Contacts of the helix formed by residues 78 - 90 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74I LEU* 3.0 36.5 + - + +
75I LEU 3.7 3.6 - - - -
77I GLN* 1.3 86.7 + - + +
79I ALA* 1.3 64.2 + - - +
80I ASP 3.3 2.5 - - - -
81I GLU* 3.4 20.6 + - - +
82I ILE* 3.1 27.1 + - + +
183I TYR* 2.9 34.4 + - + +
187I LEU* 3.5 23.1 - - + +
190I GLU* 4.7 6.4 + - - -
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Residues in contact with ALA 79 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75I LEU 3.3 3.2 + - - +
76I GLU* 3.3 20.5 + - - +
77I GLN 3.3 1.4 + - - -
78I HIS* 1.3 76.6 - - - +
80I ASP* 1.3 60.8 + - - +
82I ILE* 3.3 2.3 + - - +
83I CYS* 2.9 35.5 + - - -
98I MET* 4.0 17.0 - - + -
101I LEU* 3.5 28.3 - - + -
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Residues in contact with ASP 80 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77I GLN 5.2 0.6 + - - -
78I HIS 3.3 0.4 - - - -
79I ALA* 1.3 82.0 - - - +
81I GLU* 1.3 66.9 + - - +
83I CYS* 3.7 6.5 + - - +
84I ARG* 3.1 26.2 + - - +
98I MET* 5.4 5.2 - - - +
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Residues in contact with GLU 81 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77I GLN 4.5 4.7 - - - +
78I HIS* 3.4 32.3 + - - +
79I ALA 3.4 0.4 - - - -
80I ASP* 1.3 86.9 + - - +
82I ILE* 1.3 60.0 + - - +
84I ARG* 3.2 20.0 + - - +
85I LEU* 2.9 35.9 + - + +
183I TYR* 3.9 21.6 + - + +
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Residues in contact with ILE 82 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75I LEU* 4.0 27.4 - - + +
78I HIS 3.1 20.8 + - - +
79I ALA 3.6 3.8 - - - +
81I GLU* 1.3 73.2 - - - +
83I CYS* 1.3 61.0 + - - +
85I LEU* 3.3 9.8 + - - +
86I ILE* 2.9 34.3 + - + +
101I LEU* 4.4 19.5 - - + -
152I VAL* 3.9 27.4 - - + -
180I SER* 4.2 3.3 - - - +
183I TYR* 3.6 25.8 - - + -
184I ILE* 3.7 20.9 - - + -
187I LEU* 4.2 4.5 - - + -
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Residues in contact with CYS 83 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79I ALA 2.9 21.4 + - - +
80I ASP* 3.9 7.2 - - - +
82I ILE* 1.3 76.0 - - - +
84I ARG* 1.3 58.0 + - - +
86I ILE* 3.2 3.9 + - - +
87I GLY* 2.9 27.2 + - - -
92I LYS 5.1 0.2 - - - +
94I ALA* 4.4 9.9 - - + +
97I ALA* 3.8 21.5 - - + +
98I MET* 3.5 52.0 - - + -
101I LEU* 4.5 6.1 - - - -
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Residues in contact with ARG 84 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80I ASP 3.1 16.3 + - - +
81I GLU* 3.4 28.0 + - - +
82I ILE 3.2 0.2 - - - -
83I CYS* 1.3 77.0 - - - +
85I LEU* 1.3 87.5 + - - +
87I GLY* 3.3 1.7 + - - -
88I GLU* 2.8 58.4 + - + +
313I SER* 5.6 0.2 + - - -
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Residues in contact with LEU 85 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32I LYS* 6.2 1.8 - - - +
81I GLU* 2.9 14.2 + - + +
82I ILE* 3.5 7.9 - - - +
84I ARG* 1.3 111.6 - - - +
86I ILE* 1.3 67.0 + - - +
88I GLU* 3.7 12.6 + - - +
89I GLU* 3.6 26.9 + - - +
179I SER* 3.8 14.4 - - - +
180I SER* 3.8 20.2 + - - +
183I TYR* 3.6 47.8 - - + -
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Residues in contact with ILE 86 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82I ILE* 2.9 26.1 + - + +
83I CYS* 3.5 7.2 - - - +
85I LEU* 1.3 76.8 - - - +
87I GLY* 1.3 59.3 + - - +
88I GLU 3.3 0.2 + - - -
89I GLU 3.3 0.5 + - - -
90I HIS* 2.8 41.2 + - + +
92I LYS* 3.3 34.8 - - + -
97I ALA* 3.8 20.9 - - + +
100I GLU* 3.9 18.8 - - + +
101I LEU 5.4 0.7 - - - +
151I PRO* 3.9 9.4 - - + -
152I VAL* 3.6 22.4 - - + -
177I ASP* 6.2 0.4 - - - -
180I SER* 3.6 20.9 - - - +
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Residues in contact with GLY 87 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24I ASN* 4.9 3.1 - - - +
83I CYS 2.9 14.6 + - - -
84I ARG* 3.6 2.9 - - - -
86I ILE* 1.3 75.7 - - - +
88I GLU* 1.3 61.9 + - - +
89I GLU 3.3 0.2 - - - -
91I GLY* 3.0 23.1 - - - -
92I LYS 3.3 24.2 - - - -
313I SER* 3.8 19.1 + - - -
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Residues in contact with GLU 88 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23I PHE 3.8 0.7 - - - +
24I ASN* 3.5 43.7 - - + +
25I PRO* 3.6 1.0 - - - +
32I LYS* 4.8 16.8 + - - +
84I ARG* 2.8 47.1 + - + +
85I LEU* 3.9 12.2 - - - +
86I ILE 3.2 0.4 - - - -
87I GLY* 1.3 74.1 - - - +
89I GLU* 1.3 66.2 + - + +
179I SER* 5.7 1.4 + - - -
313I SER* 5.2 1.1 - - - -
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Residues in contact with GLU 89 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4I ILE* 4.1 0.2 - - - +
22I VAL* 3.8 13.3 - - + +
23I PHE 3.9 13.1 - - - +
25I PRO* 3.5 13.3 - - - +
32I LYS* 3.8 13.9 - - + +
85I LEU 3.6 11.9 + - - +
86I ILE 3.3 1.6 + - - -
88I GLU* 1.3 90.6 - - + +
90I HIS* 1.3 62.7 + - - +
91I GLY 3.4 0.2 - - - -
176I ARG 4.0 8.4 - - - +
177I ASP* 3.2 23.4 - - + +
178I PRO* 3.9 8.6 - - - +
179I SER* 2.5 55.1 + - - -
180I SER* 4.0 1.0 + - - -
324I ILE* 3.7 12.5 - - - +
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Residues in contact with HIS 90 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25I PRO* 3.5 10.4 - - - +
86I ILE* 2.8 24.1 + - + +
89I GLU* 1.3 74.5 - - - +
91I GLY* 1.3 57.2 + - - +
92I LYS* 3.3 41.2 + - + +
148I PHE* 3.6 28.7 - + - -
149I ASN* 3.5 27.6 + - - +
151I PRO* 4.6 2.2 - - + -
177I ASP* 3.7 11.3 - - + +
275I SER* 4.7 11.4 - - - -
276I SER* 5.5 1.1 - - - -
278I GLU* 3.4 26.6 + - - +
322I PRO 3.9 11.2 - - - +
323I VAL 4.5 1.4 - - - +
324I ILE* 4.0 13.3 - - + +
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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
------------------------------------------------------------
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