Contacts of the helix formed by residues 78 - 96 (chain C) in PDB entry 1M1J
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 78 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A LEU* 5.7 2.3 - - - +
141B ASP* 5.8 4.2 + - - -
72C LYS* 5.0 11.5 + - - -
75C LEU* 4.1 2.9 + - - -
77C GLN* 1.3 77.5 - - - +
79C ILE* 1.3 76.3 + - - +
80C GLU* 4.4 3.3 + - - -
81C GLN* 2.8 32.6 - - - +
82C LEU* 3.2 23.2 + - - +
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Residues in contact with ILE 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A LEU* 3.8 39.0 - - + +
106A ASP* 4.0 10.8 - - - +
109A TYR* 4.2 7.2 - - + -
137B ARG* 3.6 26.2 - - - +
141B ASP* 5.1 6.3 - - - +
144B LEU* 3.4 33.2 - - + -
78C SER* 1.3 86.0 + - - +
80C GLU* 1.3 55.8 + - - +
81C GLN 2.7 5.2 + - - -
82C LEU* 2.7 28.9 + - + +
83C THR* 2.8 29.8 + - + +
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Residues in contact with GLU 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A LEU* 4.1 31.5 - - + +
78C SER* 4.4 3.1 + - - -
79C ILE* 1.3 78.9 - - - +
81C GLN* 1.3 60.8 + - + +
83C THR* 3.1 23.8 + - - +
84C GLN* 3.5 18.1 + - + +
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Residues in contact with GLN 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C LYS* 5.0 6.9 - - - +
74C THR* 5.3 7.9 - - - +
75C LEU 4.9 2.0 + - - -
77C GLN* 3.0 32.5 + - + +
78C SER* 2.8 42.7 - - - +
79C ILE 2.7 1.0 + - - -
80C GLU* 1.3 82.5 - - + +
82C LEU* 1.3 59.5 + - - +
83C THR 3.3 0.4 - - - -
84C GLN* 4.5 2.2 - - - +
85C LYS* 3.1 27.9 + - - +
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Residues in contact with LEU 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A TYR* 3.6 18.9 - - + +
144B LEU* 4.2 32.5 - - + -
145B SER* 4.7 14.4 - - - +
148B ASN* 3.7 18.4 - - + +
77C GLN* 4.3 22.0 - - + +
78C SER 3.2 18.6 - - - +
79C ILE* 2.7 15.2 + - + +
81C GLN* 1.3 74.7 - - - +
83C THR* 1.3 59.7 + - - +
85C LYS* 3.3 28.8 + - - +
86C SER* 3.0 28.8 + - - -
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Residues in contact with THR 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A LEU* 4.9 1.6 - - + +
108A ASN* 5.5 3.8 - - + -
109A TYR* 3.3 45.1 - - + +
112A VAL* 4.0 9.3 - - - +
79C ILE* 2.8 25.0 + - + +
80C GLU* 3.1 20.1 + - - +
82C LEU* 1.3 75.6 - - - +
84C GLN* 1.3 64.4 + - - +
85C LYS 3.2 1.1 - - - -
86C SER* 3.2 5.3 + - - -
87C LYS* 2.9 39.7 + - - +
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Residues in contact with GLN 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C GLU* 3.5 16.9 + - + +
81C GLN* 4.5 2.9 - - - +
83C THR* 1.3 79.8 + - - +
85C LYS* 1.3 66.7 + - - +
87C LYS* 3.0 21.4 + - + +
88C LYS* 2.9 35.1 + - + +
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Residues in contact with LYS 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B ASN* 2.8 29.1 + - - +
151B MET* 5.6 1.2 - - - -
152B GLU* 3.8 17.5 + - - +
77C GLN* 4.3 20.4 - - - +
81C GLN 3.1 16.9 + - - +
82C LEU* 3.3 34.6 + - - +
84C GLN* 1.3 81.8 - - - +
86C SER* 1.3 77.1 + - - +
88C LYS* 3.5 7.4 + - - +
89C ILE* 3.3 34.5 + - + +
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Residues in contact with SER 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A TYR* 4.2 9.5 + - - -
112A VAL* 3.8 17.0 - - - -
113A SER* 5.5 1.0 - - - -
116A LEU* 3.4 27.8 - - - +
148B ASN* 4.1 4.2 + - - -
82C LEU 3.0 20.8 + - - -
83C THR* 3.2 6.6 + - - -
84C GLN 3.1 0.6 - - - -
85C LYS* 1.3 85.8 + - - +
87C LYS* 1.3 58.7 + - - +
88C LYS 3.1 1.8 - - - -
89C ILE* 3.3 4.4 + - - +
90C ILE* 3.0 32.1 + - - +
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Residues in contact with LYS 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A VAL* 3.9 26.5 - - + -
