Contacts of the helix formed by residues 12 - 25 (chain W) in PDB entry 5G04
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 LYS 12 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1317A SER* 3.1 43.9 + - - +
1318A ASP 5.2 0.2 + - - -
1319A LEU 4.4 0.4 + - - -
1320A ASN* 3.3 35.0 + - - +
514K PHE* 4.2 6.5 - - - -
10W GLU* 3.7 8.7 + - + +
11W LEU* 1.3 82.6 + - - +
13W LEU* 1.3 73.3 + - - +
14W ASP* 3.1 15.0 - - + +
15W ASP* 2.8 43.9 + - - +
16W ILE* 3.2 8.8 + - - +
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Residues in contact with LEU 13 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1311A SER* 5.7 3.8 - - - +
1320A ASN* 3.6 28.3 - - - +
1322A PRO* 3.7 25.6 - - + -
1323A GLU* 5.8 2.7 - - + +
513K THR* 5.5 4.0 - - - +
514K PHE* 5.3 10.1 - - + +
517K THR* 5.0 6.7 - - + -
12W LYS* 1.3 86.9 - - - +
14W ASP* 1.3 65.4 + - - +
16W ILE* 2.9 42.6 + - + +
17W GLU* 3.3 7.0 + - - +
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Residues in contact with ASP 14 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1312A ASN* 3.9 25.7 - - - +
1317A SER* 4.4 13.8 + - - -
12W LYS* 3.8 16.9 - - + +
13W LEU* 1.3 78.8 + - - +
15W ASP* 1.3 63.8 + - - +
17W GLU* 3.1 36.3 + - - +
18W GLU* 3.8 2.8 + - - +
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Residues in contact with ASP 15 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413K PHE* 5.9 1.6 - - - -
453K HIS* 4.7 1.2 - - - -
456K ARG* 3.3 23.4 + - - +
457K LYS* 4.4 17.7 + - - +
487K TYR* 2.4 30.4 + - + +
514K PHE* 5.1 0.7 - - + -
10W GLU 3.9 5.0 - - - +
11W LEU* 3.6 17.7 - - + -
12W LYS* 2.8 38.2 + - - +
14W ASP* 1.3 79.5 - - - +
16W ILE* 1.3 59.9 + - - -
18W GLU* 3.0 17.7 + - - +
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Residues in contact with ILE 16 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487K TYR* 4.8 0.2 - - - -
514K PHE* 3.7 16.8 - - + -
517K THR* 3.4 32.8 - - + +
518K MET* 3.5 30.7 - - + -
521K HIS* 4.9 18.8 - - + +
12W LYS 3.2 1.9 + - - +
13W LEU* 2.9 38.9 + - + +
15W ASP* 1.3 71.6 - - - +
17W GLU* 1.3 63.8 + - - +
19W PHE* 3.0 14.2 + - + +
20W GLU* 3.4 18.4 + - + +
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Residues in contact with GLU 17 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1312A ASN* 4.1 15.2 - - - +
13W LEU 3.3 7.8 + - - +
14W ASP* 3.1 23.7 + - - +
16W ILE* 1.3 75.7 - - - +
18W GLU* 1.3 61.6 + - - +
20W GLU* 3.1 22.4 + - + +
21W ASN* 3.4 18.9 + - - +
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Residues in contact with GLU 18 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456K ARG* 4.0 16.4 + - - +
457K LYS* 3.7 38.7 - - + +
459K LYS* 3.6 30.7 + - - +
487K TYR* 3.6 6.7 + - - +
491K LEU* 4.3 16.6 - - + +
14W ASP 3.8 1.9 + - - +
15W ASP* 3.0 17.5 + - - +
17W GLU* 1.3 75.2 - - - +
19W PHE* 1.3 62.6 + - - +
21W ASN* 3.2 29.9 + - - +
22W ILE* 3.5 4.9 + - - +
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Residues in contact with PHE 19 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487K TYR* 3.8 8.6 + - + +
490K SER* 3.8 29.4 - - - -
491K LEU* 4.7 7.2 - - + -
495K PHE* 3.6 34.3 - + - -
518K MET* 4.1 27.6 - - + -
521K HIS* 3.8 26.7 - + + -
522K CYS* 4.3 7.6 - - - -
525K MET* 5.1 0.7 - - + -
16W ILE* 3.0 11.8 + - + +
18W GLU* 1.3 79.2 - - - +
20W GLU* 1.3 72.5 + - - +
22W ILE* 3.3 23.1 + - + +
23W ARG* 3.2 41.9 + - + +
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Residues in contact with GLU 20 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521K HIS* 3.6 34.0 + - - -
16W ILE* 3.4 16.7 + - + +
17W GLU* 3.1 15.9 + - + +
19W PHE* 1.3 82.7 - - - +
21W ASN* 1.3 63.6 + - - +
23W ARG* 3.2 19.8 + - - +
24W LYS* 3.2 19.6 + - - +
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Residues in contact with ASN 21 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17W GLU* 3.4 16.2 + - - +
18W GLU* 3.2 18.5 + - - +
19W PHE 3.2 0.6 - - - -
20W GLU* 1.3 77.5 - - - +
22W ILE* 1.3 61.8 + - - +
24W LYS* 3.2 23.1 + - - +
25W ASP* 3.7 4.2 + - - +
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Residues in contact with ILE 22 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459K LYS* 5.3 3.1 - - - +
461K TYR* 4.7 7.9 - - + +
490K SER 5.1 1.3 - - - +
491K LEU* 3.7 42.8 - - + +
495K PHE* 5.9 2.5 - - + -
525K MET* 5.4 4.1 - - + +
18W GLU 3.5 4.9 + - - +
19W PHE* 3.3 37.8 + - + +
21W ASN* 1.3 76.0 - - - +
23W ARG* 1.3 64.7 + - - +
25W ASP* 3.3 25.0 + - + +
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Residues in contact with ARG 23 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521K HIS* 3.0 32.3 + - - -
524K GLU* 3.4 21.2 + - - +
525K MET* 3.2 51.1 - - + +
19W PHE* 3.2 38.4 + - + +
20W GLU* 3.3 29.4 - - - +
22W ILE* 1.3 74.7 - - - +
24W LYS* 1.3 65.6 + - - +
25W ASP 3.4 6.6 + - - +
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Residues in contact with LYS 24 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20W GLU 3.2 6.6 + - - +
21W ASN* 3.2 15.3 + - - +
23W ARG* 1.3 79.6 - - - +
25W ASP* 1.3 63.0 + - - +
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Residues in contact with ASP 25 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525K MET* 6.2 1.5 - - - +
21W ASN 3.7 3.9 + - - +
22W ILE* 3.3 26.7 + - + +
23W ARG 3.3 6.9 - - - +
24W LYS* 1.3 84.0 - - - +
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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