Contacts of the helix formed by residues 79 - 90 (chain G) in PDB entry 5Z3U
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 ILE 79 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75G LYS* 5.5 6.3 - - + -
77G ARG* 4.4 15.3 - - + +
78G ILE* 1.3 82.5 - - - +
80G PRO* 1.3 66.0 - - + +
81G ARG* 4.3 12.1 - - + +
82G HIS* 2.6 66.1 + - + +
83G LEU* 3.4 3.0 + - - -
52H SER* 3.8 16.4 - - - +
55H ALA* 4.4 2.5 - - - -
133J A 5.7 4.7 - - - +
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Residues in contact with PRO 80 (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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79G ILE* 1.3 88.7 - - + +
81G ARG* 1.3 63.8 + - - +
83G LEU* 2.9 10.3 + - + +
84G GLN* 2.9 22.3 + - - +
102G ILE* 4.8 2.5 - - - +
103G ALA 3.8 9.9 - - - +
104G GLN* 3.6 31.2 - - + +
52H SER* 4.4 7.0 - - - +
54H LYS* 3.8 31.4 - - + -
55H ALA* 4.6 3.5 - - + +
58H ILE* 4.1 17.5 - - + -
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Residues in contact with ARG 81 (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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55A GLN 3.9 8.6 + - - -
56A LYS* 4.3 14.9 + - - +
57A SER 5.6 0.2 + - - -
58A THR* 4.1 22.4 - - + +
79G ILE* 2.9 13.2 + - + +
80G PRO* 1.3 79.3 - - - +
82G HIS* 1.3 70.0 + - + +
84G GLN* 3.3 6.0 + - - +
85G LEU* 3.0 61.9 + - + +
104G GLN 4.2 2.6 + - - -
105G GLY 3.5 14.5 + - - -
106G GLY* 3.3 8.9 - - - -
107G VAL 2.9 49.1 + - - +
109G PRO* 3.6 13.9 - - - +
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Residues in contact with HIS 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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66G ALA* 4.2 13.3 - - - +
69G ALA* 4.5 5.3 - - + +
70G ALA* 3.2 40.4 - - + +
73G ASN* 4.4 21.1 + - - +
75G LYS* 4.1 14.1 - - + +
77G ARG 3.6 7.8 + - - -
78G ILE* 3.8 8.2 - - + -
79G ILE* 2.6 57.4 + - + +
81G ARG* 1.3 81.3 - - + +
83G LEU* 1.3 58.8 + - - +
85G LEU* 3.9 7.4 - - + +
86G ALA* 2.9 31.7 + - - +
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Residues in contact with LEU 83 (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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62G ILE* 3.8 25.6 - - + -
63G LEU* 5.1 2.9 - - + -
66G ALA* 3.7 22.7 - - + -
78G ILE* 4.3 11.0 - - + -
79G ILE 3.4 1.9 + - - +
80G PRO* 2.9 10.1 + - + +
82G HIS* 1.3 75.4 - - - +
84G GLN* 1.3 65.8 + - - +
86G ALA* 4.5 0.9 - - - -
87G VAL* 2.9 31.8 + - + +
102G ILE* 4.6 9.6 - - + -
55H ALA* 4.3 22.9 - - + +
58H ILE* 3.9 37.5 - - + -
59H MET* 4.5 11.9 - - + -
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Residues in contact with GLN 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 PRO 2.9 10.0 + - - +
81G ARG* 3.3 19.1 - - - +
83G LEU* 1.3 76.3 - - - +
85G LEU* 1.3 60.9 + - + +
87G VAL* 3.8 0.7 - - - -
88G ARG* 2.9 86.3 + - + +
102G ILE* 4.1 22.5 + - + +
105G GLY* 3.3 35.2 - - - +
106G GLY 3.2 22.4 + - - +
107G VAL* 4.9 4.4 - - - +
108G LEU 5.4 0.2 - - - +
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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
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69G ALA* 5.0 9.6 - - + -
73G ASN* 5.0 14.4 - - - +
81G ARG* 3.0 64.2 + - + +
82G HIS* 4.1 7.2 - - + +
84G GLN* 1.3 75.3 - - + +
86G ALA* 1.3 67.6 + - - +
89G ASN* 3.0 39.3 + - - +
108G LEU* 3.6 29.8 - - + +
109G PRO* 4.5 3.6 - - + -
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Residues in contact with ALA 86 (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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62G ILE* 4.5 4.0 - - + +
65G LEU* 3.7 20.8 - - + +
66G ALA* 3.4 33.4 - - + +
69G ALA* 5.0 3.8 - - + +
82G HIS 2.9 18.6 + - - +
83G LEU* 3.9 3.8 - - + +
85G LEU* 1.3 77.7 - - - +
87G VAL* 1.3 63.6 + - + +
89G ASN* 4.9 1.3 - - - +
90G ASP* 3.7 21.0 + - - +
93G LEU* 4.7 1.5 - - - +
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Residues in contact with VAL 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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62G ILE* 4.7 23.8 - - + -
83G LEU* 2.9 23.2 + - + +
84G GLN 3.9 2.5 - - - +
86G ALA* 1.3 79.5 - - - +
88G ARG* 1.3 83.9 + - - +
90G ASP* 3.0 22.3 - - - +
93G LEU* 4.3 11.8 - - + +
94G ASN 3.6 10.1 + - - +
97G LEU* 3.6 36.6 - - + -
102G ILE* 4.7 11.2 - - + -
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Residues in contact with ARG 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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84G GLN* 2.9 48.7 + - - +
87G VAL* 1.3 105.4 - - - +
89G ASN* 1.3 66.0 + - - +
90G ASP 3.9 3.3 - - - +
91G GLU* 5.3 0.2 - - - -
94G ASN* 4.1 30.8 + - - +
97G LEU* 4.5 13.7 + - - +
98G GLY* 5.3 4.8 + - - -
100G VAL* 3.1 26.9 + - - +
102G ILE* 5.0 11.4 - - - +
108G LEU* 3.5 37.3 - - + +
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Residues in contact with ASN 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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85G LEU* 3.0 29.4 + - - +
86G ALA* 4.9 1.8 - - - +
88G ARG* 1.3 76.9 - - - +
90G ASP* 1.3 66.2 + - - +
91G GLU* 3.1 6.2 + - - +
108G LEU* 3.2 26.7 - - - +
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Residues in contact with ASP 90 (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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65G LEU* 3.8 21.6 - - + +
86G ALA 3.7 18.4 + - - +
87G VAL 3.0 18.6 - - - +
89G ASN* 1.3 77.1 - - - +
91G GLU* 1.3 63.7 + - - +
92G GLU* 3.3 23.1 + - - +
93G LEU* 2.6 41.6 + - + +
94G ASN* 3.2 10.6 + - - +
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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