Contacts of the helix formed by residues 20 - 35 (chain A) in PDB entry 2GWU
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 ASP 20 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A LYS* 3.0 40.6 + - + +
19A LEU* 1.3 74.2 - - - +
21A LEU* 1.3 65.1 + - - +
22A GLU* 3.5 20.3 + - - +
23A THR* 3.1 23.7 + - - -
24A LEU 3.2 16.1 + - - -
84A PHE* 3.5 8.3 - - - -
114A ILE* 3.2 13.5 - - - -
115A ASP* 4.7 6.1 - - + +
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Residues in contact with LEU 21 (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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20A ASP* 1.3 74.5 - - + +
22A GLU* 1.3 71.6 + - + +
24A LEU* 3.0 20.1 + - + +
25A THR* 3.2 17.7 + - + +
114A ILE* 3.7 13.0 - - + +
115A ASP 5.0 1.0 + - - +
117A ARG* 5.5 0.4 - - + -
119A TYR* 3.2 51.6 - - + +
133A GLN* 5.6 7.2 - - - +
134A PRO* 5.3 6.5 - - + -
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Residues in contact with GLU 22 (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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18A LYS* 3.4 26.2 + - - -
20A ASP* 3.2 15.5 + - - +
21A LEU* 1.3 83.0 - - + +
23A THR* 1.3 60.9 + - - +
25A THR* 2.7 33.0 - - + +
26A ASP* 3.1 11.9 + - - +
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Residues in contact with THR 23 (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 TYR* 5.9 0.7 - - + -
17A ASN* 2.9 47.2 - - + +
18A LYS* 2.6 28.1 + - - +
20A ASP* 3.1 11.6 + - - -
21A LEU 3.2 0.2 - - - -
22A GLU* 1.3 80.5 - - - +
24A LEU* 1.3 63.0 + - - +
26A ASP* 3.1 9.7 + - + +
27A ILE* 2.9 35.8 + - + +
84A PHE* 4.6 6.3 - - + -
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Residues in contact with LEU 24 (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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20A ASP 3.2 9.2 + - - +
21A LEU* 3.0 15.1 + - + +
23A THR* 1.3 80.7 - - - +
25A THR* 1.3 61.7 + - - +
27A ILE* 3.3 2.8 + - - -
28A LEU* 2.7 48.0 + - + +
79A LEU* 3.9 35.9 - - + -
84A PHE* 4.0 19.2 - - + -
112A VAL* 5.0 6.1 - - + -
114A ILE* 5.6 2.2 - - + -
119A TYR* 4.2 18.4 - - + -
121A VAL* 3.8 11.2 - - + -
134A PRO* 3.2 32.1 - - + -
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Residues in contact with THR 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LEU* 3.2 12.0 + - + -
22A GLU* 2.7 30.7 - - - +
24A LEU* 1.3 78.8 - - - +
26A ASP* 1.3 73.8 + - - +
28A LEU* 3.3 3.3 + - - +
29A GLN* 3.1 26.8 + - - +
132A TRP* 5.1 4.2 + - - +
133A GLN* 4.1 20.7 + - - +
134A PRO* 3.9 16.5 - - - +
146A VAL* 5.8 2.4 - - - +
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Residues in contact with ASP 26 (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 TYR* 5.0 11.9 - - + -
22A GLU* 3.6 13.0 - - - +
23A THR* 3.1 11.9 + - + +
25A THR* 1.3 93.0 - - - +
27A ILE* 1.3 59.6 + - + +
29A GLN* 3.3 13.9 + - - +
30A HIS* 2.7 51.1 + - + -
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Residues in contact with ILE 27 (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 TYR* 4.1 7.6 - - + +
7A LEU* 5.0 13.9 - - + -
10A ILE* 3.2 16.7 - - + +
12A TYR* 6.1 2.2 - - + -
17A ASN* 4.6 9.0 - - - +
23A THR* 2.9 37.9 + - + +
24A LEU* 3.9 3.6 - - - +
26A ASP* 1.3 76.3 - - + +
28A LEU* 1.3 68.3 + - + +
30A HIS* 3.2 5.8 + - - +
31A GLN* 2.8 22.2 + - + +
75A LEU* 3.5 28.7 - - + -
78A ALA* 5.8 2.7 - - + -
79A LEU* 3.9 23.8 - - + -
82A ILE* 4.8 12.8 - - + -
84A PHE* 5.3 0.4 - - + -
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Residues in contact with LEU 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU* 2.7 50.6 + - + +
