Contacts of the helix formed by residues 3 - 21 (chain A) in PDB entry 4GGF
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 THR 3 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET 5.1 0.4 - - - +
2A LEU* 1.3 76.2 - - - +
4A GLU* 1.3 59.7 + - - +
5A LEU 3.4 3.2 + - - -
6A GLU* 2.9 30.4 + - - +
7A LYS* 2.9 28.0 + - - +
43C LYS 3.6 19.3 - - - +
44C ASP* 2.6 36.5 + - - +
46C GLN* 3.9 17.9 - - + +
47C ASN* 4.0 1.8 - - - +
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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
----------------------------------------------------------
1A MET* 5.3 1.9 - - - +
2A LEU 5.0 0.9 - - - +
3A THR* 1.3 73.8 - - - +
5A LEU* 1.3 57.8 + - - +
7A LYS* 3.4 31.9 + - - +
8A ALA* 2.9 27.9 + - - +
14C THR* 3.8 12.9 - - + +
44C ASP* 5.7 0.2 + - - -
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Residues in contact with LEU 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A THR* 3.2 7.2 + - - +
4A GLU* 1.3 79.4 - - - +
6A GLU* 1.3 63.0 + - - +
8A ALA* 3.1 13.2 + - + +
9A LEU* 3.1 16.4 + - + +
14C THR* 4.1 6.8 - - + +
15C ILE* 3.9 40.2 - - + +
18C THR* 4.1 23.1 + - + +
40C LEU* 4.2 8.3 - - + -
44C ASP* 3.9 22.1 + - + +
45C LEU* 3.7 30.5 - - + -
79C PHE* 5.0 1.3 - - + -
83C MET* 4.0 20.6 - - - -
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Residues in contact with GLU 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A LEU* 3.5 7.3 - - + +
3A THR* 2.9 33.9 + - - +
5A LEU* 1.3 77.7 - - - +
7A LYS* 1.3 60.4 + - - +
9A LEU* 3.2 6.2 + - - +
10A ASN* 3.0 21.2 + - - +
44C ASP 3.5 7.0 - - - +
45C LEU* 3.3 16.3 - - + -
47C ASN* 2.8 43.0 + - - +
48C PHE* 2.8 63.4 + - + -
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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
----------------------------------------------------------
1A MET* 3.3 36.9 - - - +
2A LEU* 3.4 32.8 - - + +
3A THR 2.9 21.2 + - - +
4A GLU* 3.7 30.2 + - - +
6A GLU* 1.3 71.6 - - - +
8A ALA* 1.3 57.8 + - - +
10A ASN* 3.3 7.5 + - - +
11A SER* 2.8 29.9 + - - -
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Residues in contact with ALA 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 2.9 14.6 + - - +
5A LEU* 3.1 13.9 + - + +
7A LYS* 1.3 78.0 - - - +
9A LEU* 1.3 58.4 + - - +
11A SER* 3.2 3.7 + - - -
12A ILE* 3.0 31.5 + - - +
11C ASN* 3.6 25.9 - - - +
14C THR* 3.9 26.7 - - + +
15C ILE* 5.0 2.2 - - + -
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Residues in contact with LEU 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU* 3.1 15.2 + - + +
6A GLU 3.2 5.8 + - - +
8A ALA* 1.3 72.7 - - - +
10A ASN* 1.3 67.3 + - - +
12A ILE* 3.1 18.1 + - + +
13A ILE* 3.3 8.6 + - - +
15C ILE* 3.9 30.7 - - + -
45C LEU* 4.6 6.5 - - + -
48C PHE* 4.0 19.5 - - + -
83C MET* 4.1 28.9 - - + +
86C LEU* 3.9 30.5 - - + -
87C THR* 3.6 30.7 - - - +
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Residues in contact with ASN 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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2A LEU* 3.5 30.1 - - - +
6A GLU 3.0 11.1 + - - +
7A LYS* 3.8 5.2 - - - +
9A LEU* 1.3 76.4 - - - +
11A SER* 1.3 62.4 + - - +
13A ILE* 3.1 10.9 + - - +
14A ASP* 3.1 25.1 + - - +
48C PHE* 3.6 14.0 - - - -
90C SER* 2.8 31.8 + - - -
94C MET* 3.6 17.2 - - + +
108C GLY* 5.3 0.2 - - - -
109C LEU 5.0 0.4 + - - -
111C GLU* 4.3 9.7 + - - -
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Residues in contact with SER 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LYS 2.8 17.9 + - - -
8A ALA* 3.5 0.4 - - - -
9A LEU 3.2 0.2 - - - -
10A ASN* 1.3 74.1 - - - +
12A ILE* 1.3 57.7 + - - +
14A ASP* 3.1 12.5 + - - +
15A VAL* 2.8 29.3 + - - +
7C GLN* 2.7 26.3 + - - +
11C ASN* 2.7 38.7 + - - -
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Residues in contact with ILE 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 ALA 3.0 20.7 + - - +
9A LEU* 3.1 16.3 + - + +
11A SER* 1.3 74.8 - - - +
13A ILE* 1.3 63.5 + - - +
15A VAL* 3.3 7.6 + - - +
16A TYR 3.2 16.6 + - - -
68A PHE* 4.9 0.9 - - + -
71A PHE* 3.7 26.5 - - + -
