Contacts of the helix formed by residues 81 - 92 (chain G) in PDB entry 3CII
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 THR 81 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80G LYS* 1.3 79.8 - - - +
82G TRP* 1.3 63.2 + - - +
83G ASN* 3.6 18.8 - - + +
84G GLU* 2.8 36.0 + - + +
85G SER* 2.9 28.1 + - - -
116G TRP* 3.6 1.1 + - - -
166G CYS 3.3 17.9 - - - +
167G GLU* 4.3 20.4 + - - +
168G ASP 3.6 8.0 + - - +
169G LYS* 5.0 9.1 - - - +
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Residues in contact with TRP 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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81G THR* 1.3 71.5 - - - +
83G ASN* 1.3 76.3 + - + +
85G SER* 2.6 21.1 + - - -
86G ARG* 3.2 44.6 + - - +
96G LEU* 3.7 12.3 - - + +
116G TRP* 3.3 56.5 - + + +
117G ILE 3.1 20.1 + - - -
118G GLY* 4.5 2.7 - - - -
119G LEU 3.8 32.1 + - - -
120G SER* 4.2 16.8 - - - -
131G GLU* 4.8 4.5 - - - -
152G CYS* 3.7 28.8 - - + +
153G ILE 4.4 1.2 + - - -
166G CYS* 3.7 10.4 + - + +
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Residues in contact with ASN 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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81G THR* 3.6 13.1 - - + +
82G TRP* 1.3 93.5 - - + +
84G GLU* 1.3 63.5 + - + +
86G ARG* 3.2 30.5 + - - +
87G HIS* 3.5 28.1 + - - -
166G CYS* 4.8 1.0 + - + +
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Residues in contact with GLU 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 LYS* 4.4 17.8 + - + +
81G THR* 2.8 40.6 + - + +
82G TRP 3.3 0.4 - - - -
83G ASN* 1.3 79.1 - - + +
85G SER* 1.3 58.0 + - - +
87G HIS* 3.3 12.0 + - - +
88G LEU* 2.9 41.7 + - + +
169G LYS* 5.7 2.8 + - - -
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Residues in contact with SER 85 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80G LYS* 4.9 0.9 - - - -
81G THR 2.9 14.9 + - - -
82G TRP* 2.6 24.6 + - - -
84G GLU* 1.3 73.4 - - - +
86G ARG* 1.3 65.8 + - - +
88G LEU* 3.1 13.0 + - - +
89G CYS* 2.9 28.4 + - - -
96G LEU* 3.8 13.6 - - - +
116G TRP* 4.0 4.1 - - - -
172G TYR* 3.8 37.4 - - - -
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Residues in contact with ARG 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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82G TRP* 3.6 34.7 - - + +
83G ASN* 3.2 30.4 + - - +
85G SER* 1.3 80.4 + - - +
87G HIS* 1.3 82.1 + - - +
89G CYS* 2.9 15.1 + - - +
90G ALA* 3.0 12.9 + - + +
94G SER 4.9 0.2 - - - +
96G LEU* 4.4 17.8 + - + +
131G GLU* 3.6 36.5 + - - +
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Residues in contact with HIS 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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83G ASN* 3.5 35.4 + - - -
84G GLU* 3.3 10.0 + - - +
86G ARG* 1.3 96.3 + - - +
88G LEU* 1.3 58.7 + - + +
90G ALA* 3.0 11.1 + - + +
91G SER* 2.9 30.7 + - - -
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Residues in contact with LEU 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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78G GLU* 5.9 0.2 - - - +
80G LYS* 3.7 31.0 - - + +
84G GLU* 2.9 34.1 + - + +
85G SER* 3.1 8.7 + - - +
87G HIS* 1.3 75.4 - - + +
89G CYS* 1.3 65.0 + - - +
91G SER* 3.3 19.9 + - - +
92G GLN* 3.6 19.5 + - - +
172G TYR* 4.0 21.5 - - - +
174G CYS* 4.7 1.7 - - - -
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Residues in contact with CYS 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 SER 2.9 16.5 + - - -
86G ARG 2.9 7.6 + - - +
88G LEU* 1.3 73.5 - - - +
90G ALA* 1.3 67.8 + - - +
92G GLN* 3.0 12.5 + - - -
93G LYS 3.0 0.3 + - - -
94G SER* 2.9 34.9 + - - +
95G SER 3.9 9.6 - - - -
96G LEU* 3.8 19.5 - - - +
172G TYR* 4.1 3.6 - - - -
173G ILE 4.0 0.2 - - - -
174G CYS* 2.0 55.0 - - - -
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Residues in contact with ALA 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 ARG* 3.0 11.9 + - + +
87G HIS* 3.0 16.8 + - + +
89G CYS* 1.3 77.3 - - - +
91G SER* 1.3 56.8 + - - +
93G LYS* 2.9 23.2 + - - +
94G SER 3.3 9.8 + - - +
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Residues in contact with SER 91 (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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87G HIS 2.9 13.9 + - - -
88G LEU* 3.3 23.4 + - - +
89G CYS 3.2 0.2 - - - -
90G ALA* 1.3 75.3 - - - +
92G GLN* 1.3 61.4 + - - +
93G LYS* 3.3 5.7 + - - +
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Residues in contact with GLN 92 (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 GLN* 4.2 16.8 + - - +
65G TRP* 4.2 27.0 - - + +
74G PHE* 3.9 29.3 - - - -
88G LEU* 3.6 12.5 + - - +
89G CYS* 3.0 10.3 + - - +
91G SER* 1.3 81.3 + - - +
93G LYS* 1.3 70.1 + - - +
94G SER* 3.3 5.5 + - - +
172G TYR* 5.4 1.4 + - - -
174G CYS* 5.3 1.2 - - - -
176G GLN* 4.5 2.8 - - - +
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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