Contacts of the helix formed by residues 112 - 129 (chain B) in PDB entry 5M7S
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 112 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102B LYS* 3.9 3.0 - - - +
110B MET 3.7 2.0 + - - -
111B TYR* 1.3 75.3 - - - +
113B VAL* 1.3 56.1 + - - +
114B GLU* 3.5 8.7 + - - +
115B GLU* 2.9 42.2 + - - +
116B ALA* 2.7 32.8 + - - +
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Residues in contact with VAL 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B SER* 1.3 73.8 - - - +
114B GLU* 1.3 68.6 + - + +
116B ALA* 3.6 6.1 - - - +
117B GLU* 3.0 24.6 + - - +
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Residues in contact with GLU 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B SER* 3.3 6.8 + - - +
113B VAL* 1.3 86.3 - - + +
115B GLU* 1.3 62.9 + - + +
117B GLU* 3.4 8.4 + - - +
118B GLN* 3.2 55.5 + - - +
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Residues in contact with GLU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B MET* 5.5 0.5 - - - +
101B TYR* 2.9 33.5 + - - -
102B LYS* 2.8 27.8 + - - -
111B TYR* 3.6 22.7 - - + -
112B SER* 2.9 34.1 + - - +
114B GLU* 1.3 73.4 - - + +
116B ALA* 1.3 62.6 + - - +
118B GLN* 3.2 9.8 + - - +
119B LEU* 3.0 23.6 + - - +
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Residues in contact with ALA 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B TYR* 4.0 5.6 - - + +
112B SER 2.7 21.3 + - - +
113B VAL* 3.6 8.3 - - - +
115B GLU* 1.3 71.6 - - - +
117B GLU* 1.3 56.8 + - - +
119B LEU* 3.3 2.3 + - - +
120B MET* 2.9 35.6 + - - +
160B GLN* 5.0 2.2 - - - +
164B PHE* 3.4 38.1 - - + -
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Residues in contact with GLU 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B VAL 3.0 13.8 + - - +
114B GLU* 3.6 14.6 - - - +
115B GLU 3.3 0.2 - - - -
116B ALA* 1.3 76.0 - - - +
118B GLN* 1.3 73.3 + - - +
120B MET* 3.4 17.8 + - - +
121B THR* 3.0 50.5 + - - +
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Residues in contact with GLN 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B MET* 3.9 35.7 - - + +
79B LYS* 5.0 6.8 + - - -
114B GLU* 3.2 40.4 + - - +
115B GLU* 3.2 10.2 + - - +
117B GLU* 1.3 83.8 - - - +
119B LEU* 1.3 57.5 + - - +
121B THR* 3.4 8.6 + - - +
122B LEU* 2.9 27.5 + - - +
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Residues in contact with LEU 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B MET* 4.1 18.6 - - + +
78B ARG* 5.7 0.2 - - - +
95B TYR* 5.1 15.3 - - + -
111B TYR* 3.7 45.8 - - + +
115B GLU 3.0 13.8 + - - +
116B ALA 3.9 2.7 - - - +
118B GLN* 1.3 72.5 - - - +
120B MET* 1.3 67.3 + - - +
122B LEU* 3.2 8.3 + - + +
123B ILE* 2.9 40.3 + - + +
133B PHE* 4.4 19.7 - - + -
135B TYR* 4.4 11.2 - - + -
161B VAL* 4.8 1.3 - - + -
164B PHE* 4.1 13.5 - - + -
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Residues in contact with MET 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B ALA* 2.9 17.0 + - - +
117B GLU* 3.7 18.6 - - - +
119B LEU* 1.3 73.2 - - - +
121B THR* 1.3 55.4 + - - +
123B ILE* 3.1 3.5 + - - +
124B SER* 2.6 37.0 + - - -
163B GLN 4.9 3.8 - - - +
164B PHE* 3.6 53.1 - - + +
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Residues in contact with THR 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B LYS* 3.7 26.5 - - - +
