Contacts of the helix formed by residues 113 - 123 (chain G) in PDB entry 4DVQ
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 LEU 113 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111G MET 3.2 4.3 + - - +
112G ILE* 1.3 71.2 - - - +
114G GLU* 1.3 64.2 + - - +
115G PRO* 3.9 13.7 - - + -
116G TRP* 3.1 36.0 + - + +
117G VAL* 3.1 21.5 + - - +
130G PHE* 4.6 7.6 - - + -
131G LEU* 4.4 13.9 - - + +
234G THR* 3.9 3.4 - - + -
238G MET* 3.6 33.9 - - + +
487G PHE* 3.4 34.8 - - + -
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Residues in contact with GLU 114 (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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112G ILE* 3.2 17.2 + - + +
113G LEU* 1.3 71.2 - - - +
115G PRO* 1.3 66.1 - - + +
117G VAL* 3.9 6.9 - - + +
118G ALA* 2.7 35.0 + - - +
121G GLN* 5.7 2.6 + - - -
237G LEU 5.9 1.1 - - - +
240G MET 5.1 1.1 - - - +
241G PRO* 4.0 6.8 - - - +
242G ARG* 3.1 48.0 + - + +
253G TRP* 4.8 2.7 - - + -
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Residues in contact with PRO 115 (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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113G LEU* 3.3 21.3 - - + -
114G GLU* 1.3 95.9 - - + +
116G TRP* 1.3 62.7 + - + +
118G ALA* 3.6 2.1 - - - +
119G TYR* 3.3 18.5 + - - +
234G THR* 4.5 8.1 - - + +
237G LEU* 3.8 39.5 - - + +
238G MET* 5.1 1.1 - - - -
253G TRP* 3.9 16.6 - - + -
256G HIS* 3.5 35.2 + - + +
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Residues in contact with TRP 116 (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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113G LEU* 3.1 29.2 + - + +
115G PRO* 1.3 78.0 - - + +
117G VAL* 1.3 65.3 + - - +
119G TYR* 3.6 5.5 + - - +
120G ARG* 2.7 33.0 + - - +
130G PHE* 3.4 35.9 - + - -
131G LEU* 3.7 18.6 - - + -
230G MET* 3.6 21.1 - - + -
231G PHE* 4.3 0.9 - + - -
234G THR* 2.9 25.0 + - - -
256G HIS* 4.0 4.3 - + - -
260G TRP* 3.6 33.4 - + - +
310G GLU* 5.9 0.4 - - + -
487G PHE* 3.8 29.2 - + - -
602G 1CA 3.5 39.5 - - + -
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Residues in contact with VAL 117 (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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112G ILE* 4.1 31.2 - - + -
113G LEU 3.1 15.9 + - - +
114G GLU* 3.9 5.8 - - + +
116G TRP* 1.3 77.5 - - - +
118G ALA* 1.3 62.8 + - - +
120G ARG* 3.0 16.8 + - - +
121G GLN* 3.3 31.8 + - - +
127G CYS* 4.4 12.8 - - - -
131G LEU* 4.0 30.3 - - + +
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Residues in contact with ALA 118 (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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114G GLU* 2.7 23.0 + - - +
115G PRO 3.6 4.9 - - - +
117G VAL* 1.3 72.7 - - - +
119G TYR* 1.3 62.2 + - - +
121G GLN* 3.4 18.1 - - - +
122G HIS* 3.1 24.6 + - - +
242G ARG* 4.1 22.9 + - - +
253G TRP* 3.8 22.0 - - + -
257G PHE* 3.8 4.9 - - + -
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Residues in contact with TYR 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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115G PRO 3.3 9.4 + - - +
116G TRP 3.7 9.0 - - - +
117G VAL 3.3 0.2 - - - -
118G ALA* 1.3 79.5 - - - +
120G ARG* 1.3 70.3 + - + +
122G HIS* 3.2 5.2 + - - +
123G ARG* 3.1 41.6 + - + +
125G HIS* 4.0 10.6 + + - -
257G PHE* 3.5 38.9 - + + -
260G TRP* 3.6 35.9 - - + -
261G ASP* 2.7 30.1 + - - -
264G PHE* 3.5 58.0 - + - +
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Residues in contact with ARG 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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116G TRP* 2.7 41.6 + - - +
117G VAL 3.0 8.0 + - - +
119G TYR* 1.3 94.6 - - + +
121G GLN* 1.3 57.9 + - - +
123G ARG 3.5 0.5 + - - -
124G GLY 3.1 5.9 + - - -
125G HIS* 2.7 52.8 + - + +
126G LYS 4.1 17.2 + - - +
127G CYS* 4.1 13.9 - - - +
128G GLY 5.3 2.2 - - - +
131G LEU* 3.4 30.9 - - - +
260G TRP* 3.3 41.0 - - - -
264G PHE* 3.8 18.6 - - + -
306G ALA 5.9 0.4 + - - -
309G MET* 5.3 3.4 - - - +
310G GLU* 5.2 12.9 + - - +
602G 1CA 5.2 1.0 + - - -
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Residues in contact with GLN 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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114G GLU* 5.7 3.2 + - - -
117G VAL* 3.3 32.5 + - - +
118G ALA* 3.4 23.7 - - - +
120G ARG* 1.3 75.6 - - - +
122G HIS* 1.3 60.2 + - - +
123G ARG 3.3 1.4 + - - -
124G GLY* 3.3 11.4 + - - +
125G HIS 4.9 1.3 - - - -
242G ARG* 5.8 4.6 - - - +
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Residues in contact with HIS 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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118G ALA 3.1 19.0 + - - +
119G TYR 3.2 4.2 + - - +
121G GLN* 1.3 76.7 - - + +
123G ARG* 1.3 83.5 + - + +
242G ARG* 5.8 3.9 + - - +
257G PHE* 3.5 32.9 - + + -
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Residues in contact with ARG 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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119G TYR* 3.1 36.2 + - + +
120G ARG 3.5 0.4 + - - +
121G GLN 3.2 0.2 - - - -
122G HIS* 1.3 102.3 + - + +
124G GLY* 1.3 65.2 + - - +
125G HIS* 3.3 33.9 + - + +
257G PHE* 4.9 7.9 - - - +
261G ASP* 3.1 36.4 + - - -
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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