Contacts of the helix formed by residues 80 - 90 (chain G) in PDB entry 6R92
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 80 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74G ASN* 6.2 0.4 - - - +
76G LYS* 5.7 10.8 - - + +
78G ARG* 3.9 17.9 - - - +
79G ILE* 1.3 85.3 - - - +
81G PRO* 1.3 78.8 - - + +
82G ARG* 3.5 24.7 - - + +
83G HIS* 2.9 43.9 + - + +
84G LEU* 3.4 3.6 + - - +
56H SER* 5.5 5.2 - - - -
59H ALA* 4.6 3.4 - - - -
132I A 6.5 0.4 - - - -
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Residues in contact with PRO 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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80G ILE* 1.3 89.1 - - + +
82G ARG* 1.3 61.4 + - - +
84G LEU* 3.0 18.2 + - + +
85G GLN* 2.9 22.7 + - - +
103G ILE* 4.3 4.7 - - + +
104G ALA 3.8 21.3 - - - +
105G GLN* 4.0 17.3 - - + +
106G GLY* 5.0 0.2 - - - -
56H SER* 5.4 5.2 - - - -
58H LYS* 4.8 9.4 - - + -
59H ALA* 4.3 15.4 - - + +
62H ILE* 3.9 20.6 - - + -
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Residues in contact with ARG 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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56A GLN 2.6 26.3 + - - -
57A LYS* 3.5 24.9 + - - +
58A SER 4.7 0.6 + - - -
59A THR* 3.9 17.5 - - + +
74G ASN* 5.3 4.5 - - - +
80G ILE* 3.1 23.1 + - + -
81G PRO* 1.3 79.6 - - - +
83G HIS* 1.3 61.4 + - + +
85G GLN* 3.2 3.2 + - - +
86G LEU* 2.9 65.9 + - + +
105G GLN 4.3 3.0 + - - -
106G GLY 3.2 27.6 + - - -
107G GLY* 4.1 2.4 - - - -
108G VAL 3.1 27.4 + - - +
110G PRO* 4.3 8.9 - - - +
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Residues in contact with HIS 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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67G ALA* 4.0 17.2 - - + +
70G ALA* 4.2 13.3 - - + +
71G ALA* 3.6 31.7 - - - +
74G ASN* 3.9 26.2 + - - +
76G LYS* 4.1 11.9 - - + +
78G ARG 3.5 19.3 - - - -
79G ILE* 3.5 13.0 - - + -
80G ILE* 2.9 42.9 + - + +
82G ARG* 1.3 83.6 - - + +
84G LEU* 1.3 55.9 + - - +
86G LEU* 3.8 5.4 - - + +
87G ALA* 2.9 30.9 + - - +
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Residues in contact with LEU 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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63G ILE* 3.5 32.3 - - + -
64G LEU* 5.4 2.9 - - + -
67G ALA* 4.1 14.1 - - + -
79G ILE* 4.6 7.9 - - + -
80G ILE 3.4 4.9 + - - +
81G PRO* 3.0 20.2 + - + +
83G HIS* 1.3 76.2 - - - +
85G GLN* 1.3 61.3 + - - +
87G ALA* 3.4 3.7 + - + +
88G ILE* 2.8 46.3 + - + +
103G ILE* 5.1 4.5 - - + -
55H ILE* 6.1 0.2 - - + -
59H ALA* 4.5 17.0 - - + +
62H ILE* 4.1 26.5 - - + -
63H MET* 4.0 17.0 - - + -
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Residues in contact with GLN 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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81G PRO 2.9 11.6 + - - +
82G ARG* 3.7 9.0 - - - +
84G LEU* 1.3 77.2 - - - +
86G LEU* 1.3 59.3 + - + +
88G ILE* 3.2 5.2 + - - +
89G ARG* 2.9 84.5 + - + +
103G ILE* 3.5 25.3 + - + +
106G GLY* 3.3 30.3 - - - +
107G GLY 2.6 26.4 + - - +
108G VAL* 4.5 5.9 - - - +
109G LEU* 5.7 0.4 - - + -
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Residues in contact with LEU 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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70G ALA* 4.9 10.8 - - + -
74G ASN* 4.9 11.4 - - - +
82G ARG* 2.9 63.2 + - + +
83G HIS* 3.8 12.8 - - + +
85G GLN* 1.3 76.2 - - + +
87G ALA* 1.3 61.3 + - - +
89G ARG* 4.3 0.2 - - - +
90G ASN* 2.4 42.5 + - - +
108G VAL 5.6 0.2 - - - -
109G LEU* 3.6 23.6 - - + -
110G PRO* 4.5 8.5 - - + -
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Residues in contact with ALA 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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63G ILE* 4.9 5.4 - - + +
66G LEU* 3.9 34.6 - - + +
67G ALA* 4.2 9.2 - - + +
70G ALA* 5.2 3.0 - - + +
83G HIS 2.9 19.5 + - - +
84G LEU* 3.6 7.6 - - + +
86G LEU* 1.3 77.2 - - - +
88G ILE* 1.3 64.0 + - + +
90G ASN* 3.3 5.8 + - - +
91G ASP* 3.1 24.8 + - - +
94G LEU* 5.5 0.9 - - - -
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Residues in contact with ILE 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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63G ILE* 4.0 25.8 - - + -
84G LEU* 2.8 33.4 + - + +
85G GLN* 3.8 4.3 - - - +
87G ALA* 1.3 76.2 - - + +
89G ARG* 1.3 77.5 + - - +
91G ASP* 3.0 22.9 + - - +
94G LEU* 4.1 20.4 - - + +
95G ASN* 3.5 7.9 + - - +
98G LEU* 4.0 37.2 - - + -
103G ILE* 4.0 22.9 - - + -
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Residues in contact with ARG 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 GLN* 2.9 59.4 + - + +
88G ILE* 1.3 84.9 - - - +
90G ASN* 1.3 60.8 + - - +
91G ASP 3.3 1.3 + - - +
95G ASN* 3.3 34.4 + - - +
98G LEU* 3.1 24.2 + - - -
99G GLY* 4.5 6.1 + - - -
101G VAL 3.1 23.0 + - - -
102G THR* 4.9 0.6 - - - +
103G ILE* 4.6 7.1 - - - +
108G VAL* 6.0 0.2 - - - -
109G LEU* 3.4 40.4 - - + +
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Residues in contact with ASN 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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86G LEU* 2.4 41.4 + - - +
87G ALA* 3.6 5.6 - - - +
88G ILE 3.1 0.6 - - - -
89G ARG* 1.3 79.4 - - - +
91G ASP* 1.3 56.1 + - - +
92G GLU 4.0 1.4 + - - -
109G LEU* 4.0 20.4 - - - +
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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