Contacts of the helix formed by residues 101 - 110 (chain M) 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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96M PHE* 4.6 2.9 - - - -
99M GLY 3.7 1.4 + - - -
100M LEU* 1.3 74.4 - - - +
102M VAL* 1.3 64.8 + - - +
103M ARG* 3.3 12.2 + - - +
104M GLU* 3.0 43.7 + - - +
105M ILE* 3.1 23.8 + - - +
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Residues in contact with VAL 102 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41M THR* 3.7 28.9 - - + -
45M MET* 3.2 26.2 - - + -
96M PHE* 3.7 14.5 - - + -
101M SER* 1.3 74.8 - - - +
103M ARG* 1.3 62.1 + - - +
105M ILE* 3.4 1.0 + - - +
106M LEU* 3.0 38.8 + - + +
316M GLU* 5.5 8.3 - - + +
317M ILE* 3.5 26.0 - - + -
320M ALA* 4.4 7.9 - - + -
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Residues in contact with ARG 103 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101M SER* 3.1 9.8 + - - +
102M VAL* 1.3 79.2 - - - +
104M GLU* 1.3 59.0 + - + +
106M LEU* 4.1 2.2 - - - +
107M ALA* 3.0 30.5 + - - +
319M ASP* 5.2 5.5 + - - +
320M ALA* 4.3 18.9 - - - +
323M PHE* 3.2 69.0 - - + +
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Residues in contact with GLU 104 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99M GLY 5.0 1.0 - - - +
100M LEU* 4.1 14.5 - - + +
101M SER* 3.0 38.4 + - - +
103M ARG* 1.3 75.4 - - + +
105M ILE* 1.3 67.6 + - - +
108M GLU* 3.1 19.6 + - - +
114M GLY 4.3 15.3 - - - +
115M GLY* 3.7 0.2 - - - -
116M CYS* 3.4 38.5 + - + +
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Residues in contact with ILE 105 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45M MET* 3.4 39.0 - - + -
92M HIS* 3.6 24.0 - - + +
95M THR* 3.5 31.4 - - + +
96M PHE* 3.6 14.4 - - + +
100M LEU* 4.2 4.7 - - + +
101M SER 3.1 15.1 + - - +
102M VAL 3.8 0.2 - - - +
104M GLU* 1.3 77.3 - - - +
106M LEU* 1.3 64.7 + - - +
108M GLU* 3.5 3.1 + - - +
109M LEU* 3.1 28.3 + - + +
116M CYS* 4.9 0.4 - - - -
126M MET* 3.8 25.3 - - + +
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Residues in contact with LEU 106 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45M MET* 4.3 26.0 - - + +
48M LYS* 4.5 6.1 - - + -
49M ALA* 4.6 5.6 - - + +
52M LEU* 4.5 15.7 - - + +
102M VAL* 3.0 26.2 + - + +
103M ARG 4.2 0.9 - - - +
105M ILE* 1.3 79.3 - - + +
107M ALA* 1.3 62.8 + - - +
109M LEU* 2.9 31.9 + - + +
110M THR* 3.0 14.2 + - - +
317M ILE* 4.4 5.6 - - + +
320M ALA* 4.0 13.2 - - + +
321M ALA* 3.6 35.9 - - + +
324M ALA* 3.6 15.2 - - + +
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Residues in contact with ALA 107 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103M ARG 3.0 18.5 + - - +
105M ILE 3.5 0.2 - - - -
106M LEU* 1.3 76.2 - - - +
108M GLU* 1.3 60.1 + - - +
110M THR* 3.3 9.2 + - - -
111M GLY 3.1 5.4 + - - -
112M ARG* 2.9 35.3 + - + -
114M GLY* 3.7 6.3 - - - +
115M GLY* 3.4 26.5 - - - +
323M PHE* 4.0 13.2 - - + -
324M ALA* 3.6 8.1 - - + +
327M ASP* 4.7 0.7 - - - +
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Residues in contact with GLU 108 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104M GLU 3.1 17.7 + - - +
105M ILE 3.5 4.7 - - - +
107M ALA* 1.3 74.3 - - - +
109M LEU* 1.3 67.0 + - - +
111M GLY* 3.1 9.5 + - - +
115M GLY* 3.4 2.4 - - - -
116M CYS* 3.3 6.4 + - - +
117M ALA* 2.5 47.0 + - + +
118M LYS 3.2 0.5 + - - -
119M GLY* 3.0 26.6 + - - -
121M GLY 3.2 3.6 + - - -
122M GLY* 2.9 38.6 + - - +
126M MET* 3.9 20.9 - - + -
304P TYR* 3.3 13.5 - - - -
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Residues in contact with LEU 109 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45M MET* 6.1 0.9 - - + -
49M ALA* 4.0 23.6 - - + -
52M LEU* 6.3 0.4 - - + -
58M ILE* 3.4 31.3 - - + +
62M CYS* 4.9 1.1 - - - -
92M HIS* 3.8 28.3 - - + +
105M ILE* 3.1 21.7 + - + +
106M LEU* 2.9 23.1 + - + +
108M GLU* 1.3 72.1 - - - +
110M THR* 1.3 57.8 + - + +
111M GLY 3.3 0.9 + - - -
122M GLY 4.4 0.7 - - - -
123M SER* 3.3 41.3 - - - +
126M MET* 4.9 3.8 - - - -
304P TYR* 2.7 27.1 + - - -
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Residues in contact with THR 110 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52M LEU* 4.5 15.0 - - + -
57M ILE* 3.5 40.7 - - + +
58M ILE* 4.2 8.3 - - + -
106M LEU 3.0 15.5 + - - +
107M ALA* 3.3 9.7 + - - -
109M LEU* 1.3 75.3 - - - +
111M GLY* 1.3 55.7 + - - +
112M ARG* 2.8 35.1 + - - +
324M ALA* 3.0 29.1 + - + +
325M THR* 4.8 1.1 - - + -
304P TYR* 4.5 1.6 - - - -
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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