Contacts of the helix formed by residues 118 - 124 (chain G) in PDB entry 2NOQ
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 LYS 118 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A G 2.5 17.5 - - + +
11A U 0.6 190.8 + - + +
12A G 2.0 33.6 + - - +
13A A 1.0 172.2 - - - +
14A U 3.9 3.1 - - - +
115G VAL* 3.8 8.1 + - - +
116G LEU 3.1 1.8 + - - -
117G ILE* 1.3 64.7 - - - +
119G GLN* 1.3 49.3 - - + +
122G ARG* 3.8 0.2 - - - -
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Residues in contact with GLN 119 (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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10A G 4.9 19.8 + - + +
11A U 5.3 2.0 - - - +
13A A 1.1 52.0 + - - -
14A U 4.2 5.2 - - - +
87G VAL* 4.1 19.4 + - - +
90G LEU* 3.2 22.7 - - + +
91G LYS* 4.3 21.3 - - + +
115G VAL* 5.0 3.7 - - - +
116G LEU* 3.0 26.5 + - - +
118G LYS* 1.3 74.8 - - + +
120G VAL* 1.3 53.4 + - - +
123G LEU* 2.8 22.6 + - + +
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Residues in contact with VAL 120 (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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13A A 1.5 35.1 - - - +
68G PHE* 4.8 8.5 - - + -
90G LEU* 3.2 15.9 - - + +
112G ALA* 4.9 7.0 - - + -
116G LEU* 3.0 24.6 + - + +
117G ILE* 3.2 14.8 - - + -
119G GLN* 1.3 69.4 - - - +
121G PRO* 1.3 68.2 - - + -
124G LEU* 2.6 42.4 + - + -
128G LEU* 4.9 0.2 - - + -
134G PHE* 4.3 10.1 - - + -
135G PRO* 4.3 15.5 - - + -
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Residues in contact with PRO 121 (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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12A G 3.7 0.2 - - - +
13A A 0.5 347.6 - - + +
14A U 1.8 25.1 - - - +
61A G 3.3 16.4 - - - +
117G ILE 2.8 18.2 - - - +
120G VAL* 1.3 46.8 - - + -
122G ARG 1.3 44.6 + - - -
134G PHE* 3.0 31.9 - - + -
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Residues in contact with ARG 122 (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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9A U 5.6 0.6 + - - -
10A G 2.3 41.2 + - - +
11A U 3.3 8.9 + - - -
13A A 0.9 90.7 - - - +
14A U 0.9 308.6 + - - +
15A C 2.3 30.2 + - - -
64A A 3.6 17.0 + - - -
94G ASN* 4.7 1.9 + - - -
119G GLN 4.0 0.2 - - - +
121G PRO 1.3 32.1 - - - +
123G LEU* 1.3 69.5 + - + +
126G PRO* 4.0 3.6 - - - +
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Residues in contact with LEU 123 (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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10A G 5.5 1.8 - - - +
13A A 2.6 17.6 + - - +
14A U 4.6 0.9 - - - +
90G LEU* 2.9 31.0 - - + -
91G LYS* 4.0 23.6 - - + +
94G ASN* 2.7 69.5 + - + +
95G LYS* 4.8 6.7 - - - +
119G GLN* 2.8 22.0 - - + +
122G ARG* 1.3 81.9 - - + +
124G LEU* 1.4 56.7 + - + +
126G PRO* 4.0 4.2 - - - +
127G GLN* 5.8 2.1 - - - +
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Residues in contact with LEU 124 (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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13A A 2.0 11.8 + - - -
85G MET* 3.5 36.3 - - + -
90G LEU* 3.0 47.3 - - + +
93G LEU* 5.3 5.4 - - + -
94G ASN* 5.4 2.0 - - - +
100G ILE* 5.1 11.7 - - + -
103G LEU* 6.1 0.7 - - + -
110G PHE* 6.5 0.2 - - + -
120G VAL* 2.6 35.5 + - + +
123G LEU* 1.4 70.4 - - + +
125G GLY* 1.3 59.7 + - - +
126G PRO 3.2 0.7 - - - -
127G GLN* 2.9 17.0 + - - +
128G LEU* 3.0 37.9 + - + +
135G PRO* 5.7 0.4 - - + -
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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