Contacts of the helix formed by residues 120 - 131 (chain E) in PDB entry 6R1T
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 MET 120 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116E ARG* 3.1 33.7 - - - +
118E THR* 4.1 4.7 - - + +
119E ILE* 1.3 78.0 - - - +
121E PRO* 1.4 72.0 - - + +
122E LYS* 3.2 18.4 - - + -
123E ASP* 2.9 30.0 + - - +
124E ILE* 3.5 5.6 + - - +
47F SER* 4.0 16.4 - - - +
50F ILE* 3.7 5.6 - - - -
-3J G 4.1 15.3 - - - +
-2J C 3.4 26.0 - - - +
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Residues in contact with PRO 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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120E MET* 1.4 92.7 - - + +
122E LYS* 1.3 56.8 + - + +
124E ILE* 3.2 18.9 + - + +
125E GLN* 3.0 40.8 + - - +
47F SER* 4.9 4.9 - - - +
49F LEU* 4.1 28.9 - - + +
50F ILE* 3.7 15.7 - - + -
53F GLU* 5.0 8.6 - - + +
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Residues in contact with LYS 122 (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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113A HIS* 3.4 34.3 - - + +
115A LYS* 5.2 13.1 - - - +
116E ARG* 4.4 12.1 - - - +
120E MET* 4.6 18.2 - - + +
121E PRO* 1.3 79.5 - - + +
123E ASP* 1.3 63.1 + - - +
125E GLN* 3.4 17.2 + - - +
126E LEU* 2.9 21.5 + - - +
-2J C 5.4 4.0 + - - -
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Residues in contact with ASP 123 (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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113A HIS* 2.3 41.8 + - - -
107E THR* 3.7 19.6 - - + +
110E CYS* 3.3 18.3 - - - +
111E ALA* 3.3 20.1 - - + +
116E ARG* 3.0 24.5 + - - -
120E MET 2.9 21.6 + - - +
122E LYS* 1.3 76.5 - - - +
124E ILE* 1.3 64.4 + - - +
126E LEU* 3.1 2.3 + - - +
127E ALA* 3.0 25.3 + - - +
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Residues in contact with ILE 124 (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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103E LEU* 3.8 22.1 - - + +
104E PHE* 5.4 6.1 - - + -
107E THR* 3.8 24.9 - - + +
119E ILE* 5.3 3.1 - - + -
120E MET 4.1 3.1 - - - +
121E PRO* 3.3 23.3 - - + +
123E ASP* 1.3 76.5 - - - +
125E GLN* 1.3 60.3 + - - +
127E ALA* 3.4 1.7 + - - +
128E ARG* 3.0 41.9 + - - +
50F ILE* 3.9 33.0 - - + +
53F GLU* 4.1 26.2 - - + -
54F THR* 4.8 3.8 - - - +
57F VAL* 4.6 3.4 - - + -
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Residues in contact with GLN 125 (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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121E PRO* 3.0 24.2 + - - +
122E LYS* 3.6 16.9 - - - +
123E ASP 3.2 0.2 - - - -
124E ILE* 1.3 77.1 - - + +
126E LEU* 1.3 62.8 + - - +
128E ARG* 3.6 8.3 + - - +
129E ARG* 3.0 24.4 + - - +
134E ARG* 3.4 31.9 + - - +
53F GLU* 4.5 21.9 + - - +
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Residues in contact with LEU 126 (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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109A LEU* 4.0 37.0 - - + +
110A CYS* 4.5 7.9 - - + -
113A HIS* 3.8 27.1 - - + +
126A LEU* 5.7 4.0 - - + -
110E CYS* 3.6 26.0 - - + -
122E LYS 2.9 14.5 + - - +
123E ASP 3.1 8.7 + - - +
125E GLN* 1.3 76.8 - - - +
127E ALA* 1.3 58.4 + - - +
129E ARG* 3.0 8.0 + - + -
130E ILE* 2.9 51.0 + - + +
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Residues in contact with ALA 127 (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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130A ILE* 4.4 5.6 - - + -
103E LEU* 4.9 6.1 - - + +
106E ASP* 4.1 33.0 - - + +
107E THR* 4.1 12.8 - - - +
110E CYS* 5.3 1.1 - - + -
123E ASP 3.0 15.1 + - - +
124E ILE 4.1 1.3 - - - +
126E LEU* 1.3 75.4 - - - +
128E ARG* 1.3 57.9 + - - +
130E ILE* 3.9 10.1 - - - +
131E ARG* 3.0 37.1 + - + +
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Residues in contact with ARG 128 (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 TYR* 4.4 0.8 + - - -
103E LEU* 3.9 16.8 - - + -
124E ILE* 3.0 31.2 + - - +
125E GLN* 3.9 6.8 - - - +
127E ALA* 1.3 76.8 - - - +
129E ARG* 1.3 60.3 + - - +
131E ARG* 3.7 0.4 + - - +
132E GLY 3.2 4.0 + - - -
133E GLU* 2.8 74.4 + - + +
134E ARG* 4.5 22.8 - - - +
53F GLU* 3.8 14.3 + - - -
57F VAL* 3.6 34.4 - - - +
60F VAL* 5.1 18.6 - - - +
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Residues in contact with ARG 129 (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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106A ASP* 4.8 0.8 - - - +
109A LEU* 3.6 35.3 - - + +
125E GLN 3.0 15.7 + - - +
126E LEU* 3.0 10.4 + - + +
128E ARG* 1.3 76.4 - - - +
130E ILE* 1.3 59.7 + - + +
132E GLY* 3.0 17.8 + - - -
133E GLU 4.6 2.7 - - - +
134E ARG* 3.1 48.8 - - + +
110G ASN* 5.4 8.5 - - - +
112G GLN* 5.6 4.4 - - - +
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Residues in contact with ILE 130 (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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106A ASP* 3.2 45.3 - - - +
109A LEU* 5.4 2.7 - - + -
110A CYS* 5.5 4.5 - - + -
126A LEU* 5.8 2.9 - - + -
127A ALA* 5.6 1.8 - - - -
130A ILE* 3.0 41.7 - - + -
131A ARG* 3.4 29.2 - - + +
126E LEU* 2.9 50.0 + - + +
127E ALA* 3.9 3.1 - - - +
128E ARG 3.3 0.2 - - - -
129E ARG* 1.3 78.7 - - + +
131E ARG* 1.3 60.9 + - - +
132E GLY 3.2 1.0 + - - -
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Residues in contact with ARG 131 (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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130A ILE* 4.8 11.6 + - + +
131A ARG* 5.4 6.7 - - - +
99E TYR* 4.0 25.1 + - - -
102E ALA* 3.0 34.8 + - - +
103E LEU* 4.0 22.7 - - - +
106E ASP* 2.7 31.5 + - - +
127E ALA* 3.0 22.6 + - + +
128E ARG 4.2 2.2 - - - +
130E ILE* 1.3 76.3 - - + +
132E GLY* 1.3 61.8 + - - +
133E GLU* 3.8 20.5 + - - +
95F ARG* 5.0 6.2 - - - +
99G ARG* 3.6 19.0 + - - -
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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