Contacts of the helix formed by residues 12 - 30 (chain A) in PDB entry 4G98
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 12 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A GLN* 1.3 76.0 - - - +
13A LEU* 1.3 66.0 + - - +
14A SER* 4.2 4.5 - - - +
15A GLU* 3.1 24.6 + - + +
16A ALA* 2.8 20.1 + - - +
187A ASN* 3.6 32.7 + - - +
196A LYS* 4.2 0.4 - - - -
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Residues in contact with LEU 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A GLN 3.7 2.0 + - - -
12A ASP* 1.3 70.4 - - - +
14A SER* 1.3 58.2 + - - +
16A ALA* 3.6 4.7 - - + +
17A LEU* 2.9 36.5 + - + +
130A VAL* 4.4 5.6 - - + -
186A MET* 3.7 37.9 - - + +
187A ASN* 3.1 11.7 + - - +
189A LEU* 4.1 9.4 - - + -
191A MET* 3.7 29.6 - - + -
196A LYS* 3.9 30.0 - - + +
199A VAL* 4.0 24.9 - - + -
200A THR* 4.8 4.5 - - + -
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Residues in contact with SER 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU* 1.3 74.2 - - - +
15A GLU* 1.3 66.8 + - - +
17A LEU* 3.9 2.8 - - - +
18A LYS* 3.3 26.2 + - - +
134A TYR* 4.7 2.7 - - - -
183A ARG* 3.9 40.1 + - - +
186A MET* 3.9 16.6 - - - +
187A ASN* 2.8 34.0 + - - -
301A HEM 4.4 4.0 - - - +
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Residues in contact with GLU 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A GLN* 4.2 14.9 - - + +
12A ASP* 3.1 29.7 + - + +
14A SER* 1.3 85.5 + - - +
16A ALA* 1.3 64.8 + - - +
17A LEU 3.1 1.1 - - - -
18A LYS* 3.2 10.6 + - + +
19A GLU* 3.0 27.0 + - - +
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Residues in contact with ALA 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A GLN* 3.7 28.5 - - - +
12A ASP 2.8 13.1 + - - +
13A LEU* 3.6 8.7 - - - +
15A GLU* 1.3 74.9 - - - +
17A LEU* 1.3 56.7 + - - +
19A GLU* 3.9 1.7 - - - +
20A ALA* 2.9 32.1 + - - +
196A LYS* 4.1 23.6 - - + -
200A THR* 4.0 11.5 - - + +
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Residues in contact with LEU 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 LEU* 2.9 30.0 + - + +
14A SER 3.9 3.4 - - - +
16A ALA* 1.3 73.8 - - - +
18A LYS* 1.3 60.3 + - - +
20A ALA* 3.3 1.3 + - - -
21A THR* 2.6 39.5 + - - +
130A VAL* 4.7 2.0 - - + +
131A ALA* 5.1 0.9 - - - -
134A TYR* 3.8 29.8 - - + -
186A MET* 3.1 35.7 - - + -
199A VAL* 4.2 12.8 - - + -
200A THR* 4.1 18.2 - - + -
203A ALA* 3.4 33.4 - - + -
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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 SER 3.3 13.2 + - - +
15A GLU* 3.2 10.0 + - + +
17A LEU* 1.3 79.7 - - - +
19A GLU* 1.3 62.1 + - - +
21A THR* 3.5 1.8 + - - -
22A LYS* 3.1 27.1 + - + +
134A TYR* 3.3 9.8 + - - -
183A ARG* 4.9 7.7 - - - +
301A HEM 3.3 68.5 + - + +
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Residues in contact with GLU 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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11A GLN* 3.2 26.0 + - - +
15A GLU* 3.0 15.1 + - - +
16A ALA* 3.9 2.5 - - - +
18A LYS* 1.3 80.1 - - - +
20A ALA* 1.3 61.0 + - - +
22A LYS* 3.2 42.6 - - - +
23A GLU* 5.0 4.3 + - - +
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Residues in contact with ALA 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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16A ALA 2.9 20.9 + - - +
17A LEU* 3.9 3.8 - - - +
19A GLU* 1.3 75.9 - - - +
21A THR* 1.3 60.1 + - + +
22A LYS 3.6 0.2 - - - -
23A GLU* 5.0 6.0 + - - +
24A VAL* 4.7 1.9 + - - +
200A THR* 3.8 27.6 - - - +
204A LYS* 3.7 31.8 - - - +
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Residues in contact with THR 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 LEU 2.6 23.1 + - - +
18A LYS 3.5 4.2 + - - -
19A GLU 3.2 0.2 - - - -
20A ALA* 1.3 81.5 - - + +
22A LYS* 1.3 59.4 + - - +
23A GLU 3.3 3.1 - - - -
24A VAL* 3.3 8.7 - - + +
25A HIS* 2.9 29.7 + - - +
134A TYR* 3.5 16.4 + - + -
