Contacts of the helix formed by residues 108 - 121 (chain E) in PDB entry 2AMT
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 HIS 108 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23E VAL* 3.8 18.0 - - + +
24E ARG 4.6 2.1 + - - -
25E ILE* 3.4 48.8 - - + +
26E PRO* 4.0 15.2 - - + +
104E LYS 3.4 24.5 + - - -
105E MET 2.8 5.8 + - - +
107E PRO* 1.3 94.5 + - + +
109E ILE* 1.3 64.7 + - - +
110E PRO* 3.5 1.6 - - - -
111E GLN* 3.3 11.0 + - - +
112E MET* 3.1 25.9 + - + +
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Residues in contact with ILE 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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56D ASP* 5.7 1.1 - - - +
98E ILE* 4.6 0.2 - - + -
105E MET* 2.9 38.8 + - + +
106E LEU* 3.9 19.3 - - + +
108E HIS* 1.3 74.0 - - - +
110E PRO* 1.4 75.5 - - + +
112E MET* 2.8 23.5 + - - +
113E ARG* 3.0 20.3 + - + +
129E VAL* 3.4 46.2 - - + +
130E LYS* 4.1 16.4 - - - -
131E ALA* 4.1 7.0 - - + +
4901E 1AA 5.8 1.3 - - - +
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Residues in contact with PRO 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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106E LEU* 3.3 17.7 - - + +
107E PRO 4.2 10.3 - - - +
108E HIS 3.7 0.4 - - - -
109E ILE* 1.4 94.7 - - + +
111E GLN* 1.3 61.6 + - + +
113E ARG* 3.4 14.5 + - + +
114E VAL* 3.2 26.8 + - - +
124E MET* 4.2 6.1 - - + +
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Residues in contact with GLN 111 (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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23E VAL* 3.4 26.2 - - + -
107E PRO 5.6 0.9 - - - +
108E HIS* 3.3 12.1 + - - +
109E ILE 3.1 0.8 - - - -
110E PRO* 1.3 77.6 - - + +
112E MET* 1.3 64.9 + - - +
114E VAL* 3.4 16.5 + - - +
115E PHE* 3.1 52.1 + - + -
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Residues in contact with MET 112 (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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20E ILE* 3.4 41.1 - - + +
21E GLY* 3.5 18.4 - - - +
23E VAL* 3.5 5.6 - - + -
25E ILE* 3.7 24.0 - - + -
40E ALA* 5.4 1.1 - - - -
98E ILE* 3.8 25.1 - - + -
105E MET* 4.2 7.9 - - - +
108E HIS* 3.1 24.5 + - + +
109E ILE* 2.8 16.6 + - - +
111E GLN* 1.3 71.8 - - - +
113E ARG* 1.3 58.2 + - - +
115E PHE* 3.4 1.7 + - - +
116E ILE* 2.9 36.3 + - + +
129E VAL* 4.0 18.4 - - + -
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Residues in contact with ARG 113 (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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53D ALA* 4.2 17.1 + - - +
59D LYS* 6.0 4.2 - - - +
109E ILE* 3.0 25.4 + - - +
110E PRO* 3.5 14.1 - - - +
112E MET* 1.3 73.3 - - - +
114E VAL* 1.3 59.1 + - - +
116E ILE* 3.8 0.9 - - - +
117E ALA* 2.8 33.8 + - - +
124E MET* 2.6 57.4 + - - +
125E ASP* 3.9 7.9 + - - +
127E VAL* 2.6 35.8 + - + +
128E ASN* 4.4 3.5 + - - +
129E VAL* 4.0 22.2 - - + +
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Residues in contact with VAL 114 (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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110E PRO 3.2 16.5 + - - +
111E GLN* 3.6 21.3 - - - +
112E MET 3.3 0.2 - - - -
113E ARG* 1.3 77.0 - - - +
115E PHE* 1.3 66.0 + - + +
117E ALA* 3.3 2.1 + - - +
118E GLU* 2.9 53.3 + - + +
124E MET* 3.7 24.9 - - + -
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Residues in contact with PHE 115 (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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21E GLY 3.8 9.4 - - - +
22E GLY* 3.3 36.6 - - - -
23E VAL* 3.9 3.8 - - + -
41E LEU* 6.3 0.7 - - + -
74E ARG* 3.2 40.4 - - + +
111E GLN* 3.1 53.3 + - + +
112E MET 3.4 4.2 + - - +
114E VAL* 1.3 77.3 - - + +
116E ILE* 1.3 57.1 + - + +
118E GLU* 3.4 12.2 + - - +
119E ASP* 2.9 36.6 + - - +
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Residues in contact with ILE 116 (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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21E GLY* 4.8 4.3 - - - +
40E ALA* 6.0 2.0 - - + +
41E LEU* 3.7 28.0 - - + -
44E LEU* 3.7 28.7 - - + -
77E LEU* 4.8 2.2 - - + -
94E VAL* 4.4 2.2 - - + -
96E VAL* 4.8 7.2 - - + -
112E MET* 2.9 26.1 + - + +
113E ARG 3.9 2.5 - - - +
115E PHE* 1.3 75.1 - - - +
117E ALA* 1.3 56.8 + - - +
119E ASP* 3.3 5.5 + - - -
120E LEU* 2.9 42.0 + - + +
127E VAL* 3.7 23.3 - - + -
129E VAL* 4.0 25.1 - - + -
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Residues in contact with ALA 117 (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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113E ARG 2.8 23.1 + - - +
114E VAL* 3.7 3.8 - - - +
116E ILE* 1.3 73.6 - - - +
118E GLU* 1.3 56.8 + - + +
121E GLY* 2.9 8.1 + - - -
122E CYS* 2.8 53.9 + - - +
123E HIS 4.0 16.4 - - - +
124E MET* 4.1 11.4 - - + +
127E VAL* 3.9 4.7 - - + +
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Residues in contact with GLU 118 (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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74E ARG* 3.9 14.2 + - - +
114E VAL* 2.9 38.3 + - + +
115E PHE* 3.7 14.1 - - - +
117E ALA* 1.3 75.6 - - + +
119E ASP* 1.3 67.1 + - - +
121E GLY* 3.3 12.2 + - - -
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Residues in contact with ASP 119 (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 LEU* 5.7 0.2 - - - +
74E ARG* 2.8 47.0 + - - +
77E LEU* 3.8 22.0 - - + +
78E ARG* 2.7 52.7 + - + +
81E TRP* 3.6 14.6 - - - -
115E PHE 2.9 18.7 + - - +
116E ILE 3.8 3.6 - - - +
118E GLU* 1.3 76.4 - - - +
120E LEU* 1.3 60.8 + - - +
121E GLY 3.4 0.4 + - - -
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Residues in contact with LEU 120 (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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44E LEU* 4.5 1.8 - - + -
48E LEU* 3.7 30.3 - - + -
77E LEU* 4.1 13.0 - - + -
81E TRP* 2.9 60.5 + - + +
85E GLN* 4.9 0.3 - - - +
91E LEU* 3.8 27.1 - - + +
94E VAL* 4.2 10.8 - - + -
116E ILE* 2.9 36.7 + - + +
119E ASP* 1.3 77.5 - - - +
121E GLY* 1.3 64.3 + - - +
122E CYS* 3.3 14.3 + - - +
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Residues in contact with GLY 121 (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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81E TRP* 5.0 0.4 - - - -
117E ALA 2.9 7.5 + - - -
118E GLU* 3.3 11.3 + - - -
119E ASP 3.4 0.6 + - - -
120E LEU* 1.3 79.0 - - - +
122E CYS* 1.3 58.5 + - - +
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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