Contacts of the helix formed by residues 78 - 90 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74F LEU* 3.0 36.2 + - + +
75F LEU 3.3 4.5 - - - +
77F GLN* 1.3 87.6 + - + +
79F ALA* 1.3 59.1 + - - -
81F GLU* 3.4 23.0 + - - +
82F ILE* 3.1 26.0 + - - +
183F TYR* 3.2 35.0 + - + +
187F LEU* 3.5 28.9 - - + +
190F GLU* 4.9 7.4 + - - -
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Residues in contact with ALA 79 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75F LEU 3.2 6.0 + - - +
76F GLU* 3.2 20.2 - - - +
77F GLN 3.2 4.6 + - - -
78F HIS* 1.3 73.4 - - - +
80F ASP* 1.3 67.4 + - - +
82F ILE* 3.8 0.7 - - - +
83F CYS* 3.0 35.8 + - - -
98F MET* 4.0 16.6 - - + -
101F LEU* 3.7 21.1 - - + -
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Residues in contact with ASP 80 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77F GLN 5.0 1.3 + - - -
78F HIS 3.5 0.2 - - - -
79F ALA* 1.3 82.0 - - - +
81F GLU* 1.3 62.2 + - - +
83F CYS* 3.5 5.0 + - - +
84F ARG* 3.0 28.1 + - - +
98F MET* 5.4 4.7 - - - +
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Residues in contact with GLU 81 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77F GLN 4.0 4.0 - - - +
78F HIS* 3.4 41.7 + - - +
80F ASP* 1.3 77.3 + - + +
82F ILE* 1.3 65.7 + - - +
84F ARG* 3.3 19.5 + - - +
85F LEU* 2.9 30.7 + - + +
183F TYR* 3.7 23.9 + - + +
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Residues in contact with ILE 82 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75F LEU* 4.0 24.0 - - + +
78F HIS* 3.1 26.3 + - + +
79F ALA 3.8 3.6 - - - +
80F ASP 3.4 0.2 - - - -
81F GLU* 1.3 76.7 - - - +
83F CYS* 1.3 58.7 + - - +
85F LEU* 3.0 9.1 + - - +
86F ILE* 2.9 45.8 + - + +
101F LEU* 4.1 25.6 - - + -
152F VAL* 3.9 15.9 - - + -
180F SER* 4.3 3.1 - - - +
183F TYR* 3.6 25.4 - - + -
184F ILE* 3.6 21.1 - - + -
187F LEU* 4.4 1.3 - - + -
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Residues in contact with CYS 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79F ALA 3.0 22.7 + - - +
80F ASP* 4.0 4.9 - - - +
82F ILE* 1.3 76.2 - - - +
84F ARG* 1.3 57.0 + - - +
86F ILE* 4.0 3.6 - - - -
87F GLY* 3.1 21.3 + - - -
92F LYS 4.7 0.9 - - - +
94F ALA* 4.6 11.9 + - + +
97F ALA* 3.4 23.1 - - + +
98F MET* 3.2 53.8 - - + -
101F LEU* 4.4 7.2 - - - -
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Residues in contact with ARG 84 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80F ASP 3.0 17.8 + - - +
81F GLU* 3.5 23.0 + - - +
82F ILE 3.1 0.2 - - - -
83F CYS* 1.3 76.4 - - - +
85F LEU* 1.3 91.9 + - - +
87F GLY* 3.2 1.5 + - - -
88F GLU* 2.7 56.3 + - + +
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Residues in contact with LEU 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81F GLU* 2.9 13.2 + - + +
82F ILE* 3.6 7.4 - - - +
84F ARG* 1.3 113.4 - - - +
86F ILE* 1.3 63.3 + - - +
88F GLU* 4.1 10.8 - - - +
89F GLU* 3.7 27.2 + - - +
177F ASP* 5.5 0.2 - - - +
179F SER* 3.9 16.2 - - - +
180F SER* 3.7 21.2 + - - +
183F TYR* 3.5 47.3 - - + -
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Residues in contact with ILE 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82F ILE* 2.9 25.3 + - + +
83F CYS* 4.0 4.7 - - - +
85F LEU* 1.3 74.4 - - - +
87F GLY* 1.3 60.6 + - - +
89F GLU* 3.1 2.6 + - - -
90F HIS* 2.8 40.7 + - + +
92F LYS* 3.3 36.3 - - + -
97F ALA* 4.0 20.6 - - + +
100F GLU* 4.0 16.2 - - - +
101F LEU* 5.3 0.4 - - + -
151F PRO* 4.1 7.6 - - + -
152F VAL* 3.6 25.1 - - + -
177F ASP* 6.2 0.7 - - - -
180F SER* 3.5 23.1 - - - +
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Residues in contact with GLY 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24F ASN* 5.3 1.7 - - - +
83F CYS 3.1 12.4 + - - -
84F ARG* 3.2 4.0 + - - -
86F ILE* 1.3 79.4 - - - +
88F GLU* 1.3 60.3 + - - +
91F GLY* 3.3 15.2 - - - -
92F LYS 3.1 27.1 + - - -
313F SER* 2.9 26.5 + - - -
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Residues in contact with GLU 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23F PHE 4.0 0.2 - - - +
24F ASN* 3.5 42.9 - - + +
25F PRO* 3.6 2.8 - - - +
31F GLY* 6.2 0.2 - - - -
32F LYS* 5.3 15.3 + - - +
84F ARG* 2.7 44.3 + - + +
85F LEU* 4.2 13.0 - - - +
86F ILE 3.1 0.2 + - - -
87F GLY* 1.3 74.9 - - - +
89F GLU* 1.3 67.1 + - + +
179F SER* 5.8 1.9 - - - -
313F SER* 4.8 1.3 - - - -
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Residues in contact with GLU 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4F ILE* 3.9 0.7 - - - +
22F VAL* 3.5 25.5 - - + +
23F PHE 3.7 14.6 - - - +
25F PRO* 3.1 19.8 - - - +
32F LYS* 4.1 4.6 - - + +
85F LEU 3.7 12.6 + - - +
86F ILE 3.1 1.6 + - - -
88F GLU* 1.3 90.4 - - + +
90F HIS* 1.3 60.1 + - - +
91F GLY 3.4 0.7 - - - -
176F ARG 4.1 6.1 - - - +
177F ASP* 3.5 18.3 - - + +
178F PRO* 3.5 14.6 - - - +
179F SER* 2.8 52.6 + - - -
180F SER 3.8 0.9 + - - -
324F ILE* 3.9 9.2 - - - +
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Residues in contact with HIS 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25F PRO* 3.5 10.4 - - - +
86F ILE* 2.8 25.3 + - + +
89F GLU* 1.3 75.9 - - - +
91F GLY* 1.3 56.4 + - - +
92F LYS* 3.4 38.1 + - + +
148F PHE* 3.3 34.1 - + - -
149F ASN* 3.6 25.9 + - - +
151F PRO* 4.9 1.1 - - + -
177F ASP* 3.5 11.8 - - - +
275F SER* 4.1 11.0 - - - -
276F SER* 5.4 0.7 - - - -
278F GLU* 3.4 27.2 + - - +
322F PRO 3.8 12.4 - - - +
324F ILE* 3.9 14.7 - - + +
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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