Contacts of the helix formed by residues 10 - 20 (chain P) in PDB entry 2IMW
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 TYR 10 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9P ASP* 1.3 85.4 - - + +
11P PHE* 1.3 63.3 + - - +
12P TYR 3.5 1.3 - - - -
13P ALA* 3.2 6.5 + - + -
14P GLN* 3.0 52.4 + - + +
17P GLU* 3.1 36.0 + - - -
45P THR* 4.8 1.3 - - - +
46P ALA 3.6 11.4 - - - +
47P ASN* 3.4 22.4 - - + -
48P TYR* 3.5 24.0 - + + -
51P ARG* 3.5 17.0 - - - +
139P THR* 4.6 4.1 + - - +
160P PRO* 5.3 2.5 - - + -
401P DDS 2.8 32.7 + - - -
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Residues in contact with PHE 11 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8P PHE* 3.6 31.4 - + + -
9P ASP 2.7 9.3 + - - -
10P TYR* 1.3 71.8 - - - +
12P TYR* 1.3 80.3 + + + +
14P GLN* 3.3 1.2 + - - -
15P VAL* 2.9 49.3 + - + +
81P TYR* 3.5 34.3 - - + -
84P VAL* 4.1 8.7 - - + -
85P SER* 3.8 22.4 - - - -
88P ILE* 4.2 5.8 - - + -
104P ILE* 4.2 6.7 - - + -
105P ASP* 3.7 33.2 - - + +
138P ILE* 4.5 11.2 - - + -
401P DDS 3.0 8.2 + - - +
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Residues in contact with TYR 12 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10P TYR 3.2 1.0 + - - -
11P PHE* 1.3 82.0 - + + +
13P ALA* 1.3 62.7 + - - +
15P VAL 3.4 0.3 + - - -
16P GLU* 3.2 25.5 + - - +
30P VAL* 4.1 9.0 - - + -
44P ALA* 4.5 0.7 - - + -
45P THR* 3.6 22.4 - - + +
76P MET* 3.3 39.5 - - + -
78P LYS* 3.0 30.4 + - + -
81P TYR* 3.3 50.5 - + + -
104P ILE* 3.8 28.4 - - + +
401P DDS 3.9 23.6 + + - -
1801S G 6.0 0.2 + - - -
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Residues in contact with ALA 13 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10P TYR* 3.2 14.1 + - + +
12P TYR* 1.3 78.8 - - - +
14P GLN* 1.3 62.7 + - - +
16P GLU* 3.3 5.2 + - - +
17P GLU* 3.1 24.8 + - - +
28P VAL* 4.1 14.9 - - + +
30P VAL* 3.7 19.9 - - + +
45P THR* 3.9 4.1 - - + +
46P ALA 4.1 4.9 - - - -
47P ASN* 3.8 28.3 - - + +
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Residues in contact with GLN 14 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9P ASP* 2.8 24.9 - - - +
10P TYR* 3.0 40.2 + - + +
11P PHE* 3.7 4.2 - - - +
13P ALA* 1.3 74.3 - - - +
15P VAL* 1.3 58.4 + - - +
17P GLU* 3.2 9.0 + - + +
18P VAL* 2.9 29.4 + - + +
137P LYS 3.8 4.9 + - - -
138P ILE* 3.4 22.8 - - + +
139P THR* 2.7 58.9 + - - +
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Residues in contact with VAL 15 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11P PHE* 2.9 53.1 + - + +
12P TYR 3.7 0.4 - - - +
13P ALA 3.3 0.2 - - - -
14P GLN* 1.3 74.4 - - - +
16P GLU* 1.3 64.4 + - - +
18P VAL* 3.1 7.5 + - - +
19P LEU* 3.0 35.5 + - + +
80P VAL* 4.1 7.4 - - + -
81P TYR* 3.6 32.1 - - + -
84P VAL* 3.9 29.4 - - + -
138P ILE* 4.3 4.5 - - + -
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Residues in contact with GLU 16 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12P TYR 3.2 15.4 + - - +
13P ALA* 3.5 8.5 - - - +
15P VAL* 1.3 76.5 - - - +
17P GLU* 1.3 56.8 + - - +
19P LEU* 3.5 4.5 + - - +
20P ASN* 2.9 31.4 + - - +
23P LEU* 3.5 6.1 - - + +
28P VAL* 4.8 1.1 - - + -
30P VAL* 4.4 8.5 - - + -
74P LEU* 3.8 35.3 - - + +
75P PRO 4.1 2.8 - - - +
77P ARG* 2.8 45.8 + - - +
81P TYR* 2.6 29.0 + - + +
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Residues in contact with GLU 17 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10P TYR* 3.1 39.1 + - - -
13P ALA 3.1 12.8 + - - +
14P GLN* 3.3 10.5 - - + +
15P VAL 3.2 0.4 - - - -
16P GLU* 1.3 72.9 - - - +
18P VAL* 1.3 60.5 + - + +
20P ASN 2.9 7.8 - - - +
21P PRO* 2.9 33.6 - - - +
23P LEU* 4.1 18.4 - - + +
24P LYS* 4.2 30.0 - - + +
25P GLY 5.4 1.2 + - - -
28P VAL* 4.6 4.3 - - + -
47P ASN* 3.0 28.4 + - - +
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Residues in contact with VAL 18 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14P GLN* 2.9 18.8 + - + +
15P VAL* 3.1 10.0 + - - +
17P GLU* 1.3 77.6 - - + +
19P LEU* 1.3 71.1 + - + +
20P ASN 3.5 0.2 + - - -
21P PRO* 3.7 12.7 - - - +
84P VAL* 6.5 0.7 - - + -
136P GLU* 3.9 15.5 - - - +
137P LYS* 3.4 33.2 - - + +
138P ILE* 3.7 15.7 - - + -
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Residues in contact with LEU 19 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15P VAL* 3.0 32.0 + - + +
16P GLU 4.0 3.6 - - - +
18P VAL* 1.3 89.3 - - + +
20P ASN* 1.3 59.2 + - + +
21P PRO* 3.7 4.5 - - - +
77P ARG* 3.6 28.9 - - - +
80P VAL* 3.8 22.7 - - + -
84P VAL* 5.2 6.5 - - + -
87P ARG* 6.3 0.2 - - - +
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Residues in contact with ASN 20 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16P GLU* 2.9 13.2 + - - +
17P GLU 2.9 7.5 - - - +
19P LEU* 1.3 80.3 - - + +
21P PRO* 1.4 64.6 - - - +
22P SER* 2.7 30.8 + - - -
23P LEU* 3.0 39.1 + - + +
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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