Contacts of the helix formed by residues 101 - 110 (chain Q) 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 Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96Q PHE* 4.8 3.8 - - - -
99Q GLY 3.8 1.0 + - - -
100Q LEU* 1.3 72.4 - - - +
102Q VAL* 1.3 65.3 + - - +
103Q ARG* 3.3 17.4 - - - +
104Q GLU* 3.0 44.9 + - - +
105Q ILE* 3.1 16.1 + - - +
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Residues in contact with VAL 102 (chain Q).
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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41Q THR* 3.7 28.0 - - + -
45Q MET* 3.3 31.6 - - + -
96Q PHE* 3.7 13.4 - - + -
101Q SER* 1.3 73.2 - - - +
103Q ARG* 1.3 63.1 + - - +
106Q LEU* 3.0 39.8 + - + +
316Q GLU* 5.3 9.6 - - + -
317Q ILE* 3.4 26.2 - - + -
320Q ALA* 4.0 9.6 - - + -
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Residues in contact with ARG 103 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101Q SER* 3.3 14.5 - - - +
102Q VAL* 1.3 77.6 - - - +
104Q GLU* 1.3 59.8 + - + +
106Q LEU* 3.9 1.0 - - - +
107Q ALA* 2.9 30.0 + - - +
319Q ASP* 4.6 13.1 + - - +
320Q ALA* 3.8 22.6 - - + +
323Q PHE* 3.2 62.3 - - + +
324Q ALA* 4.8 0.9 - - - +
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Residues in contact with GLU 104 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100Q LEU* 3.8 15.7 - - + +
101Q SER* 3.0 38.4 + - - +
103Q ARG* 1.3 78.0 - - + +
105Q ILE* 1.3 63.0 + - - +
107Q ALA* 4.1 4.9 - - - -
108Q GLU* 2.8 31.9 + - - +
114Q GLY 4.2 9.3 - - - +
115Q GLY 5.2 0.5 - - - +
116Q CYS* 3.3 32.9 + - + +
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Residues in contact with ILE 105 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45Q MET* 3.4 38.6 - - + -
92Q HIS* 3.8 15.9 - - + +
95Q THR* 3.5 39.7 - - + -
96Q PHE* 3.8 12.6 - - + +
100Q LEU* 4.5 5.6 - - + +
101Q SER 3.1 12.1 + - - +
104Q GLU* 1.3 74.6 - - - +
106Q LEU* 1.3 66.9 + - + +
108Q GLU* 3.4 1.7 + - - +
109Q LEU* 3.0 32.1 + - + +
116Q CYS* 5.0 0.2 - - - -
126Q MET* 4.1 26.5 - - + +
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Residues in contact with LEU 106 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45Q MET* 4.3 12.8 - - + +
48Q LYS* 4.1 20.2 - - + -
49Q ALA* 4.2 22.7 - - + +
52Q LEU* 4.7 8.7 - - + -
58Q ILE* 5.2 0.9 - - + -
102Q VAL* 3.0 38.9 + - + +
103Q ARG 4.4 0.4 - - - +
105Q ILE* 1.3 78.6 - - + +
107Q ALA* 1.3 57.2 + - - +
109Q LEU* 3.2 22.3 + - + +
110Q THR* 3.0 33.4 + - - +
317Q ILE* 4.4 4.9 - - + +
320Q ALA* 4.4 1.6 - - + +
321Q ALA* 4.0 23.1 - - + +
324Q ALA* 3.7 14.8 - - + -
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Residues in contact with ALA 107 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103Q ARG 2.9 21.8 + - - +
105Q ILE 3.3 0.2 - - - -
106Q LEU* 1.3 75.7 - - - +
108Q GLU* 1.3 58.9 + - - +
110Q THR* 3.4 8.9 + - - -
112Q ARG* 2.8 35.3 + - + +
114Q GLY* 3.5 26.0 - - - +
115Q GLY* 3.4 6.3 - - - +
323Q PHE* 4.0 16.8 - - + +
324Q ALA* 3.8 7.1 - - + +
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Residues in contact with GLU 108 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104Q GLU 2.8 17.1 + - - +
105Q ILE 4.0 2.2 - - - +
107Q ALA* 1.3 75.0 - - - +
109Q LEU* 1.3 62.4 + - - +
110Q THR 3.2 0.7 - - - -
111Q GLY* 2.9 18.5 + - - -
115Q GLY* 3.4 2.4 - - - -
116Q CYS* 3.7 17.5 - - - +
117Q ALA* 2.8 27.1 + - + -
118Q LYS 3.4 0.3 + - - -
119Q GLY* 2.8 28.5 + - - -
120Q LYS 3.2 5.9 + - - -
121Q GLY* 2.8 31.1 + - - -
122Q GLY* 2.9 23.9 + - - +
126Q MET* 4.3 7.4 - - + -
304T TYR* 3.5 9.4 - - - -
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Residues in contact with LEU 109 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45Q MET* 6.4 0.4 - - + -
46Q GLU* 5.4 0.2 - - - +
49Q ALA* 3.9 23.3 - - + -
58Q ILE* 3.3 34.6 - - + +
62Q CYS* 4.7 2.5 - - - -
92Q HIS* 3.8 27.6 - - + +
105Q ILE* 3.0 28.1 + - + +
106Q LEU* 3.2 14.3 + - + +
108Q GLU* 1.3 78.1 - - - +
110Q THR* 1.3 55.7 + - - +
111Q GLY 3.1 0.2 - - - -
122Q GLY 4.5 0.4 - - - +
123Q SER* 3.2 42.4 - - - +
126Q MET* 5.3 2.7 - - + -
304T TYR* 2.9 24.9 + - - -
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Residues in contact with THR 110 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52Q LEU* 4.0 21.3 - - + -
57Q ILE* 3.8 24.0 - - + +
58Q ILE* 3.9 15.5 - - + -
106Q LEU 3.0 16.0 + - - +
107Q ALA* 3.4 4.7 + - - -
109Q LEU* 1.3 78.8 - - - +
111Q GLY* 1.3 56.5 + - - +
112Q ARG* 2.9 36.0 + - - +
324Q ALA* 2.9 30.7 + - + +
325Q THR* 4.9 0.4 - - + -
304T TYR* 4.4 2.0 - - - -
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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