83C THR* 2.9 19.4 + - - +
84C GLN* 3.0 31.0 + - + +
86C SER* 1.3 77.1 - - - +
88C LYS* 1.3 61.4 + - + +
90C ILE* 3.6 11.3 + - + +
91C GLU* 3.2 29.0 + - - +
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Residues in contact with LYS 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C GLN* 2.9 30.6 + - + +
85C LYS* 3.7 8.1 - - - +
86C SER 3.1 0.2 - - - -
87C LYS* 1.3 76.8 - - + +
89C ILE* 1.3 65.1 + - + +
91C GLU* 3.0 31.5 + - - +
92C GLU* 3.0 26.1 + - - +
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Residues in contact with ILE 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A LEU* 3.5 23.3 - - + -
120A ILE* 4.4 1.8 - - + -
151B MET* 4.2 21.5 - - + -
152B GLU* 4.4 18.4 - - + +
155B TYR* 4.1 41.7 - - + -
85C LYS* 3.3 24.7 + - + +
86C SER 3.3 8.0 + - - +
88C LYS* 1.3 77.0 - - + +
90C ILE* 1.3 62.7 + - - +
92C GLU* 3.1 12.0 + - - +
93C ILE* 3.0 25.5 + - + +
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Residues in contact with ILE 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A VAL* 3.9 18.2 - - + +
115A GLU* 3.8 22.2 - - + +
116A LEU* 3.4 44.0 - - + +
119A ARG* 3.3 26.4 + - + +
86C SER 3.0 18.9 + - - +
87C LYS* 3.6 10.8 - - + +
88C LYS 3.1 0.2 - - - -
89C ILE* 1.3 77.8 - - - +
91C GLU* 1.3 62.2 + - + +
93C ILE* 3.6 7.7 + - - +
94C ILE* 3.3 26.9 + - + +
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Residues in contact with GLU 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C LYS* 3.2 18.9 + - - +
88C LYS* 3.0 33.0 + - - +
90C ILE* 1.3 77.2 - - + +
92C GLU* 1.3 66.8 + - - +
94C ILE* 3.1 10.0 + - + +
95C ARG* 2.9 35.9 + - + +
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Residues in contact with GLU 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B TYR* 2.5 45.5 + - + +
159B LYS* 3.4 26.7 + - - +
88C LYS* 3.0 22.5 + - - +
89C ILE* 3.1 10.3 + - - +
91C GLU* 1.3 76.7 - - - +
93C ILE* 1.3 62.1 + - - +
95C ARG* 3.2 7.8 + - - +
96C TYR* 3.0 31.5 + - + -
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Residues in contact with ILE 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A LEU* 4.6 1.3 - - + -
119A ARG* 4.0 24.5 - - + +
120A ILE* 3.2 49.6 - - + +
123A LEU* 3.8 27.8 - - + +
155B TYR* 3.7 20.4 - - + -
89C ILE* 3.0 21.4 + - + +
90C ILE* 3.8 5.8 - - - +
92C GLU* 1.3 75.3 - - - +
94C ILE* 1.3 63.9 + - + +
96C TYR* 3.3 21.4 - - - +
97C GLU* 3.9 1.9 + - - -
100C ILE* 4.9 3.1 - - - +
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Residues in contact with ILE 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ARG* 3.4 35.4 - - - +
90C ILE* 3.3 18.1 + - + +
91C GLU* 3.1 11.0 + - + +
93C ILE* 1.3 72.1 - - + +
95C ARG* 1.3 61.3 + - + +
96C TYR 2.9 4.5 - - - -
97C GLU* 2.7 39.5 + - + +
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Residues in contact with ARG 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C GLU* 2.9 28.6 + - + +
92C GLU* 3.6 8.7 - - - +
94C ILE* 1.3 81.1 - - + +
96C TYR* 1.3 59.4 + - - +
97C GLU 3.1 1.8 + - - -
98C ASN* 4.0 11.0 + - - +
99C THR* 4.2 8.1 - - - +
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Residues in contact with TYR 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A LEU* 4.7 4.7 - - + -
155B TYR* 3.4 30.3 - + - -
158B ILE* 5.1 0.4 - - + -
159B LYS* 2.9 32.3 + - + +
162B LEU* 3.8 26.7 - - + -
163B ASP* 2.7 40.8 + - - -
92C GLU* 3.0 22.4 + - + -
93C ILE* 3.3 16.2 - - - +
94C ILE 2.9 1.6 + - - -
95C ARG* 1.3 75.1 - - - +
97C GLU* 1.3 68.4 + - - +
98C ASN 3.5 0.4 - - - -
99C THR* 3.0 24.4 + - + -
100C ILE* 3.0 32.0 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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