Contacts of the helix formed by residues 78 - 90 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74G LEU* 2.8 41.0 + - + +
75G LEU 3.7 2.7 - - - -
76G GLU 3.3 0.2 - - - -
77G GLN* 1.3 84.9 + - + +
79G ALA* 1.3 62.9 + - - +
80G ASP 3.3 2.6 + - - -
81G GLU* 3.3 22.1 + - - +
82G ILE* 3.0 23.6 + - + +
183G TYR* 2.9 34.7 + - + +
187G LEU* 3.7 29.2 - - + +
190G GLU* 4.8 4.9 + - - -
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Residues in contact with ALA 79 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75G LEU 3.3 12.4 + - - +
76G GLU* 3.5 16.8 - - - +
77G GLN 3.4 3.8 + - - -
78G HIS* 1.3 76.8 - - - +
80G ASP* 1.3 66.7 + - - +
82G ILE* 3.4 0.9 + - - +
83G CYS* 3.0 32.0 + - - -
98G MET* 3.9 18.2 - - + -
101G LEU* 3.6 18.2 - - + -
105G ILE* 6.1 0.7 - - + -
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Residues in contact with ASP 80 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77G GLN 5.1 0.2 + - - -
78G HIS 3.3 0.2 - - - -
79G ALA* 1.3 81.5 - - - +
81G GLU* 1.3 65.5 + - + +
83G CYS* 3.4 5.6 + - - +
84G ARG* 3.0 29.3 + - - +
98G MET* 5.2 5.2 - - - +
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Residues in contact with GLU 81 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77G GLN 4.1 5.5 - - - +
78G HIS* 3.4 42.4 + - - +
80G ASP* 1.3 82.5 + - + +
82G ILE* 1.3 58.1 + - - +
84G ARG* 3.5 20.4 + - - +
85G LEU* 3.0 35.3 + - + +
183G TYR* 3.9 19.9 + - + +
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Residues in contact with ILE 82 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75G LEU* 4.0 23.8 - - + +
78G HIS* 3.0 22.4 - - + +
79G ALA 3.6 4.9 - - - +
80G ASP 3.2 0.4 - - - -
81G GLU* 1.3 76.0 - - - +
83G CYS* 1.3 54.7 + - - +
85G LEU* 3.2 7.6 + - - +
86G ILE* 2.8 43.3 + - + +
101G LEU* 4.1 23.3 - - + -
152G VAL* 3.9 26.2 - - + -
180G SER* 5.0 3.1 - - - +
183G TYR* 3.7 21.8 - - + -
184G ILE* 3.7 23.3 - - + -
187G LEU* 4.5 1.6 - - + -
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Residues in contact with CYS 83 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79G ALA 3.0 26.3 + - - +
80G ASP* 3.9 5.2 - - - +
82G ILE* 1.3 73.3 - - - +
84G ARG* 1.3 59.7 + - - +
86G ILE* 3.8 4.0 - - - +
87G GLY* 2.9 23.6 + - - -
92G LYS 4.9 0.5 - - - +
94G ALA* 4.5 11.2 - - + +
97G ALA* 3.6 23.5 - - + +
98G MET* 3.5 49.4 - - + +
101G LEU* 4.3 7.6 - - - -
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Residues in contact with ARG 84 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80G ASP 3.0 18.3 + - - +
81G GLU* 3.5 27.6 + - - +
83G CYS* 1.3 76.8 - - - +
85G LEU* 1.3 75.6 + - - +
87G GLY* 3.0 2.8 + - - -
88G GLU* 2.6 64.1 + - + +
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Residues in contact with LEU 85 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32G LYS* 5.4 4.7 - - - +
81G GLU* 3.0 22.5 + - + +
82G ILE* 3.2 5.6 + - - +
84G ARG* 1.3 104.7 - - - +
86G ILE* 1.3 63.0 + - - +
88G GLU* 3.7 12.5 + - - +
89G GLU* 3.6 26.3 + - - +
179G SER* 3.9 20.4 - - - +
180G SER* 3.8 18.3 + - - +
183G TYR* 3.5 48.0 - - + -
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Residues in contact with ILE 86 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82G ILE* 2.8 28.8 + - + +
83G CYS* 3.9 4.7 - - - +
85G LEU* 1.3 75.9 - - - +
87G GLY* 1.3 59.5 - - - +
88G GLU 3.3 0.2 + - - -
89G GLU* 3.4 0.6 + - - -
90G HIS* 2.9 43.4 + - + +
92G LYS* 3.5 33.2 - - + -
97G ALA* 4.1 22.9 - - + +
100G GLU* 4.0 17.3 - - - +
101G LEU* 5.3 0.7 - - + -
151G PRO* 4.3 8.1 - - + -
152G VAL* 3.6 24.2 - - + -
177G ASP* 6.2 0.4 - - - -
180G SER* 3.7 19.7 - - - +
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Residues in contact with GLY 87 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24G ASN* 5.1 1.0 - - - +
83G CYS 2.9 16.7 + - - -
84G ARG* 3.4 3.6 - - - -
86G ILE* 1.3 75.7 - - - +
88G GLU* 1.3 62.8 + - - +
91G GLY* 3.0 22.0 - - - -
92G LYS 3.4 23.3 + - - -
313G SER* 3.6 20.2 + - - -
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Residues in contact with GLU 88 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24G ASN* 3.5 29.1 - - + +
25G PRO* 3.4 16.8 - - - +
32G LYS* 4.5 19.6 + - - +
84G ARG* 2.6 47.4 + - + +
85G LEU* 3.9 16.1 - - - +
86G ILE 3.3 0.4 - - - -
87G GLY* 1.3 74.9 - - - +
89G GLU* 1.3 64.9 + - + +
179G SER* 5.5 0.2 + - - -
313G SER* 5.1 1.1 - - - -
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Residues in contact with GLU 89 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4G ILE* 4.1 0.2 - - - +
22G VAL* 3.7 21.3 - - + +
23G PHE 3.8 14.9 - - - +
25G PRO* 3.2 18.1 - - - +
32G LYS* 3.7 6.4 - - + +
85G LEU 3.6 10.1 + - - +
86G ILE 3.4 1.8 + - - -
88G GLU* 1.3 88.5 - - + +
90G HIS* 1.3 63.0 + - - +
91G GLY 3.4 0.2 - - - -
176G ARG 4.0 5.6 - - - +
177G ASP* 3.1 27.1 - - + +
178G PRO* 3.8 8.5 - - - +
179G SER* 2.5 54.0 + - - -
180G SER* 4.1 2.6 + - - -
324G ILE* 3.7 10.9 - - - +
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Residues in contact with HIS 90 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G PRO* 3.5 10.1 - - - +
86G ILE* 2.9 22.5 + - + +
89G GLU* 1.3 78.0 - - - +
91G GLY* 1.3 57.8 + - - +
92G LYS* 3.3 38.6 + - + +
148G PHE* 3.4 31.8 - + - -
149G ASN* 3.4 26.2 + - - +
151G PRO* 4.7 0.9 - - + -
177G ASP* 3.5 12.9 - - + +
275G SER* 4.5 9.8 - - - -
276G SER* 5.3 0.9 - - - -
278G GLU* 3.5 26.4 + - - +
322G PRO 3.8 12.8 - - - +
324G ILE* 3.9 15.5 - - + +
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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