Contacts of the helix formed by residues 114 - 124 (chain G) in PDB entry 5EIG
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 TYR 114 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91G LEU* 3.8 9.4 - - + -
113G VAL* 1.3 73.3 - - - +
115G GLY* 1.3 69.9 + - - +
116G GLY* 3.4 23.1 - - - -
117G THR* 2.8 44.1 + - - +
118G ASN 2.9 10.4 + - - -
157G GLU* 2.9 23.8 + - - +
161G ASN* 4.0 9.9 - - - +
212G 5OW 3.1 84.1 - + + +
355G THR 4.4 4.0 - - - -
356G HIS* 3.7 8.3 - + - -
501G CYS* 3.5 14.3 + - + +
62H ARG* 2.5 29.8 + - - -
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Residues in contact with GLY 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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114G TYR* 1.3 77.8 - - - +
116G GLY* 1.3 51.6 + - - +
118G ASN* 3.3 3.0 + - - +
119G ARG* 2.8 35.0 + - - +
355G THR 4.0 6.3 - - - -
356G HIS* 3.5 12.9 + - - -
358G SER* 3.3 22.4 + - - +
359G VAL* 3.8 20.0 - - - -
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Residues in contact with GLY 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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91G LEU* 3.9 11.0 - - - +
114G TYR* 3.2 24.2 - - - -
115G GLY* 1.3 72.8 - - - +
117G THR* 1.3 59.5 + - - +
119G ARG* 3.6 29.2 + - - +
120G TYR* 2.9 30.8 + - - +
355G THR 5.1 0.2 + - - -
358G SER* 4.1 0.6 + - - -
501G CYS 5.6 0.4 - - - -
242H SER 5.1 0.3 - - - +
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Residues in contact with THR 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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91G LEU* 4.5 9.0 - - - +
94G THR* 4.7 10.4 + - + -
113G VAL* 3.6 17.0 - - + -
114G TYR* 2.8 28.3 + - - +
116G GLY* 1.3 72.6 - - - +
118G ASN* 1.3 67.6 + - - +
120G TYR* 3.5 4.1 + - - +
121G PHE* 3.3 44.3 + - + -
155G TRP* 3.6 27.6 - - + +
157G GLU* 4.2 3.3 + - - -
187G ASP* 4.7 2.8 + - - -
212G 5OW 4.4 5.7 + - - -
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Residues in contact with ASN 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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111G ASP 4.6 8.5 + - - -
113G VAL* 3.4 19.6 + - + +
114G TYR 2.9 6.2 + - - +
115G GLY 3.4 9.9 - - - +
117G THR* 1.3 78.0 - - - +
119G ARG* 1.3 56.1 + - - +
122G ARG* 3.0 45.6 + - - +
134G PHE* 3.6 32.8 - - - -
358G SER 4.9 1.7 - - - +
359G VAL* 3.9 35.3 - - + +
363G ASP* 5.2 5.5 + - - +
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Residues in contact with ARG 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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91G LEU* 3.9 16.0 - - - +
115G GLY 2.8 18.7 + - - +
116G GLY* 3.6 20.5 + - - +
118G ASN* 1.3 75.6 - - - +
120G TYR* 1.3 56.9 + - - +
122G ARG* 4.8 3.1 - - - +
123G GLN* 2.9 51.9 + - - +
124G VAL* 3.9 1.4 + - + +
358G SER* 3.6 30.2 + - - +
501G CYS* 2.3 44.2 + - - -
238H PHE* 3.9 28.9 - - + -
241H ASN* 3.5 17.6 + - - +
242H SER* 3.6 11.6 + - - +
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Residues in contact with TYR 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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91G LEU* 5.4 3.6 - - + -
94G THR* 4.2 12.1 - - + -
95G VAL* 3.7 37.3 + - + +
98G THR* 3.4 40.5 - - - +
99G HIS* 4.5 5.5 + - - -
116G GLY 2.9 16.7 + - - +
117G THR* 4.0 4.3 - - - +
118G ASN 3.4 0.2 - - - -
119G ARG* 1.3 75.7 - - - +
121G PHE* 1.3 77.3 + + - +
124G VAL* 2.9 37.1 + - + +
125G ALA* 2.8 38.0 + - + +
99H HIS* 4.8 3.4 + - - -
242H SER* 4.4 13.9 - - - +
243H LEU* 3.8 21.1 - - + -
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Residues in contact with PHE 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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94G THR* 4.2 10.1 - - + -
98G THR* 3.6 22.4 - - - -
107G ILE* 3.8 34.3 - - + -
109G CYS* 3.7 30.5 - - + -
117G THR* 3.3 36.8 + - + +
118G ASN 4.0 2.5 - - - +
120G TYR* 1.3 90.7 - + - +
122G ARG* 1.3 62.4 + - - +
125G ALA* 3.9 4.0 - - + -
126G SER* 3.3 21.5 + - - -
132G ILE* 3.3 30.3 - - + +
134G PHE* 4.3 3.1 - + + -
153G LEU* 4.7 2.2 - - + -
155G TRP* 4.0 27.8 - + + -
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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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118G ASN* 3.0 34.3 + - - +
119G ARG* 4.4 1.4 - - - +
121G PHE* 1.3 78.8 - - - +
123G GLN* 1.3 93.8 + - - +
126G SER* 2.6 22.6 + - - -
132G ILE* 5.0 2.9 - - - -
134G PHE* 4.2 18.4 - - + -
358G SER 4.3 12.9 + - - -
359G VAL* 6.0 0.2 - - - +
360G LEU* 3.9 45.7 - - - +
363G ASP* 5.1 4.3 - - - -
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Residues in contact with GLN 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 ARG* 2.9 40.0 + - + +
122G ARG* 1.3 115.8 + - - +
124G VAL* 1.3 65.6 + - + +
126G SER* 3.9 3.4 - - - -
127G GLU* 3.4 20.1 - - - +
358G SER* 4.8 2.1 - - - +
238H PHE* 4.3 17.1 - - + -
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Residues in contact with VAL 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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119G ARG 4.4 2.0 - - - +
120G TYR* 2.9 39.1 + - + +
122G ARG 3.7 0.4 - - - -
123G GLN* 1.3 82.4 - - - +
125G ALA* 1.3 64.9 + - - +
126G SER 3.1 1.3 - - - -
127G GLU* 3.0 22.2 + - - +
128G PHE* 3.3 11.3 - - + -
99H HIS* 3.7 31.6 - - + +
238H PHE* 4.0 25.4 - - + -
239H LEU* 4.5 14.4 - - + -
242H SER* 4.6 6.3 - - - -
243H LEU* 4.2 3.8 - - + -
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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