Contacts of the helix formed by residues 99 - 110 (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 SER 99 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93G ALA* 3.4 3.6 - - - +
98G VAL* 1.3 87.8 - - - +
100G GLN* 1.3 64.2 + - - +
101G GLN* 3.2 23.4 - - - +
102G ALA 3.1 9.2 + - - -
103G VAL 3.5 1.6 + - - -
45I T 3.0 27.9 + - - +
46I T 3.3 26.9 - - - +
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Residues in contact with GLN 100 (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* 2.9 38.1 - - + +
90G LYS* 3.9 22.6 - - + +
93G ALA* 3.5 13.7 - - - +
99G SER* 1.3 71.1 - - - +
101G GLN* 1.3 90.9 + - - +
103G VAL* 2.9 16.7 + - - +
104G SER* 3.2 9.4 + - - -
8H T 3.5 27.4 - - + +
9H A 3.3 24.0 - - - +
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Residues in contact with GLN 101 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99G SER* 3.2 12.6 - - - +
100G GLN* 1.3 94.9 + - - +
102G ALA* 1.3 61.4 + - - +
104G SER* 3.3 17.9 + - - -
105G ASN* 3.5 14.2 + - - +
9H A 2.5 53.5 + - - -
10H C 2.7 23.9 - - - +
11H A 4.0 2.0 - - - +
45I T 4.4 4.5 - - + +
46I T 2.8 33.9 - - + +
47I G 2.8 13.5 - - - +
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Residues in contact with ALA 102 (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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72G TYR* 3.4 11.7 + - - +
98G VAL* 3.9 16.4 - - + -
99G SER* 3.1 8.0 + - - +
101G GLN* 1.3 78.2 - - - +
103G VAL* 1.3 59.1 + - - +
105G ASN* 3.3 15.0 + - - +
106G ARG* 3.1 23.7 + - - +
44I C 4.1 14.5 + - - +
45I T 3.5 26.9 - - + +
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Residues in contact with VAL 103 (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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72G TYR* 4.1 7.9 - - - +
77G LEU* 4.3 10.1 - - + -
89G GLN* 4.2 12.8 - - + +
92G LEU* 4.2 20.6 - - + -
93G ALA* 3.4 40.4 - - + +
96G LEU* 4.7 4.9 - - + -
98G VAL* 3.9 9.9 - - + -
99G SER 3.6 2.9 - - - +
100G GLN 2.9 7.0 + - - +
102G ALA* 1.3 73.4 - - - +
104G SER* 1.3 64.2 + - - +
106G ARG* 4.1 1.7 - - - -
107G LEU* 3.1 43.9 + - + +
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Residues in contact with SER 104 (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* 3.6 27.7 - - - +
100G GLN* 3.2 8.0 + - - -
101G GLN* 3.4 12.8 - - - -
103G VAL* 1.3 77.5 - - - +
105G ASN* 1.3 65.7 + - - +
107G LEU* 3.8 3.1 - - - +
108G ARG* 3.3 20.0 + - - +
9H A 2.8 50.7 + - - +
10H C 5.9 0.4 - - - -
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Residues in contact with ASN 105 (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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101G GLN* 3.5 17.7 + - - +
102G ALA* 3.3 13.7 + - - +
104G SER* 1.3 76.0 + - - +
106G ARG* 1.3 56.9 + - + +
108G ARG* 2.8 39.7 + - - +
109G GLU* 2.8 25.0 + - + +
10H C 5.5 7.3 - - - -
44I C 5.0 8.5 - - - -
45I T 4.7 12.5 + - - +
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Residues in contact with ARG 106 (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 LYS* 3.8 21.3 - - - +
72G TYR* 2.1 80.4 + - + +
73G GLU 3.9 2.0 + - - -
74G ASP* 2.9 30.6 + - - +
77G LEU* 4.3 7.9 - - + -
102G ALA 3.1 6.5 + - - +
103G VAL 4.1 2.7 - - - +
104G SER 3.5 0.2 - - - -
105G ASN* 1.3 79.2 - - + +
107G LEU* 1.3 57.8 + - - +
109G GLU* 3.1 17.5 + - + +
110G MET* 2.9 38.0 + - - +
43I A 4.6 3.4 - - - -
44I C 2.7 35.9 + - - +
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Residues in contact with LEU 107 (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* 4.2 16.2 - - + -
81G LEU* 4.1 20.0 - - + -
89G GLN* 4.0 23.8 - - + +
92G LEU* 4.7 7.2 - - + -
103G VAL* 3.1 41.9 + - + +
104G SER 3.8 3.8 - - - +
106G ARG* 1.3 75.8 - - - +
108G ARG* 1.3 52.9 + - - +
110G MET* 2.7 30.1 - - - +
112G LYS* 3.4 44.6 + - + +
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Residues in contact with ARG 108 (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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104G SER* 3.3 12.6 + - - +
105G ASN* 2.8 22.5 + - - +
107G LEU* 1.3 77.1 - - - +
109G GLU* 1.3 65.5 + - - +
110G MET 2.8 11.1 - - - +
112G LYS 4.8 4.3 - - - -
9H A 3.8 12.1 + - - +
10H C 2.6 43.9 + - - -
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Residues in contact with GLU 109 (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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74G ASP* 5.4 3.6 - - - +
105G ASN* 2.8 27.3 + - + +
106G ARG* 3.1 26.0 + - + +
108G ARG* 1.3 84.0 - - - +
110G MET* 1.3 62.4 + - + +
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Residues in contact with MET 110 (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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74G ASP* 3.3 55.0 - - + +
77G LEU* 4.5 18.2 - - + -
78G GLN* 3.6 29.8 - - + +
106G ARG* 2.9 25.9 + - - +
107G LEU* 2.7 20.8 - - - +
108G ARG* 2.8 13.3 - - - +
109G GLU* 1.3 76.2 - - + +
111G GLY* 1.3 60.5 + - - +
112G LYS* 3.0 24.5 + - + +
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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