Contacts of the helix formed by residues 1 - 19 (chain A) in PDB entry 2M5W
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 1 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A SER* 1.3 87.2 + - - +
4A GLU* 3.3 15.9 + - - +
5A THR* 2.7 40.2 + - - -
60A LEU* 5.7 7.9 - - + -
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Residues in contact with SER 2 (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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1A MET* 1.3 97.0 - - - +
3A GLU* 1.3 63.0 + - - +
4A GLU* 4.6 1.6 - - - -
6A SER* 3.0 28.2 + - - -
60A LEU* 4.9 4.2 - - - +
63A GLU* 4.9 2.6 - - - +
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Residues in contact with GLU 3 (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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2A SER* 1.3 75.8 - - - +
4A GLU* 1.3 61.7 + - - +
6A SER* 4.2 6.1 - - - -
7A THR* 2.7 39.5 + - - +
67A LYS* 2.9 34.1 + - + +
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Residues in contact with GLU 4 (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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1A MET* 3.6 12.9 + - - +
2A SER* 3.2 2.6 - - - -
3A GLU* 1.3 76.6 - - - +
5A THR* 1.3 60.4 + - - +
7A THR* 3.7 2.1 - - - -
8A GLN* 2.8 34.7 + - + +
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Residues in contact with THR 5 (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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1A MET* 2.7 38.3 + - - +
4A GLU* 1.3 74.3 - - - +
6A SER* 1.3 66.0 + - - +
8A GLN* 3.2 8.4 + - + +
9A ILE* 3.0 33.6 + - + +
54A ILE* 3.8 25.6 - - + +
55A SER* 5.2 1.6 - - - +
60A LEU* 4.4 11.4 - - + -
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Residues in contact with SER 6 (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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2A SER 3.0 22.0 + - - -
3A GLU* 4.2 7.6 - - - -
5A THR* 1.3 77.7 - - - +
7A THR* 1.3 56.8 + - - +
9A ILE* 3.2 4.6 + - - +
10A LEU* 2.9 31.5 + - - +
60A LEU* 3.9 12.9 - - - +
63A GLU* 2.8 31.6 + - - -
64A ALA* 4.1 16.4 + - - +
67A LYS* 4.3 8.1 - - - +
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Residues in contact with THR 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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3A GLU* 2.7 31.7 + - - +
4A GLU* 3.9 2.0 - - - -
6A SER* 1.3 73.8 - - - +
8A GLN* 1.3 64.2 + - - +
10A LEU* 3.7 14.3 - - + +
11A LYS* 2.9 61.5 + - + +
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Residues in contact with GLN 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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4A GLU* 2.8 21.3 + - + +
5A THR* 3.2 13.9 + - + +
7A THR* 1.3 75.4 - - - +
9A ILE* 1.3 63.3 + - - +
11A LYS* 3.5 8.0 + - - +
12A GLN* 3.0 33.8 + - - +
54A ILE* 4.4 19.8 - - + +
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Residues in contact with ILE 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 THR* 3.0 28.5 + - + +
6A SER 3.5 6.1 - - - +
8A GLN* 1.3 73.9 - - - +
10A LEU* 1.3 56.1 + - - +
12A GLN* 2.9 7.6 + - - +
13A VAL* 2.7 38.2 + - + +
51A MET* 3.9 17.3 - - + -
54A ILE* 3.5 21.8 - - + -
55A SER* 3.3 40.2 - - - +
60A LEU* 4.2 14.1 - - + +
61A ILE* 4.6 3.4 - - + -
64A ALA* 3.5 22.0 - - + -
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Residues in contact with LEU 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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6A SER* 2.9 18.7 + - - +
7A THR* 3.3 22.4 - - + +
9A ILE* 1.3 76.7 - - - +
11A LYS* 1.3 63.6 + - + +
13A VAL* 3.4 7.6 + - + +
14A GLU* 3.2 23.0 + - - +
64A ALA* 3.7 16.8 - - - +
67A LYS* 3.3 32.8 - - + +
68A SER* 3.6 7.9 - - - +
69A THR* 3.1 52.4 - - + +
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Residues in contact with LYS 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 THR* 2.9 51.7 + - + +