25A THR 3.7 6.3 - - - +
27A ILE* 1.3 80.4 - - + +
29A GLN* 1.3 56.9 + - - +
31A GLN* 3.2 4.0 + - - +
32A ILE* 2.9 36.5 + - + +
75A LEU* 4.1 12.1 - - + -
121A VAL* 3.0 33.0 - - + -
122A ASP 4.5 5.4 - - - +
123A ALA* 4.6 12.3 - - + +
131A MET 4.8 8.7 - - - +
132A TRP 3.7 14.8 - - - +
133A GLN 5.1 0.9 - - - -
134A PRO* 3.7 18.2 - - + -
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Residues in contact with GLN 29 (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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25A THR* 3.1 13.2 + - - +
26A ASP* 3.6 16.4 + - - +
28A LEU* 1.3 77.7 - - - +
30A HIS* 1.3 71.6 + - - +
32A ILE* 2.7 32.4 - - - +
33A ARG* 2.8 58.3 + - - +
132A TRP* 3.6 26.6 + - + +
146A VAL* 5.0 4.3 - - - +
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Residues in contact with HIS 30 (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 ILE* 2.9 37.5 - - + +
11A GLY* 4.5 11.5 + - - -
12A TYR* 3.6 34.3 - + + +
26A ASP* 2.7 44.4 + - + -
27A ILE* 4.0 3.2 + - - +
29A GLN* 1.3 87.1 + - - +
31A GLN* 1.3 60.5 + - - +
33A ARG* 3.3 20.7 + - - +
34A ALA* 3.0 25.6 + - - +
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Residues in contact with GLN 31 (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 TYR* 2.7 40.6 + - - +
10A ILE* 3.1 13.9 - - + +
27A ILE* 2.8 18.8 + - + +
28A LEU* 3.6 6.1 - - + +
30A HIS* 1.3 76.5 - - - +
32A ILE* 1.3 64.1 + - - +
34A ALA* 4.4 0.8 - - - +
35A VAL* 2.7 58.4 + - - +
59A VAL* 5.3 0.2 - - - +
71A VAL* 5.2 8.0 - - + +
74A LEU* 4.8 4.7 - - - +
75A LEU* 5.5 5.6 - - + -
123A ALA* 4.2 23.6 - - + -
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Residues in contact with ILE 32 (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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28A LEU* 2.9 28.1 + - + +
29A GLN* 2.7 24.5 - - - +
31A GLN* 1.3 78.2 - - + +
33A ARG* 1.3 69.2 + - + +
35A VAL 4.1 8.1 - - - +
123A ALA* 5.3 3.1 - - + -
130A GLN* 3.4 39.5 + - - +
131A MET 4.4 6.7 - - - +
132A TRP* 2.9 65.3 - - + +
225A LEU* 4.1 2.6 - - - +
226A GLN* 3.1 29.5 + - + +
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Residues in contact with ARG 33 (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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29A GLN* 2.8 67.9 + - - +
30A HIS* 3.3 19.9 + - - +
31A GLN 3.2 0.4 - - - -
32A ILE* 1.3 85.6 - - + +
34A ALA* 1.3 60.7 + - + +
36A PRO* 5.5 0.3 - - - +
132A TRP* 3.9 9.0 - - - -
225A LEU* 4.3 17.2 - - - +
226A GLN 3.1 16.6 - - - +
227A THR* 4.2 13.4 - - + +
228A PRO* 3.4 29.0 - - - +
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Residues in contact with ALA 34 (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 ARG* 3.5 34.1 + - - +
10A ILE* 3.6 17.3 - - + +
30A HIS 3.0 18.8 + - - +
31A GLN 3.2 1.5 + - - +
33A ARG* 1.3 79.2 - - + +
35A VAL* 1.4 67.8 + - + +
36A PRO* 3.5 8.5 - - - +
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Residues in contact with VAL 35 (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 TYR* 5.6 0.7 - - + -
9A ARG* 3.5 28.5 - - + +
31A GLN* 2.7 43.9 + - - +
32A ILE* 4.1 8.3 - - - +
33A ARG 5.1 0.7 - - - -
34A ALA* 1.4 78.4 - - + +
36A PRO* 1.3 71.2 - - + +
37A PHE 4.0 0.5 + - - -
59A VAL* 3.2 35.2 - - + +
64A ARG 3.7 2.7 - - - +
65A GLY* 3.5 20.4 - - - -
66A GLY 4.7 0.9 - - - +
71A VAL* 5.1 8.6 - - + +
74A LEU* 5.4 0.7 - - + -
130A GLN* 5.9 0.5 + - - -
225A LEU* 5.4 0.3 - - - -
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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