Contacts of the helix formed by residues 1 - 16 (chain A) in PDB entry 4K06
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 SER 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 LEU* 1.3 64.2 + - - +
3A PHE* 3.1 29.5 + - - +
4A GLU* 2.5 34.0 + - - +
5A LEU* 2.9 22.5 + - - +
69A PRO 3.5 16.9 + - - -
70A LYS 3.2 17.3 - - - -
71A LYS* 3.6 15.3 - - - -
72A ASP 2.7 27.4 + - - -
73A ARG* 3.6 2.9 - - - +
74A TYR* 3.3 17.0 - - - -
96A LEU* 4.7 0.8 - - - +
100A ASP* 4.2 1.6 - - - +
32B LEU* 5.7 0.7 - - - -
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Residues in contact with LEU 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 SER* 1.3 74.5 - - - +
3A PHE* 1.3 55.7 + - + +
5A LEU* 4.0 22.0 - - + -
6A GLY* 2.7 31.7 + - - -
53A TYR* 6.0 1.8 - - + +
69A PRO 4.0 1.7 + - - +
70A LYS* 3.1 31.9 + - + +
201A PGE 3.6 23.9 - - - +
32B LEU* 3.8 36.6 - - + +
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Residues in contact with PHE 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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1A SER* 3.3 17.5 - - - +
2A LEU* 1.3 79.4 - - + +
4A GLU* 1.3 65.3 + - - +
6A GLY 4.0 0.3 - - - -
7A LYS* 3.0 30.2 + - - +
71A LYS 5.9 0.2 - - - -
73A ARG* 4.1 26.5 - - + -
201A PGE 4.3 15.9 - - - +
32B LEU* 3.9 48.9 - - + -
122B LYS* 5.4 12.8 - - + -
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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
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1A SER* 2.5 44.2 + - - +
3A PHE* 1.3 81.4 - - - +
5A LEU* 1.3 60.2 + - - +
7A LYS* 3.3 7.2 + - + +
8A MET* 2.9 36.5 + - - +
73A ARG* 3.3 21.2 - - - +
74A TYR* 3.4 56.9 + - + +
76A TYR* 4.0 14.6 - - + -
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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
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1A SER 2.9 16.1 + - - +
2A LEU* 3.7 18.8 - - + +
4A GLU* 1.3 77.5 - - - +
6A GLY* 1.3 62.9 + - - +
8A MET* 3.7 2.0 - - - +
9A ILE* 3.1 42.0 + - + +
49A HIS* 3.5 20.9 - - + +
53A TYR* 3.7 8.3 - - + +
100A ASP* 3.8 30.4 + - + +
103A VAL* 3.6 30.5 - - + -
201A PGE 4.3 15.9 - - - +
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Residues in contact with GLY 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 LEU 2.7 17.1 + - - -
5A LEU* 1.3 73.7 - - - +
7A LYS* 1.3 56.6 + - - +
9A ILE* 3.3 0.9 + - - -
10A LEU* 2.9 24.8 + - - +
19A PRO* 3.3 23.5 - - - +
201A PGE 3.3 32.3 + - - -
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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
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3A PHE 3.0 20.6 + - - +
4A GLU* 3.6 4.5 - - + +
6A GLY* 1.3 75.1 - - - +
8A MET* 1.3 57.5 + - - +
10A LEU* 3.3 14.1 + - + +
11A GLN* 2.9 51.9 + - + +
76A TYR* 3.2 28.1 + - + +
201A PGE 4.1 5.4 - - - -
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Residues in contact with MET 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 15.9 + - - +
5A LEU 3.7 4.0 - - - +
7A LYS* 1.3 72.1 - - - +
9A ILE* 1.3 60.2 - - - +
11A GLN* 3.1 9.5 + - - +
12A GLU* 2.8 34.7 + - - +
74A TYR* 3.4 20.0 - - - +
76A TYR* 3.5 37.2 - - + +
83A ILE* 3.6 23.8 - - + -
97A CYS* 3.6 23.6 - - - +
100A ASP* 3.5 11.4 - - - +
101A LYS* 3.4 31.0 - - - -
104A ALA* 3.7 8.5 - - + -
