Contacts of the helix formed by residues 6 - 17 (chain A) in PDB entry 1M1B
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 LYS 6 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A VAL* 1.3 77.1 - - - +
7A LYS* 1.3 65.8 + - - +
8A THR* 3.8 9.8 + - - +
9A THR* 3.2 18.9 + - - +
10A GLN* 3.2 18.4 + - - +
151A ASP* 3.1 38.7 + - - -
152A PRO* 5.1 4.0 - - - +
153A ASP* 5.0 3.0 + - - -
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Residues in contact with LYS 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A VAL 3.7 0.8 + - - -
6A LYS* 1.3 69.5 - - - +
8A THR* 1.3 66.9 + - + +
10A GLN* 3.1 12.2 + - - +
11A LEU 2.9 19.6 + - - -
75A SER* 2.9 46.5 + - - +
78A SER* 3.0 19.2 + - - -
79A ASP* 3.8 22.9 - - - +
80A VAL 4.1 10.1 + - - +
81A PRO* 3.4 21.6 - - + +
82A ILE* 5.2 2.4 - - + +
107A GLY* 3.3 24.3 + - - +
109A ALA* 4.0 4.3 - - + -
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Residues in contact with THR 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LYS* 3.8 11.1 - - - +
7A LYS* 1.3 76.7 - - + +
9A THR* 1.3 63.7 + - - +
11A LEU* 3.2 1.9 + - - +
12A LYS* 2.8 25.8 + - - +
104A GLU* 6.1 0.9 - - + -
107A GLY 6.0 0.4 - - - +
108A VAL 4.4 2.2 - - - +
109A ALA* 3.7 22.0 - - - +
151A ASP* 2.9 29.0 + - + +
153A ASP* 3.3 30.0 - - - +
154A PHE* 3.5 28.5 - - + -
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Residues in contact with THR 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A VAL* 4.9 8.1 - - + -
6A LYS* 3.2 32.6 + - - +
8A THR* 1.3 78.4 + - - +
10A GLN* 1.3 56.9 + - + +
12A LYS* 3.1 3.6 + - + +
13A GLN* 2.8 58.7 + - + +
153A ASP* 2.4 31.0 + - - +
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Residues in contact with GLN 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A VAL* 3.0 40.4 + - + +
6A LYS 3.3 11.9 + - - +
7A LYS* 3.1 8.5 + - - +
9A THR* 1.3 76.5 - - - +
11A LEU* 1.3 64.7 + - - +
13A GLN* 3.1 15.8 + - - +
14A MET* 2.9 30.4 + - - +
41A LYS 4.8 1.2 - - - +
79A ASP 3.9 16.0 + - - +
80A VAL* 4.3 7.4 - - - +
81A PRO* 3.4 27.4 - - + +
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Residues in contact with LEU 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A LYS 2.9 5.9 + - - -
8A THR 3.7 6.1 - - - +
10A GLN* 1.3 76.2 - - - +
12A LYS* 1.3 64.0 + - - +
14A MET* 3.3 6.6 + - - +
15A LEU* 3.1 29.0 + - + +
23A ILE* 4.8 6.3 - - + -
81A PRO* 3.8 16.3 - - + +
83A LEU* 4.2 29.4 - - + +
109A ALA* 3.7 31.2 - - + -
110A GLY* 3.9 8.7 - - - +
155A CYS* 3.7 27.1 - - + -
234A MET* 4.0 24.9 - - + -
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Residues in contact with LYS 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A THR 2.8 17.4 + - - +
9A THR* 3.3 13.7 - - + +
11A LEU* 1.3 73.9 - - - +
13A GLN* 1.3 58.7 + - + +
15A LEU* 3.7 3.4 - - + +
16A ASN* 3.0 54.6 + - - +
146A LYS* 4.4 3.4 - - - +
152A PRO 3.7 20.5 + - - -
153A ASP* 3.9 21.1 - - + +
154A PHE 4.0 3.6 + - - -
155A CYS* 3.6 17.6 - - - -
185A ASP* 2.6 34.2 + - + +
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Residues in contact with GLN 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A VAL* 5.8 6.1 - - - +
9A THR* 2.8 47.3 + - + +
10A GLN* 3.5 14.3 - - - +
12A LYS* 1.3 75.2 - - + +
14A MET* 1.3 59.4 + - + +
16A ASN* 3.7 5.6 - - - +
17A SER* 2.9 32.1 + - - -
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Residues in contact with MET 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A GLN* 2.9 22.7 + - + +
11A LEU* 3.3 7.8 + - - +
13A GLN* 1.3 75.7 - - + +
15A LEU* 1.3 62.8 + - - +
17A SER* 2.6 21.6 + - - -
21A GLU* 3.1 42.4 - - + +
22A PHE 4.0 13.5 - - - +
23A ILE* 4.0 11.0 - - + -
41A LYS* 3.4 65.1 - - + +
42A GLY* 4.6 1.1 - - - -
81A PRO* 4.5 10.1 - - - -
233A SER* 3.4 4.5 + - - -
234A MET* 3.9 9.4 - - + -
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Residues in contact with LEU 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A LEU* 3.1 21.5 + - + +
12A LYS* 3.7 4.7 - - + +
14A MET* 1.3 77.4 - - - +
16A ASN* 1.3 62.2 + - - +
17A SER 4.1 0.2 - - - +
83A LEU* 5.6 1.6 - - + -
155A CYS* 3.6 38.6 - - + -
157A VAL* 4.4 9.4 - - + -
185A ASP* 4.0 26.7 - - + +
186A ALA* 4.1 17.3 - - + -
211A PRO* 3.2 16.6 - - + +
213A VAL* 4.1 9.4 - - + -
233A SER* 2.5 22.8 + - - -
234A MET* 3.8 30.7 - - + -
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Residues in contact with ASN 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A LYS* 3.0 45.9 + - - +
13A GLN* 3.7 5.1 - - - +
15A LEU* 1.3 79.8 - - - +
17A SER* 1.3 63.0 + - - +
18A LYS* 3.6 16.6 + - - -
185A ASP* 4.6 4.3 - - - +
211A PRO* 3.9 17.2 - - - +
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Residues in contact with SER 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A GLN 2.9 15.7 + - - -
14A MET 2.6 18.8 + - - -
15A LEU 4.1 0.2 - - - +
16A ASN* 1.3 78.4 - - - +
18A LYS* 1.3 65.0 + - - +
19A ASP* 2.8 16.8 + - - +
21A GLU* 2.6 24.8 + - - -
233A SER* 3.3 15.6 + - - -
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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