8A GLN* 3.6 8.5 - - - +
10A LEU* 1.3 77.6 - - + +
12A GLN* 1.3 62.3 + - - +
14A GLU* 3.4 11.1 + - - +
15A TYR* 2.8 32.0 + - - +
69A THR* 6.3 0.2 - - + -
90A ILE 5.4 0.9 - - - +
91A ASP* 2.7 75.8 + - + +
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Residues in contact with GLN 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 GLN* 3.0 22.2 + - - +
9A ILE* 2.9 11.3 + - + +
11A LYS* 1.3 81.0 - - - +
13A VAL* 1.3 62.3 + - - +
15A TYR* 3.5 31.6 - - + +
16A TYR* 3.6 3.3 + - - -
50A ARG* 2.8 44.0 + - + +
51A MET* 3.3 30.3 - - + +
54A ILE* 4.5 19.1 - - + +
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Residues in contact with VAL 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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9A ILE* 2.7 31.3 + - + +
10A LEU* 3.7 8.5 - - + +
12A GLN* 1.3 70.4 - - - +
14A GLU* 1.3 67.8 + - + +
15A TYR 3.2 0.7 + - - -
16A TYR* 3.3 11.1 + - - +
17A PHE* 3.3 22.1 - - + -
45A ILE* 4.3 17.0 - - + -
48A PHE* 5.4 1.3 - - + -
51A MET* 3.6 27.8 - - + -
61A ILE* 4.4 4.3 - - + -
64A ALA* 5.1 4.5 - - + -
65A LEU* 4.3 16.8 - - + -
68A SER* 5.3 2.2 - - - +
71A LEU* 3.6 25.1 - - + -
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Residues in contact with GLU 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 LEU 3.2 9.6 + - - +
11A LYS* 3.8 9.5 - - - +
13A VAL* 1.3 78.8 - - - +
15A TYR* 1.3 60.9 + - - +
17A PHE* 2.9 14.8 + - - +
18A SER* 2.9 33.7 + - - -
69A THR* 3.1 26.8 - - + +
70A ARG* 3.4 21.3 - - - +
71A LEU* 4.2 17.3 - - + -
87A PRO* 4.6 3.5 - - + +
90A ILE* 3.2 48.3 - - - +
91A ASP* 4.0 6.9 + - - +
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Residues in contact with TYR 15 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A LYS 2.8 18.5 + - - +
12A GLN* 3.5 27.8 - - + +
13A VAL 3.1 0.4 - - - -
14A GLU* 1.3 76.7 - - - +
16A TYR* 1.3 88.9 + + - +
18A SER* 3.9 8.1 - - - -
19A ASP* 2.8 73.4 + - + +
21A ASN* 5.8 1.4 + - + -
50A ARG* 4.4 22.7 + - - -
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Residues in contact with TYR 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 GLN 3.6 3.3 + - - -
13A VAL 3.3 8.6 + - - +
14A GLU 3.3 0.8 - - - -
15A TYR* 1.3 104.5 - + - +
17A PHE* 1.3 62.2 + - + +
21A ASN* 3.4 30.5 + - + +
22A PHE* 3.3 21.5 + - - -
28A LEU* 4.2 6.9 - - + +
48A PHE* 3.4 67.0 + + + -
50A ARG* 3.2 36.7 - - - +
51A MET* 3.4 25.4 - - + -
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Residues in contact with PHE 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 VAL* 3.3 24.2 - - + -
14A GLU* 2.9 9.4 + - - +
16A TYR* 1.3 79.3 - - + +
18A SER* 1.3 61.8 + - - +
19A ASP 3.3 1.0 + - - -
20A SER* 3.6 12.5 + - - -
21A ASN 4.2 0.5 + - - -
22A PHE* 4.0 19.2 + + + +
23A PRO* 5.6 0.3 - - - +
28A LEU* 3.3 31.4 - - + -
32A ALA* 6.1 0.2 - - + -
37A ASP* 3.6 24.2 - - - -
40A ILE* 3.5 37.7 - - + -
45A ILE* 6.2 2.0 - - + -
48A PHE* 5.0 5.8 - + - -
71A LEU* 4.1 21.8 - - + -
80A VAL* 5.9 0.7 - - + -
82A ARG* 4.0 26.0 + - + +
87A PRO* 4.6 7.0 - - + +
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Residues in contact with SER 18 (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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14A GLU* 2.9 22.8 + - - +
15A TYR* 2.9 11.4 + - - -
17A PHE* 1.3 73.2 - - - +
19A ASP* 1.3 56.1 + - - +
20A SER* 3.0 13.9 + - - -
87A PRO* 3.1 42.9 + - - +
89A ASN 5.3 2.1 + - - -
90A ILE* 4.9 10.1 + - - +
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Residues in contact with ASP 19 (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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15A TYR* 2.8 55.9 + - + +
17A PHE 3.3 0.4 - - - -
18A SER* 1.3 74.7 - - - +
20A SER* 1.3 56.0 + - - +
21A ASN* 2.8 31.1 + - + +
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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