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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 LEU* 3.1 37.4 + - + +
6A GLY 3.6 6.7 - - - +
7A LYS 3.3 0.2 - - - -
8A MET* 1.3 74.6 - - - +
10A LEU* 1.3 52.9 + - - +
13A THR* 2.5 47.9 + - + +
19A PRO* 4.0 11.9 - - + -
23A TYR* 3.4 40.6 - - + -
103A VAL* 4.9 1.6 - - + -
104A ALA* 3.9 16.6 - - + +
107A LEU* 3.9 20.6 - - + -
201A PGE 4.1 17.5 - - - +
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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 GLY 2.9 13.6 + - - +
7A LYS* 3.4 16.8 - - + +
9A ILE* 1.3 78.6 - - - +
11A GLN* 1.3 60.2 + - + +
16A GLY* 2.8 42.6 + - - +
17A LYS 3.6 22.8 + - - +
18A ASN* 4.5 2.5 - - - +
19A PRO* 4.2 6.3 - - + -
201A PGE 5.0 10.3 - - - +
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Residues in contact with GLN 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 LYS* 2.9 33.1 + - + +
8A MET* 3.1 11.0 + - - +
10A LEU* 1.3 82.0 - - + +
12A GLU* 1.3 60.8 + - + +
16A GLY* 4.5 1.4 + - - -
76A TYR* 3.0 37.6 + - - -
78A TRP* 3.8 61.1 - - + +
83A ILE* 3.9 2.9 - - - +
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Residues in contact with GLU 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 MET 2.8 19.1 + - - +
9A ILE 4.2 0.7 - - - +
11A GLN* 1.3 80.6 - - - +
13A THR* 1.3 62.3 + - - +
78A TRP* 3.7 17.4 - - - -
81A LYS 4.6 1.7 - - - +
83A ILE* 3.5 24.9 + - + +
104A ALA* 3.2 36.1 - - + +
105A ILE* 3.9 11.7 - - - +
108A ARG* 2.6 65.5 + - + +
202A SO4 4.1 8.6 + - - -
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Residues in contact with THR 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* 2.5 36.1 + - + +
12A GLU* 1.3 74.6 - - - +
16A GLY* 1.3 56.7 + - - +
17A LYS* 2.9 33.1 + - - +
23A TYR* 3.9 13.0 - - + +
104A ALA 4.2 3.8 - - - +
107A LEU* 3.8 29.2 - - + -
108A ARG* 3.8 11.0 - - - +
111A LEU* 3.6 28.1 - - + +
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Residues in contact with GLY 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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10A LEU* 2.8 29.1 + - - +
11A GLN 4.4 1.3 + - - -
12A GLU 3.6 1.0 - - - -
13A THR* 1.3 77.0 - - - +
17A LYS* 1.3 64.0 + - - +
18A ASN 4.1 0.5 + - - -
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Residues in contact with LYS 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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10A LEU* 3.6 15.3 - - - -
13A THR* 2.9 32.3 + - - +
16A GLY* 1.3 81.4 - - - +
18A ASN* 1.3 64.9 + - - +
19A PRO* 3.0 11.1 - - - +
22A SER* 3.9 27.8 - - - +
23A TYR* 4.2 4.0 - - + +
111A LEU* 4.3 25.8 - - + -
114A TYR* 6.5 0.2 - - + -
119A ARG* 5.6 0.2 - - - +
204A SO4 4.2 16.8 + - - +
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Residues in contact with ASN 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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10A LEU* 4.5 3.9 - - - +
16A GLY 4.1 1.2 + - - -
17A LYS* 1.3 69.0 - - - +
19A PRO* 1.3 70.5 - - - +
20A ALA* 3.3 12.6 + - - +
21A LYS* 3.2 29.7 + - + +
22A SER* 3.1 23.2 + - - -
201A PGE 5.3 3.4 + - - -
119B TYR* 4.2 19.6 + - - +
121B LEU* 5.1 9.3 - - - +
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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