Contacts of the helix formed by residues 88 - 97 (chain G) in PDB entry 4U7B
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 88 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87G GLN* 1.3 78.1 - - - +
89G GLN* 1.3 62.5 - - - +
90G LYS* 3.9 8.5 + - - +
91G GLN* 3.1 36.3 + - - +
92G LEU* 3.2 23.9 + - - +
7H G 3.5 50.2 + - - +
8H T 3.6 11.9 - - - +
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Residues in contact with GLN 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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88G THR* 1.3 68.7 - - - +
90G LYS* 1.3 60.1 + - - +
92G LEU* 3.0 5.5 + - + +
93G ALA* 2.8 30.4 + - - +
100G GLN* 2.9 37.9 - - + +
103G VAL* 4.1 10.6 - - + +
104G SER* 3.6 19.0 - - - +
107G LEU* 4.0 25.9 - - + +
8H T 2.8 46.0 + - - +
9H A 2.8 27.0 + - - -
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Residues in contact with LYS 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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88G THR* 3.4 7.7 + - - +
89G GLN* 1.3 79.0 - - - +
91G GLN* 1.3 58.4 + - + +
93G ALA* 3.5 3.4 + - - +
94G GLU* 2.9 48.2 + - + +
100G GLN* 3.9 22.7 - - + +
7H G 4.5 18.2 - - + +
8H T 4.3 2.8 + - + +
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Residues in contact with GLN 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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84G ASP* 5.1 2.3 - - - +
86G ALA 5.2 1.0 + - - -
87G GLN* 3.6 28.8 - - + +
88G THR* 3.1 45.4 + - - +
90G LYS* 1.3 79.9 - - + +
92G LEU* 1.3 60.7 + - - +
94G GLU* 3.4 20.0 + - - +
95G GLN* 3.1 19.5 + - - +
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Residues in contact with LEU 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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77G LEU* 4.7 9.2 - - + -
80G LEU* 3.9 25.1 - - + +
81G LEU* 4.0 24.9 - - + -
87G GLN* 3.6 40.8 - - + +
88G THR 3.3 18.6 - - - +
89G GLN* 3.0 6.7 + - + +
91G GLN* 1.3 75.4 - - - +
93G ALA* 1.3 65.6 + - - +
95G GLN* 3.3 8.8 + - - +
96G LEU* 3.1 27.1 + - + +
103G VAL* 4.2 22.7 - - + -
107G LEU* 4.7 9.0 - - + -
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Residues in contact with ALA 93 (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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89G GLN 2.8 11.8 + - - +
90G LYS* 3.8 4.9 - - - +
92G LEU* 1.3 78.6 - - - +
94G GLU* 1.3 56.1 + - - +
96G LEU 3.1 0.7 + - - +
97G GLU* 2.8 27.2 + - - -
98G VAL* 3.1 31.8 + - - +
99G SER 3.4 24.0 - - - +
100G GLN* 3.5 4.9 - - - +
103G VAL* 3.4 16.4 - - + +
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Residues in contact with GLU 94 (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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90G LYS* 2.9 36.1 + - + +
91G GLN* 3.5 11.1 - - - +
92G LEU 3.2 0.4 - - - -
93G ALA* 1.3 75.4 - - - +
95G GLN* 1.3 60.8 + - + +
97G GLU* 4.0 10.2 + - - +
98G VAL 5.0 0.9 - - - -
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Residues in contact with GLN 95 (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 LEU* 3.7 27.1 - - + +
87G GLN* 2.9 31.6 + - - +
91G GLN* 3.1 19.5 + - - +
92G LEU* 3.3 9.8 + - - +
93G ALA 3.2 0.2 - - - -
94G GLU* 1.3 76.4 - - + +
96G LEU* 1.3 63.7 + - - +
97G GLU* 3.2 15.2 + - - +
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Residues in contact with LEU 96 (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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71G ARG* 5.5 4.0 - - - +
72G TYR* 3.7 51.7 - - + +
76G GLU* 4.8 18.3 - - + +
77G LEU* 3.9 22.4 - - + +
80G LEU* 3.4 32.3 - - + -
92G LEU* 3.1 18.9 + - + +
93G ALA 3.1 3.5 + - - +
95G GLN* 1.3 77.8 - - - +
97G GLU* 1.3 70.2 + - - +
98G VAL* 3.1 14.4 + - + +
103G VAL* 4.7 7.2 - - + -
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Residues in contact with GLU 97 (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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93G ALA 2.8 6.9 + - - -
94G GLU* 4.0 8.3 + - - +
95G GLN 3.2 12.6 - - - +
96G LEU* 1.3 82.1 - - - +
98G VAL* 1.3 58.0 + - - +
45I T 4.5 3.3 + - - -
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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