203A ALA* 3.7 33.0 - - + -
204A LYS* 4.3 4.3 - - + +
207A PHE* 3.6 30.9 - - + -
301A HEM 5.6 0.9 - - - +
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Residues in contact with LYS 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LYS* 3.1 12.6 + - + +
19A GLU* 3.2 41.3 - - - +
20A ALA 3.6 0.4 - - - -
21A THR* 1.3 76.7 - - - +
23A GLU* 1.3 76.8 + - + +
25A HIS* 3.5 7.4 + - - +
26A ILE* 3.3 30.7 + - + +
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Residues in contact with GLU 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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19A GLU 5.2 3.0 - - - +
20A ALA 5.0 5.9 + - - +
21A THR 3.3 0.4 - - - -
22A LYS* 1.3 94.0 - - + +
24A VAL* 1.3 63.4 + - - +
26A ILE* 3.1 22.3 + - + +
27A ARG* 3.1 30.0 + - - +
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Residues in contact with VAL 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ALA 4.7 1.7 + - - +
21A THR* 3.3 26.9 - - + +
23A GLU* 1.3 76.2 - - - +
25A HIS* 1.3 59.2 + - - +
27A ARG* 3.2 29.0 + - - +
28A ALA* 2.8 28.4 + - - +
204A LYS* 4.7 19.3 - - + +
207A PHE* 3.7 35.4 - - + -
208A LEU 4.8 0.9 - - - +
211A ILE* 3.9 14.8 - - + -
303A FMT 3.7 12.3 - - - +
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Residues in contact with HIS 25 (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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21A THR* 2.9 19.3 + - - +
22A LYS* 3.6 9.2 - - - +
23A GLU 3.2 0.2 - - - -
24A VAL* 1.3 77.6 - - - +
26A ILE* 1.3 58.2 + - + +
28A ALA* 3.1 2.5 + - - +
29A GLU* 2.9 63.8 + - + +
207A PHE* 3.8 13.7 - + + -
301A HEM 2.1 92.1 + + + -
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Residues in contact with ILE 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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22A LYS* 3.3 19.0 + - + +
23A GLU* 3.1 12.4 + - + +
25A HIS* 1.3 76.7 - - - +
27A ARG* 1.3 66.1 + - + +
29A GLU* 3.5 15.3 + - - +
30A ASN* 2.8 40.6 + - - +
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Residues in contact with ARG 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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23A GLU* 3.1 29.7 + - - +
24A VAL* 3.2 26.4 + - - +
26A ILE* 1.3 82.2 - - + +
28A ALA* 1.3 61.5 + - - +
30A ASN* 3.1 14.5 + - - +
31A SER* 3.2 11.6 + - - -
204A LYS* 6.4 0.2 - - - +
211A ILE* 4.3 11.8 - - + +
303A FMT 2.8 40.6 + - - +
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Residues in contact with ALA 28 (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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24A VAL 2.8 19.9 + - - +
25A HIS* 3.1 4.7 + - - +
27A ARG* 1.3 72.0 - - - +
29A GLU* 1.3 59.7 + - - +
30A ASN 3.2 0.3 + - - -
31A SER* 3.0 25.3 + - - -
34A MET* 3.7 9.0 - - - +
207A PHE* 4.2 12.6 - - + +
211A ILE* 3.7 25.0 - - + +
214A PHE* 4.4 1.8 - - + -
301A HEM 3.8 26.9 - - + -
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Residues in contact with GLU 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 HIS* 2.9 50.3 + - + +
26A ILE* 3.6 21.5 - - - +
28A ALA* 1.3 74.9 - - - +
30A ASN* 1.3 66.2 + - - +
31A SER 3.4 0.4 - - - -
34A MET* 3.5 10.2 - - - +
35A ARG* 3.8 2.8 + - - +
38A GLN* 3.0 34.2 + - - +
301A HEM 3.8 38.3 - - + +
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Residues in contact with ASN 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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26A ILE* 2.8 36.2 + - + +
27A ARG* 3.1 10.4 + - - +
29A GLU* 1.3 86.9 + - - +
31A SER* 1.3 65.4 + - - +
32A GLU 3.6 0.2 + - - -
35A ARG* 3.1 41.7 + - - +
38A GLN* 5.5 1.4 + - - -
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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
------------------------------------------------------------
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