Contacts of the helix formed by residues 11 - 22 (chain A) in PDB entry 3GTU
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 GLY 11 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A TYR* 3.8 11.0 - - - -
9A ILE* 3.6 3.9 - - - +
10A ARG* 1.3 88.2 - - - +
12A LEU* 1.3 60.0 + - - -
13A ALA 3.1 2.8 + - - -
14A HIS* 3.3 8.3 + - - +
161A ASP* 4.1 1.9 - - - +
165A ARG* 3.3 27.3 + - - -
207A VAL 3.1 17.4 + - - -
208A PHE* 5.5 3.1 - - - -
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Residues in contact with LEU 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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6A TYR* 3.1 21.4 + - + +
11A GLY* 1.3 70.8 - - - -
13A ALA* 1.3 58.3 + - - +
14A HIS 3.5 0.4 - - - -
15A SER* 4.6 5.2 + - - -
16A ILE* 3.7 17.2 - - - +
59A LEU 4.5 6.1 - - - +
60A PRO* 4.2 15.3 - - + -
72A SER* 3.5 30.6 + - - +
104A MET* 5.0 4.3 - - + -
107A ARG* 3.6 39.3 - - - +
108A MET* 4.5 11.4 - - + -
161A ASP* 5.5 1.1 - - - -
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Residues in contact with ALA 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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4A LEU* 4.7 7.2 - - + -
6A TYR* 3.3 36.6 - - + -
10A ARG 3.2 1.1 + - - +
11A GLY 3.1 1.6 + - - -
12A LEU* 1.3 78.0 - - - +
14A HIS* 1.3 66.5 + - - +
15A SER 3.4 1.6 - - - -
16A ILE* 3.0 13.4 + - - +
17A ARG* 2.9 47.9 + - + +
60A PRO* 4.9 2.2 - - + -
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Residues in contact with HIS 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 ARG* 3.0 44.5 + - + +
11A GLY 3.3 11.3 + - - +
13A ALA* 1.3 74.5 - - - +
15A SER* 1.3 63.5 + - - +
17A ARG* 3.3 10.7 + - - +
18A LEU* 3.1 51.2 + - + +
160A TYR* 3.8 20.4 + + - -
161A ASP* 3.5 27.1 - - + +
196A TYR* 5.8 1.5 + + - -
202A PHE* 4.2 23.6 + + - -
203A LEU 4.0 16.0 + - - -
204A PRO* 4.2 11.0 - - + -
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Residues in contact with SER 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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12A LEU 4.6 4.9 + - - -
13A ALA 3.4 0.6 - - - -
14A HIS* 1.3 76.7 - - - +
16A ILE* 1.3 59.1 + - - +
18A LEU* 3.5 8.3 + - - +
19A LEU* 3.0 28.9 + - - +
76A LEU* 3.9 24.1 - - - +
107A ARG* 3.8 5.9 + - - -
157A PHE* 2.9 37.6 + - - +
158A ILE* 3.6 5.0 - - - -
161A ASP* 3.3 18.7 + - - +
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Residues in contact with ILE 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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4A LEU* 3.7 26.2 - - + -
12A LEU 3.7 19.1 - - - +
13A ALA* 3.0 10.5 + - - +
15A SER* 1.3 73.7 - - - +
17A ARG* 1.3 67.8 + - - +
19A LEU* 3.0 4.0 + - - +
20A LEU* 2.8 31.9 + - + +
60A PRO* 3.9 23.3 - - + -
62A LEU* 5.4 0.2 - - + -
72A SER* 4.6 5.8 - - - +
75A ILE* 3.9 33.2 - - + -
76A LEU* 3.8 24.2 - - + -
79A ILE* 4.1 12.6 - - + -
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Residues in contact with ARG 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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4A LEU* 3.7 16.5 - - + +
6A TYR* 4.2 4.0 - - - +
7A TRP 3.4 16.4 + - - -
9A ILE 2.8 29.9 + - - -
10A ARG* 3.5 16.2 + - - +
13A ALA* 2.9 32.7 + - - +
14A HIS* 3.7 9.3 + - - +
16A ILE* 1.3 73.4 - - - +
18A LEU* 1.3 63.6 + - - +
20A LEU* 3.1 12.0 + - - +
21A GLU* 3.0 29.7 + - - +
27A TYR* 4.2 5.5 + - - +
29A GLU* 3.1 31.3 + - - +
31A LYS* 4.8 3.8 - - - +
196A TYR* 3.6 24.2 - - + +
201A ARG 5.3 1.1 - - - -
202A PHE 4.9 2.7 - - - -
203A LEU* 3.7 26.6 + - - +
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Residues in contact with LEU 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 HIS* 3.1 34.6 + - + +
15A SER* 3.7 9.0 - - - +
17A ARG* 1.3 79.4 - - - +
19A LEU* 1.3 57.9 + - - +
21A GLU* 3.3 3.6 + - - +
22A TYR* 2.9 30.1 + - - +
157A PHE* 3.9 15.0 - - + +
160A TYR* 3.6 33.0 - - + -
187A PHE* 4.0 8.1 - - + -
193A ILE* 4.1 27.3 - - + +
196A TYR* 3.8 30.7 - - + -
197A MET* 5.8 0.2 - - - -
202A PHE* 4.5 10.5 - - + -
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Residues in contact with LEU 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 SER 3.0 18.1 + - - +
16A ILE* 3.0 5.1 + - - +
18A LEU* 1.3 75.6 - - - +
20A LEU* 1.3 60.3 + - - +
22A TYR* 3.4 1.0 + - - +
23A THR* 2.9 31.0 + - + +
76A LEU* 3.7 41.1 - - + +
79A ILE* 4.0 24.9 - - + -
80A ALA 4.3 2.9 - - - +
85A LEU* 3.7 30.5 - - + -
154A PHE* 4.3 13.0 - - + -
157A PHE* 3.7 30.5 - - + -
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Residues in contact with LEU 20 (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 MET* 4.4 14.4 - - - -
4A LEU* 4.1 22.7 - - + -
16A ILE* 2.8 22.6 + - + +
17A ARG* 3.4 7.2 - - - +
19A LEU* 1.3 77.1 - - - +
21A GLU* 1.3 57.9 + - - +
23A THR* 3.0 17.2 + - - -
24A ASP 3.1 0.2 + - - -
25A SER* 3.0 39.4 + - - +
27A TYR* 3.6 47.8 - - + -
62A LEU* 4.9 4.3 - - + -
79A ILE* 3.5 28.5 - - + -
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Residues in contact with GLU 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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17A ARG 3.0 17.9 + - - +
18A LEU 3.6 7.2 - - - +
20A LEU* 1.3 72.0 - - - +
22A TYR* 1.3 66.2 + - - +
24A ASP* 2.8 26.1 + - - +
25A SER 5.7 0.2 - - - -
27A TYR* 2.8 29.7 + - - +
192A LYS* 4.2 10.7 - - - +
193A ILE* 5.5 1.3 - - + -
196A TYR* 3.4 44.8 - - + +
201A ARG* 3.3 32.9 + - - -
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Residues in contact with TYR 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 LEU 2.9 17.2 + - - +
19A LEU 3.7 3.8 - - - +
21A GLU* 1.3 76.0 - - - +
23A THR* 1.3 61.6 + - + +
85A LEU* 4.1 28.0 - - + +
152A ILE* 3.4 28.5 - - + +
157A PHE* 3.8 24.2 - + + -
190A LEU* 3.8 38.5 - - + +
192A LYS* 3.1 53.9 + - + +
193A ILE* 4.1 12.5 - - + +
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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