117B GLU* 3.0 33.8 + - - +
118B GLN* 3.6 9.0 - - - +
120B MET* 1.3 75.5 - - - +
122B LEU* 1.3 63.5 + - - +
124B SER* 3.3 8.4 + - - -
125B ALA* 3.0 22.3 + - - +
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Residues in contact with LEU 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B MET* 3.6 25.1 - - - +
78B ARG* 3.7 23.6 - - + +
79B LYS* 3.7 30.9 - - + +
82B PHE* 3.4 30.1 - - + -
93B TYR* 4.6 3.6 - - + -
95B TYR* 5.8 1.1 - - + -
118B GLN 2.9 16.7 + - - +
119B LEU* 3.2 11.9 + - + +
121B THR* 1.3 77.1 - - - +
123B ILE* 1.3 55.6 + - - +
125B ALA* 3.2 3.6 + - - +
126B ALA 3.0 22.5 + - - -
133B PHE* 3.2 37.2 - - + -
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Residues in contact with ILE 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B LEU* 2.9 31.6 + - + +
120B MET 3.7 2.7 - - - +
122B LEU* 1.3 72.5 - - - +
124B SER* 1.3 64.5 + - - +
126B ALA* 3.3 8.4 + - - +
127B ARG* 3.2 42.9 + - - +
133B PHE* 3.6 44.1 - - + +
161B VAL* 4.7 3.8 - - + +
164B PHE* 3.9 22.4 - - + +
165B GLY 3.8 14.8 - - - +
166B CYS* 4.0 19.1 - - + +
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Residues in contact with SER 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B MET 2.6 27.8 + - - -
121B THR* 3.3 9.3 + - - -
123B ILE* 1.3 73.7 - - - +
125B ALA* 1.3 62.8 + - - +
127B ARG* 3.3 27.6 + - - +
128B GLU* 3.0 23.5 + - - +
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Residues in contact with ALA 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B LYS* 4.0 29.4 - - + -
82B PHE* 3.9 6.5 - - + -
121B THR 3.0 14.2 + - - +
122B LEU 3.2 9.8 + - - +
124B SER* 1.3 76.6 - - - +
126B ALA* 1.3 61.2 + - - +
128B GLU* 3.2 13.6 + - - +
129B TYR* 3.1 35.2 + - + -
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Residues in contact with ALA 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B PHE* 3.5 30.3 - - + -
122B LEU 3.0 8.8 + - - +
123B ILE 3.3 9.8 + - - +
125B ALA* 1.3 74.9 - - - +
127B ARG* 1.3 61.2 + - - +
129B TYR 3.2 2.6 + - - -
130B GLU 3.2 4.5 + - - -
131B ILE* 2.9 46.2 + - + +
133B PHE* 4.0 20.6 - - + -
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Residues in contact with ARG 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B ILE* 3.2 24.7 + - - +
124B SER* 3.5 36.1 - - - +
126B ALA* 1.3 78.1 - - - +
128B GLU* 1.3 62.1 + - - +
130B GLU* 3.2 17.4 + - - +
131B ILE 4.2 3.1 + - - +
164B PHE 4.5 1.4 + - - -
165B GLY* 3.3 33.5 + - - -
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Residues in contact with GLU 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B GLN* 4.6 5.2 + - - -
124B SER 3.0 13.1 + - - +
125B ALA* 3.2 17.9 + - - +
127B ARG* 1.3 77.6 - - - +
129B TYR* 1.3 81.8 + - + +
130B GLU* 3.4 3.8 + - - +
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Residues in contact with TYR 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B LYS* 4.1 15.3 - - + -
82B PHE* 3.7 32.5 - + + +
83B ARG* 4.0 31.5 - - + +
86B GLN* 3.3 46.4 - - - +
125B ALA* 3.1 31.6 + - + +
126B ALA 3.2 3.3 + - - +
128B GLU* 1.3 101.7 + - - +
130B GLU* 1.3 69.7 + - - +
131B ILE* 3.3 4.8 - - + +
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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