C ARG* 3.8 1.8 - - - -
86C ILE* 1.3 78.3 - - - +
88C GLU* 1.3 58.1 + - - +
91C GLY* 2.9 28.1 + - - -
92C LYS 3.4 23.6 - - - -
313C SER* 3.8 18.5 + - - -
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Residues in contact with GLU 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C PHE 3.8 0.9 - - - +
24C ASN* 3.4 42.7 - - + +
25C PRO* 3.7 0.9 - - - +
32C LYS* 4.5 18.4 + - - +
84C ARG* 2.9 44.9 + - - +
85C LEU* 4.3 15.0 - - - +
86C ILE 3.3 0.4 - - - -
87C GLY* 1.3 77.0 - - - +
89C GLU* 1.3 64.3 + - + +
179C SER* 5.6 0.2 + - - -
313C SER* 5.1 1.6 - - - -
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Residues in contact with GLU 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C ILE* 4.2 0.5 - - - +
22C VAL* 3.7 11.5 - - + +
23C PHE 3.8 14.4 - - - +
25C PRO* 3.3 14.4 - - - +
32C LYS* 3.7 16.7 - - + +
85C LEU* 3.8 12.2 + - - +
86C ILE 3.3 1.8 + - - -
87C GLY 3.3 0.2 - - - -
88C GLU* 1.3 88.3 - - + +
90C HIS* 1.3 65.6 + - - +
176C ARG 3.8 7.9 - - - +
177C ASP* 3.2 28.5 - - + +
178C PRO* 3.9 6.5 - - - -
179C SER* 2.6 52.5 + - - -
180C SER 4.2 0.2 + - - -
324C ILE* 3.5 12.0 - - - +
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Residues in contact with HIS 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C PRO* 3.4 12.3 - - - +
86C ILE* 2.9 22.4 + - + +
89C GLU* 1.3 80.6 - - - +
91C GLY* 1.3 57.1 + - - +
92C LYS* 3.3 37.8 + - + +
148C PHE* 3.5 31.3 - + - -
149C ASN* 3.5 27.2 + - - +
151C PRO* 4.8 1.6 - - + -
177C ASP* 3.6 11.9 - - + +
275C SER* 4.5 10.0 - - - -
276C SER* 5.3 0.9 - - - -
278C GLU* 3.4 26.7 + - - +
322C PRO 3.9 12.0 - - - +
323C VAL 4.7 0.3 - - - +
324C ILE* 3.8 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