Contacts of the helix formed by residues 101 - 110 (chain G) in PDB entry 3EXG
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 101 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96G PHE* 4.8 3.8 - - - -
99G GLY 3.5 3.2 + - - -
100G LEU* 1.3 72.0 - - - +
102G VAL* 1.3 58.7 + - - +
103G ARG* 2.7 34.8 + - - +
104G GLU* 2.8 33.8 + - - +
105G ILE* 3.1 12.6 + - - +
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Residues in contact with VAL 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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41G THR* 3.6 31.6 - - + -
45G MET* 3.4 33.7 - - + -
96G PHE* 3.6 12.3 - - + -
100G LEU 4.0 0.8 + - - -
101G SER* 1.3 72.9 - - - +
103G ARG* 1.3 60.3 + - - +
105G ILE* 3.9 1.1 - - - +
106G LEU* 3.2 27.6 + - + +
316G GLU* 4.3 13.2 - - + +
317G ILE* 3.6 25.4 - - + -
320G ALA* 3.9 17.3 - - + +
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Residues in contact with ARG 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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101G SER* 2.7 20.2 + - - +
102G VAL* 1.3 74.7 - - - +
104G GLU* 1.3 58.7 + - + +
106G LEU* 4.0 1.0 - - - +
107G ALA* 3.0 28.9 + - - +
319G ASP 5.3 2.4 + - - -
320G ALA* 4.2 20.0 - - + +
322G GLN* 6.0 0.6 - - - +
323G PHE* 3.4 64.9 - - + +
324G ALA* 4.7 0.2 - - - +
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Residues in contact with GLU 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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100G LEU* 3.2 21.7 - - + +
101G SER* 2.8 38.6 + - - +
103G ARG* 1.3 74.6 - - + +
105G ILE* 1.3 65.0 + - - +
107G ALA 3.8 0.7 - - - -
108G GLU* 3.2 17.8 + - - +
114G GLY 3.8 16.8 - - - +
116G CYS* 3.2 36.4 + - + +
323G PHE* 5.5 0.2 - - - -
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Residues in contact with ILE 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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45G MET* 3.5 42.4 - - + -
92G HIS* 4.2 9.6 - - + +
95G THR* 3.6 33.2 - - + -
96G PHE* 3.7 17.3 - - + +
100G LEU* 3.8 19.3 - - + +
101G SER 3.1 9.3 + - - +
104G GLU* 1.3 79.2 - - - +
106G LEU* 1.3 67.5 + - + +
108G GLU* 3.4 2.6 + - - +
109G LEU* 3.2 31.0 + - + +
116G CYS* 5.4 0.7 - - - -
126G MET* 4.5 20.0 - - + +
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Residues in contact with LEU 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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45G MET* 4.5 23.1 - - + +
48G LYS* 3.9 13.2 - - + -
49G ALA* 4.5 9.4 - - - -
52G LEU* 4.5 9.6 - - + -
58G ILE* 5.2 0.4 - - + -
102G VAL* 3.2 26.0 + - + +
103G ARG 4.3 0.7 - - - +
105G ILE* 1.3 81.4 - - + +
107G ALA* 1.3 60.2 + - - +
109G LEU* 3.3 26.2 + - + +
110G THR* 3.3 24.3 + - - +
317G ILE* 4.9 2.5 - - + +
320G ALA* 4.5 4.9 - - + +
321G ALA* 3.7 37.9 - - + +
324G ALA* 3.6 13.3 - - + +
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Residues in contact with ALA 107 (chain G).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103G ARG 3.0 19.4 + - - +
105G ILE 3.3 0.2 - - - -
106G LEU* 1.3 74.1 - - - +
108G GLU* 1.3 59.5 + - - +
110G THR* 3.2 8.5 + - - -
112G ARG* 2.9 33.3 + - + +
114G GLY* 3.6 10.1 - - - -
115G GLY* 3.5 20.9 - - - +
323G PHE* 3.7 16.8 - - + -
324G ALA* 3.5 13.6 - - + +
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Residues in contact with GLU 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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304F TYR* 3.3 12.6 - - - -
104G GLU 3.2 18.4 + - - +
105G ILE 3.7 3.8 - - - +
106G LEU 3.3 0.2 - - - -
107G ALA* 1.3 73.0 - - - +
109G LEU* 1.3 69.1 + - - +
110G THR 3.1 1.6 - - - -
111G GLY* 2.8 13.7 + - - -
112G ARG 4.9 0.2 - - - +
115G GLY* 3.3 4.6 - - - -
116G CYS* 3.8 16.8 - - - +
117G ALA* 2.5 37.2 + - - -
118G LYS 3.3 0.5 + - - -
119G GLY* 2.8 27.1 + - - -
121G GLY* 2.9 14.4 + - - -
122G GLY* 2.9 38.4 + - - +
126G MET* 4.3 6.3 - - + -
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Residues in contact with LEU 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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304F TYR* 2.5 31.0 + - - -
45G MET* 6.4 0.2 - - - -
49G ALA* 4.1 13.5 - - + -
58G ILE* 3.2 39.3 - - + +
62G CYS* 4.7 1.8 - - - -
92G HIS* 3.9 23.6 - - + +
105G ILE* 3.2 17.4 + - + +
106G LEU* 3.5 26.2 - - + +
108G GLU* 1.3 80.5 - - - +
110G THR* 1.3 55.4 + - - +
111G GLY 3.2 0.2 - - - -
122G GLY* 4.4 1.6 - - - -
123G SER* 3.4 39.0 - - - -
126G MET* 4.7 4.5 - - - -
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Residues in contact with THR 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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304F TYR* 4.4 2.2 - - - -
52G LEU* 4.9 6.7 - - + -
57G ILE* 3.5 42.7 - - + +
58G ILE* 4.0 13.0 - - + -
106G LEU 3.3 12.3 + - - +
107G ALA 3.2 11.6 + - - -
109G LEU* 1.3 75.5 - - - +
111G GLY* 1.3 57.1 + - - +
112G ARG* 3.0 24.1 + - - +
324G ALA* 3.0 28.2 + - + +
325G THR* 4.5 7.4 - - + -
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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