Contacts of the helix formed by residues 16 - 21 (chain A) in PDB entry 4DQ6
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 16 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A ARG* 3.3 47.2 + - - +
14A ASN* 3.9 5.2 - - - -
15A PHE* 1.3 74.5 - - - +
17A SER* 1.3 59.1 + - - +
18A LYS* 3.3 7.8 + - - +
19A TRP* 3.2 25.5 + - - -
20A SER* 2.9 35.5 + - - -
62B TYR 3.5 5.8 + - - -
64B THR* 4.1 0.8 - - - +
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Residues in contact with SER 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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15A PHE 3.8 1.8 + - - -
16A SER* 1.3 70.5 - - - +
18A LYS* 1.3 65.6 + - - +
21A GLU* 2.9 39.2 + - - +
35A TRP* 3.5 7.2 - - - -
36A VAL* 4.6 8.7 - - - +
62B TYR* 3.0 34.0 + - - +
64B THR* 3.9 10.2 - - - +
269B ARG* 3.5 32.4 + - - -
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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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11A ARG* 3.7 8.1 - - - +
16A SER* 3.2 10.0 + - - +
17A SER* 1.3 82.4 + - - +
19A TRP* 1.3 62.5 + - + +
22A MET* 3.6 5.4 - - - +
33A PRO* 3.4 39.1 - - + +
34A MET* 4.6 1.7 - - - +
35A TRP* 2.9 37.9 + - + +
36A VAL* 3.7 26.9 - - + +
38A ASP* 3.0 43.3 + - - +
40A ASP* 2.7 31.3 + - - +
368A ASN* 3.3 15.0 + - - +
370A ALA 4.5 1.6 + - - -
371A CYS* 5.3 1.4 - - - +
375A MET* 5.0 0.6 - - - +
62B TYR 4.8 0.4 + - - -
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Residues in contact with TRP 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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9A VAL 5.4 3.1 - - - -
10A ASP* 5.0 11.4 - - - -
11A ARG* 3.6 40.6 - - + +
12A SER* 5.0 10.5 - - - +
16A SER* 3.2 24.1 + - - +
17A SER 3.2 0.2 - - - -
18A LYS* 1.3 82.7 - - + +
20A SER* 1.3 61.0 + - - +
21A GLU 3.9 0.4 - - - -
22A MET* 3.6 18.2 - - + +
29A ASN* 3.7 9.4 + - - +
31A LEU 5.0 3.8 - - - -
32A LEU* 5.6 2.2 - - + -
33A PRO* 3.6 34.6 - - + +
40A ASP* 2.7 31.0 + - - -
375A MET* 4.0 19.5 - - + -
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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
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11A ARG 5.3 0.9 + - - -
12A SER* 5.0 8.1 + - - -
15A PHE* 4.9 1.6 + - - -
16A SER 2.9 23.5 + - - -
19A TRP* 1.3 81.8 + - - +
21A GLU* 1.3 60.4 + - - +
23A GLU* 4.9 1.9 + - - +
29A ASN* 3.1 26.8 + - - +
64B THR* 3.9 21.7 + - - +
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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 SER* 2.9 21.1 + - - +
20A SER* 1.3 77.9 - - - +
22A MET* 1.3 63.8 + - - +
23A GLU* 3.3 3.7 + - - +
24A LYS* 3.5 27.3 - - + +
25A LYS* 3.9 3.1 + - - +
35A TRP* 4.0 18.5 - - + -
64B THR* 2.7 30.4 + - - +
65B ARG 4.4 1.2 + - - -
269B ARG* 2.9 42.8 + - - -
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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