Contacts of the helix formed by residues 18 - 31 (chain A) in PDB entry 3Q37
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 18 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A GLY* 1.3 74.7 - - - -
19A GLN* 1.3 65.3 + - - +
20A GLN* 3.6 5.9 + - - +
21A SER* 3.0 28.9 + - - -
22A LEU* 3.0 25.3 + - - +
48A HIS* 4.4 5.6 - - - -
86B ASP* 3.5 26.5 - - - -
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Residues in contact with GLN 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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18A SER* 1.3 71.0 - - - +
20A GLN* 1.3 59.2 + - - +
22A LEU 4.1 0.2 - - - -
23A SER* 2.5 35.3 + - - +
48A HIS* 4.6 2.2 + - + -
51A MET* 3.2 38.8 - - + +
86B ASP* 2.9 41.7 + - - +
87B TYR* 3.6 30.9 + - + -
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Residues in contact with GLN 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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18A SER* 3.2 6.5 + - - +
19A GLN* 1.3 78.0 - - - +
21A SER* 1.3 66.5 + - - +
23A SER* 3.3 8.7 + - - -
24A GLU* 3.1 34.7 + - - +
86B ASP* 5.2 1.5 + - - +
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Residues in contact with SER 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 GLY* 3.8 6.8 - - - -
18A SER* 3.0 37.2 + - - -
20A GLN* 1.3 77.9 - - - +
22A LEU* 1.3 65.7 + - - +
24A GLU* 3.4 9.3 + - - +
25A LEU* 3.1 22.5 + - - +
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Residues in contact with LEU 22 (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 TRP* 3.8 47.8 - - + -
16A ASN 4.2 1.3 - - - +
17A GLY* 3.8 18.6 - - - -
18A SER 3.0 16.7 + - - +
19A GLN 4.5 0.9 - - - +
21A SER* 1.3 79.4 + - - +
23A SER* 1.3 60.9 + - - +
25A LEU* 3.8 7.0 - - + +
26A ILE* 2.9 41.4 + - + +
48A HIS* 3.3 45.5 - - + +
51A MET* 4.8 7.4 - - - -
52A THR* 5.4 0.4 - - - +
239A LEU* 4.1 13.0 - - + -
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Residues in contact with SER 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 GLN* 2.5 26.8 + - - +
20A GLN* 3.6 11.0 - - - -
22A LEU* 1.3 77.0 - - - +
24A GLU* 1.3 57.1 + - - +
26A ILE* 3.4 1.1 + - - -
27A ASP* 3.0 37.3 + - - +
51A MET* 4.8 7.9 - - - +
55A ARG* 3.7 38.3 + - - +
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Residues in contact with GLU 24 (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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20A GLN* 3.1 23.9 + - - +
21A SER* 3.6 12.1 - - - +
22A LEU 3.3 0.2 - - - -
23A SER* 1.3 78.8 - - - +
25A LEU* 1.3 61.9 + - - +
27A ASP* 3.4 10.1 + - - +
28A LEU* 3.3 19.9 + - - +
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Residues in contact with LEU 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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13A TRP* 3.6 23.8 - - + +
21A SER 3.1 16.3 + - - +
22A LEU* 3.8 11.7 - - + +
23A SER 3.2 0.2 - - - -
24A GLU* 1.3 73.6 - - - +
26A ILE* 1.3 65.8 + - - +
28A LEU* 3.1 14.4 + - + +
29A PHE* 3.0 46.0 + - + -
238A SER 3.6 21.8 - - - +
239A LEU* 3.7 20.2 - - - +
240A LYS* 4.0 22.9 - - - +
241A PRO* 4.4 4.3 - - + -
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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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13A TRP* 4.0 19.5 - - + -
22A LEU* 2.9 29.2 + - + +
23A SER* 3.9 6.3 - - - +
25A LEU* 1.3 75.4 - - - +
27A ASP* 1.3 60.5 + - - +
29A PHE* 3.2 8.6 + - + +
30A ASN* 2.8 34.1 + - - +
51A MET* 4.8 4.9 - - + +
52A THR* 3.8 38.8 - - + +
55A ARG* 4.0 13.5 - - + -
56A LEU* 3.8 41.1 - - + +
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Residues in contact with ASP 27 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A SER 3.0 19.5 + - - +
24A GLU* 3.7 9.0 - - - +
25A LEU 3.2 0.2 - - - -
26A ILE* 1.3 77.4 - - - +
28A LEU* 1.3 62.6 + - - +
30A ASN* 3.3 13.8 + - - +
31A SER* 3.1 22.2 + - - -
55A ARG* 3.0 42.1 + - - +
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Residues in contact with LEU 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 GLU 3.3 9.8 + - - +
25A LEU* 3.1 18.2 + - + +
27A ASP* 1.3 77.1 - - - +
29A PHE* 1.3 66.3 + - + +
31A SER* 2.9 25.3 + - - +
32A THR* 2.8 26.1 + - - +
241A PRO* 3.5 42.8 - - + -
244A VAL* 4.4 13.0 - - + -
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Residues in contact with PHE 29 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A ALA* 5.2 0.2 - - + -
13A TRP* 4.0 17.3 - + - -
25A LEU* 3.0 42.6 + - + -
26A ILE* 3.6 14.4 - - + +
28A LEU* 1.3 82.7 - - + +
30A ASN* 1.3 60.9 + - - +
32A THR* 3.2 14.9 + - - -
42A VAL* 3.8 22.4 - - + -
56A LEU* 4.4 11.2 - - + -
58A ASN* 2.9 26.2 + - - -
61A PHE* 3.8 31.5 - + + -
238A SER 4.0 10.3 - - - -
240A LYS 4.7 1.1 - - - -
243A PHE* 3.7 33.4 - + + -
244A VAL* 5.0 7.2 - - + -
247A ILE* 5.8 0.9 - - + -
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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 21.5 + - - +
27A ASP* 3.5 18.6 + - - +
28A LEU 3.2 0.2 - - - -
29A PHE* 1.3 75.4 - - - +
31A SER* 1.3 58.4 + - - +
32A THR 3.2 1.8 + - - +
55A ARG* 2.9 25.1 + - - +
56A LEU* 3.3 12.6 - - - +
57A THR* 2.8 40.5 + - - +
58A ASN* 3.4 12.1 + - - +
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Residues in contact with SER 31 (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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27A ASP 3.1 12.2 + - - -
28A LEU* 2.9 28.0 + - - +
30A ASN* 1.3 75.8 - - - +
32A THR* 1.3 60.6 + - - +
33A SER* 3.7 2.8 + - - -
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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