Contacts of the helix formed by residues 109 - 117 (chain l) in PDB entry 5GJQ
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 VAL 109 (chain l).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73l HIS* 5.1 0.7 - - + -
74l ILE* 3.7 23.3 - - + -
107l MET 3.8 0.6 + - - -
108l THR* 1.3 71.6 - - - +
110l GLU* 1.3 62.6 + - - +
112l VAL* 3.4 2.0 + - + +
113l THR* 2.8 34.5 + - - +
143l PHE* 4.2 20.6 - - + +
145l GLY* 3.7 37.7 - - - +
146l VAL 3.9 4.0 - - - +
147l ASP* 3.1 16.6 + - + +
152l GLN* 3.9 13.0 - - + +
154l PHE* 3.8 19.7 - - + -
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Residues in contact with GLU 110 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108l THR* 3.1 9.4 + - - +
109l VAL* 1.3 80.8 - - - +
111l SER* 1.3 56.2 + - - +
113l THR* 3.5 2.9 + - - -
114l GLN* 2.9 38.6 + - - +
149l LYS* 5.6 9.6 + - + +
152l GLN* 4.1 7.6 + - - +
154l PHE* 3.7 35.0 - - + -
162l PHE* 4.1 9.3 - - + -
61m LYS* 3.5 18.9 + - - +
78t SER 4.6 2.8 - - - +
79t ASN 4.3 9.4 - - - +
80t ASN* 3.2 31.1 + - - +
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Residues in contact with SER 111 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107l MET* 3.7 26.0 - - - +
108l THR* 2.9 22.9 + - - +
110l GLU* 1.3 75.9 - - - +
112l VAL* 1.3 68.1 + - - +
114l GLN* 3.7 10.8 - - - -
115l ALA* 4.0 7.6 - - - -
78t SER* 3.4 16.9 + - - +
79t ASN* 2.8 24.7 - - - +
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Residues in contact with VAL 112 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70l ILE* 4.1 21.5 - - + -
74l ILE* 3.8 16.4 - - + -
92l ALA* 4.2 16.2 - - + -
95l GLU* 6.2 0.2 - - + -
96l THR* 3.5 17.5 - - + -
107l MET* 3.5 37.5 - - + -
108l THR 3.0 6.5 + - - +
109l VAL 3.7 6.1 - - - +
111l SER* 1.3 75.4 + - - +
113l THR* 1.3 65.4 + - - +
115l ALA* 3.1 5.3 + - - +
116l VAL* 3.0 22.5 + - - +
143l PHE* 4.2 18.4 - - + -
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Residues in contact with THR 113 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109l VAL 2.8 18.9 + - - -
110l GLU 3.8 4.3 - - - -
112l VAL* 1.3 79.3 - - - +
114l GLN* 1.3 56.8 + - - +
116l VAL* 3.4 2.8 + - - +
117l SER* 2.8 32.9 + - - +
143l PHE* 3.7 33.9 - - + +
154l PHE* 3.7 25.7 - - + +
156l MET* 4.5 6.5 - - - +
162l PHE* 3.4 35.2 - - + -
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Residues in contact with GLN 114 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110l GLU* 2.9 31.0 + - - +
111l SER* 4.1 6.0 - - - -
113l THR* 1.3 77.3 - - - +
115l ALA* 1.3 63.0 + - - +
117l SER* 3.6 14.8 - - - -
118l ASN* 4.1 17.7 - - - +
162l PHE* 3.9 26.2 - - + -
61m LYS* 4.6 8.1 + - - -
82m ARG* 3.7 27.1 - - - +
89m ARG* 6.1 1.0 + - - -
77t HIS 5.4 1.8 - - - +
78t SER* 3.8 23.8 - - - +
80t ASN* 4.8 3.3 - - - -
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Residues in contact with ALA 115 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91l LYS* 3.8 16.0 + - + +
92l ALA* 6.1 0.2 - - - -
95l GLU* 4.1 35.0 - - + +
107l MET* 4.7 2.5 - - + -
111l SER 4.0 4.7 - - - -
112l VAL* 3.1 17.8 + - + +
114l GLN* 1.3 74.4 + - - +
116l VAL* 1.3 65.8 + - + +
118l ASN* 3.1 24.9 + - - +
119l LEU* 3.8 2.8 + - - +
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Residues in contact with VAL 116 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88l LEU* 4.0 34.7 - - + +
91l LYS* 5.2 2.9 - - + +
92l ALA* 3.8 31.6 - - + +
112l VAL 3.0 13.7 + - - +
113l THR 3.8 5.8 - - - +
115l ALA* 1.3 76.4 - - + +
117l SER* 1.3 61.0 + - - +
119l LEU* 3.2 23.8 + - + +
120l ALA* 4.1 2.3 + - - -
141l LEU* 4.1 9.4 - - + -
143l PHE* 3.8 16.2 - - + -
156l MET* 4.0 23.5 - - + +
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Residues in contact with SER 117 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113l THR 2.8 23.6 + - - -
114l GLN 4.0 4.5 - - - -
115l ALA 3.2 0.2 - - - -
116l VAL* 1.3 77.2 - - - +
118l ASN* 1.3 57.3 + - - +
119l LEU 3.2 0.2 - - - -
120l ALA* 2.9 26.9 - - - +
156l MET* 3.1 30.5 - - - +
160l GLY* 4.1 5.8 - - - -
162l PHE* 3.5 19.4 - - - +
82m ARG* 3.1 27.1 + - - -
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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