Contacts of the helix formed by residues 101 - 110 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96E PHE* 4.9 1.8 - - - -
99E GLY 3.8 1.3 + - - -
100E LEU* 1.3 76.5 - - - +
102E VAL* 1.3 65.8 + - - +
103E ARG* 3.4 11.7 + - - +
104E GLU* 2.8 45.2 + - - +
105E ILE* 3.1 25.7 + - - +
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Residues in contact with VAL 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E THR* 3.7 29.4 - - + -
45E MET* 3.5 33.2 - - + -
96E PHE* 3.7 11.8 - - + -
100E LEU 4.0 0.2 + - - -
101E SER* 1.3 73.5 - - - +
103E ARG* 1.3 57.4 + - - +
105E ILE* 3.7 0.7 - - - +
106E LEU* 2.9 33.0 + - + +
316E GLU* 5.6 8.5 - - + -
317E ILE* 3.6 25.6 - - + -
320E ALA* 4.0 15.5 - - + -
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Residues in contact with ARG 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101E SER* 3.1 11.4 - - - +
102E VAL* 1.3 75.0 - - - +
104E GLU* 1.3 63.4 + - + +
106E LEU* 3.3 2.3 + - - +
107E ALA* 2.9 33.8 + - - +
319E ASP* 4.9 5.7 + - - +
320E ALA* 4.2 21.1 - - - +
322E GLN* 5.9 0.8 - - - +
323E PHE* 3.3 63.5 - - + +
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Residues in contact with GLU 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99E GLY 5.4 0.2 - - - +
100E LEU* 3.3 23.4 - - + +
101E SER* 2.8 34.8 + - - +
103E ARG* 1.3 77.1 - - + +
105E ILE* 1.3 63.8 + - - +
108E GLU* 3.2 17.8 + - - +
114E GLY 4.1 13.2 - - - +
115E GLY* 3.4 0.7 - - - -
116E CYS* 3.2 37.6 + - + +
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Residues in contact with ILE 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E MET* 3.3 37.2 - - + -
92E HIS* 3.7 29.4 - - + +
95E THR* 3.5 32.5 - - + +
96E PHE* 3.7 13.2 - - + +
100E LEU* 4.0 6.1 - - + -
101E SER 3.1 17.5 + - - +
104E GLU* 1.3 74.9 - - - +
106E LEU* 1.3 68.3 + - + +
108E GLU* 3.1 12.8 + - - +
109E LEU* 3.2 20.1 + - + +
116E CYS* 5.0 0.9 - - - -
126E MET* 4.5 14.9 - - + +
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Residues in contact with LEU 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E MET* 4.1 26.2 - - + +
48E LYS* 3.8 13.7 - - + -
49E ALA* 4.4 17.7 - - + -
52E LEU* 4.5 8.0 - - + +
58E ILE* 5.3 0.8 - - + +
102E VAL* 2.9 32.2 + - + +
103E ARG* 4.1 2.0 - - - +
105E ILE* 1.3 75.5 - - + +
107E ALA* 1.3 58.4 + - - +
109E LEU* 3.0 29.6 + - + +
110E THR* 3.1 15.1 + - - +
317E ILE* 4.7 3.6 - - + +
320E ALA* 4.4 4.0 - - + -
321E ALA* 3.7 38.6 - - + +
324E ALA* 3.9 12.3 - - + -
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Residues in contact with ALA 107 (chain E).
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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103E ARG 2.9 19.1 + - - +
106E LEU* 1.3 78.8 - - - +
108E GLU* 1.3 56.9 + - - +
110E THR* 3.1 10.4 + - - -
111E GLY 3.1 5.4 + - - -
112E ARG* 3.1 32.4 + - + +
114E GLY* 4.0 2.2 - - - -
115E GLY* 3.7 22.0 - - - +
323E PHE* 3.9 18.6 - - + -
324E ALA* 3.7 9.8 - - + +
327E ASP* 5.4 0.7 - - + +
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Residues in contact with GLU 108 (chain E).
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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104E GLU 3.2 17.0 + - - +
105E ILE 3.1 6.7 + - - +
107E ALA* 1.3 73.4 - - - +
109E LEU* 1.3 67.6 + - - +
110E THR 3.1 1.3 - - - -
111E GLY 3.1 8.6 + - - +
115E GLY* 3.5 4.2 - - - -
116E CYS* 4.1 13.0 - - - -
117E ALA* 2.4 42.5 + - + +
118E LYS 3.1 0.5 + - - -
119E GLY* 2.7 39.9 + - - -
121E GLY 3.1 1.7 + - - -
122E GLY* 3.0 33.2 + - - +
126E MET* 4.5 7.2 - - + -
304H TYR* 3.2 14.7 - - - -
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Residues in contact with LEU 109 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E ALA* 4.1 13.2 - - + -
58E ILE* 3.4 40.3 - - + +
62E CYS* 4.9 1.8 - - - -
92E HIS* 4.0 30.1 - - + +
105E ILE* 3.4 18.2 - - + +
106E LEU* 3.0 17.2 + - + +
108E GLU* 1.3 80.4 - - - +
110E THR* 1.3 56.5 + - - +
122E GLY 4.1 1.3 - - - +
123E SER* 3.5 37.2 - - - +
126E MET* 5.0 4.9 - - - -
304H TYR* 2.7 27.1 + - - -
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Residues in contact with THR 110 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52E LEU* 5.1 6.7 - - + -
57E ILE* 3.6 34.4 - - + +
58E ILE* 4.2 10.1 - - + -
106E LEU 3.1 13.5 + - - +
107E ALA* 3.1 18.5 + - - -
109E LEU* 1.3 78.3 - - - +
111E GLY* 1.3 59.1 + - - +
112E ARG* 2.9 31.8 + - - +
324E ALA* 3.2 24.5 + - + +
325E THR* 4.6 7.0 - - + -
329E GLU* 5.7 0.2 - - - +
304H TYR* 4.3 2.2 - - - -
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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