72A LEU* 4.4 3.8 - - + -
75A VAL* 3.9 26.9 - - + -
8C LEU* 4.0 10.8 - - + -
11C ASN* 3.8 20.6 - - + +
12C ILE* 5.0 1.6 - - + -
15C ILE* 4.0 27.6 - - + -
87C THR* 4.2 15.7 - - + +
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Residues in contact with ILE 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU 3.3 3.8 + - - +
10A ASN* 3.1 31.5 + - - +
12A ILE* 1.3 75.8 - - - +
14A ASP* 1.3 66.4 + - - +
16A TYR* 3.2 3.6 + - - +
17A HIS* 2.8 50.6 + - + +
68A PHE* 3.7 15.7 - - + -
87C THR* 3.5 36.3 - - + +
90C SER* 3.9 1.8 - - - -
91C HIS* 3.7 27.8 - - + +
94C MET* 3.7 13.5 - - + -
105C HIS* 3.9 11.4 - - + -
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Residues in contact with ASP 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ASN* 3.1 15.3 + - - +
11A SER* 3.1 14.8 + - - +
13A ILE* 1.3 81.8 - - - +
15A VAL* 1.3 62.8 + - - +
17A HIS* 3.1 8.2 + - - +
18A LYS* 3.0 26.6 + - + +
7C GLN* 4.0 12.3 + - - +
94C MET* 5.9 2.1 - - - +
105C HIS* 5.2 6.6 + - - -
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Residues in contact with VAL 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A SER 2.8 23.1 + - - +
12A ILE* 3.6 10.8 - - - +
14A ASP* 1.3 72.1 - - - +
16A TYR* 1.3 63.6 + - - +
18A LYS* 3.2 13.8 + - - +
19A TYR* 3.1 26.2 - - + -
37A LEU* 5.2 0.7 - - + -
41A GLU* 3.7 32.5 - - + +
71A PHE* 4.6 7.0 - - + -
7C GLN* 3.5 33.2 - - + +
8C LEU* 4.0 24.7 - - + +
11C ASN* 4.0 7.9 - - - +
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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 ILE 3.2 2.0 + - - -
13A ILE 3.2 9.3 + - - +
15A VAL* 1.3 79.8 - - - +
17A HIS* 1.3 68.2 + + - +
19A TYR* 3.0 10.1 + - - +
20A SER* 2.8 44.3 + - - -
27A HIS* 3.0 35.3 + + - -
28A ALA 3.4 0.7 + - - -
29A VAL* 3.4 19.9 + - + -
37A LEU* 5.0 1.6 - - + -
66A VAL* 2.7 23.8 + - + -
67A ASN* 3.1 19.4 - - - -
68A PHE* 3.5 37.0 - + + -
71A PHE* 3.6 39.5 - + + -
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Residues in contact with HIS 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 ILE* 2.8 30.8 + - + +
14A ASP* 3.1 10.7 + - - +
16A TYR* 1.3 90.1 - + + +
18A LYS* 1.3 65.6 + - - +
20A SER* 3.3 16.8 - - - -
21A LEU* 3.0 42.0 + - + +
26A PHE 4.2 0.9 - - - -
27A HIS* 3.4 6.4 + + - -
68A PHE* 4.9 1.1 - + - -
91C HIS* 3.1 22.6 + + - -
103C HIS* 3.2 28.9 + + - -
105C HIS* 3.3 12.8 + + + -
201C MN 2.3 22.8 + - - -
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Residues in contact with LYS 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 ASP* 3.0 20.6 + - + +
15A VAL* 3.4 10.3 - - - +
17A HIS* 1.3 78.4 - - - +
19A TYR* 1.3 75.1 + - + +
21A LEU* 5.2 0.7 - - - +
22A ILE* 3.5 17.5 + - - +
36A LYS* 5.0 3.1 + - - -
40A THR* 5.1 2.8 - - - +
41A GLU* 2.8 30.5 + - - -
7C GLN* 3.4 27.6 + - - +
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Residues in contact with TYR 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 VAL* 3.1 21.5 - - + -
16A TYR 3.0 5.1 + - - +
18A LYS* 1.3 94.2 - - + +
20A SER* 1.3 63.9 + - - +
21A LEU 3.3 2.0 - - - -
22A ILE* 3.3 25.4 + - + +
23A LYS 4.9 0.2 + - - -
29A VAL* 4.0 13.7 - - + -
33A ASP* 4.0 27.3 - - + +
36A LYS* 3.6 41.5 - - + -
37A LEU* 3.6 34.8 - - + -
40A THR* 3.2 21.3 - - - +
41A GLU* 2.7 37.5 + - + -
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Residues in contact with SER 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A TYR* 2.8 43.1 + - - -
17A HIS* 3.3 19.6 - - - -
19A TYR* 1.3 77.6 - - - +
21A LEU* 1.3 61.3 + - - +
22A ILE 3.2 1.3 + - - -
23A LYS 3.5 6.4 - - - +
25A ASN 3.2 21.3 - - - +
26A PHE* 2.7 26.4 + - - +
28A ALA 3.5 14.3 - - - +
29A VAL* 3.7 5.1 - - - +
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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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17A HIS* 3.0 33.2 + - + +
18A LYS 5.2 0.7 - - - +
20A SER* 1.3 78.8 - - - +
22A ILE* 1.3 64.4 + - - +
23A LYS* 3.4 2.1 - - - -
26A PHE* 3.6 35.2 - - + +
103C HIS* 3.8 29.6 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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