Contacts of the helix formed by residues 21 - 31 (chain A) in PDB entry 2P3L
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 GLY 21 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A ALA 3.5 2.6 + - - -
20A LEU* 1.3 74.9 - - - +
22A LYS* 1.3 62.5 + - - -
23A SER 3.3 2.0 - - - -
24A GLU* 3.3 19.8 + - - -
25A PHE* 2.9 27.8 + - - +
1002A G3A 5.1 0.2 - - - -
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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
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20A LEU 5.4 2.8 + - - -
21A GLY* 1.3 73.3 - - - +
23A SER* 1.3 61.4 + - - +
25A PHE* 3.5 6.6 + - - +
26A GLN* 3.2 27.6 + - - +
1002A G3A 3.8 44.5 + - + +
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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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21A GLY 3.3 0.4 - - - -
22A LYS* 1.3 76.2 - - - +
24A GLU* 1.3 65.9 + - - +
26A GLN* 3.5 5.8 + - - +
27A ILE* 3.1 36.8 + - - +
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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 LEU* 4.2 22.2 - - + +
21A GLY* 3.5 25.9 + - - +
23A SER* 1.3 78.6 - - - +
25A PHE* 1.3 56.0 + - - +
27A ILE* 3.5 9.2 + - - +
28A TYR* 2.9 30.0 + - - +
246A ARG* 5.7 3.1 + - - -
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Residues in contact with PHE 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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17A LEU* 3.7 17.0 - - + -
20A LEU* 3.8 10.0 - - + +
21A GLY 2.9 17.6 + - - +
22A LYS 3.7 5.4 - - - +
24A GLU* 1.3 73.7 - - - +
26A GLN* 1.3 84.9 + - - +
28A TYR* 3.2 2.8 + + - +
29A LYS* 2.8 44.5 + - + +
214A SER* 3.6 26.9 - - - -
1002A G3A 3.3 87.9 - + + +
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Residues in contact with GLN 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 3.2 17.1 + - - +
23A SER* 3.9 7.0 - - - +
25A PHE* 1.3 102.7 - - + +
27A ILE* 1.3 63.9 + - + +
29A LYS* 3.6 27.5 - - - +
30A LYS* 4.0 13.9 + - - +
1002A G3A 5.6 0.4 + - - -
1004A GOL 4.5 8.9 + - - -
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Residues in contact with ILE 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 SER* 3.1 30.9 + - - +
24A GLU* 3.7 7.2 - - - +
25A PHE 3.2 0.2 - - - -
26A GLN* 1.3 76.2 - - + +
28A TYR* 1.3 65.5 + - - +
29A LYS 3.3 0.5 + - - -
30A LYS* 3.4 10.6 + - - +
31A SER* 2.8 26.0 + - - +
245A MET 5.8 3.1 - - - +
247A HIS* 5.6 6.1 - - - +
248A LYS 4.6 13.4 - - - +
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Residues in contact with TYR 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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13A TRP* 3.0 15.5 + - - -
17A LEU* 3.7 24.2 - - + -
20A LEU* 3.9 8.1 - - + -
24A GLU 2.9 19.8 + - - +
25A PHE 3.2 3.8 + - - +
27A ILE* 1.3 77.3 - - - +
29A LYS* 1.3 55.9 + - - +
30A LYS 3.0 1.0 + - - -
31A SER* 3.2 8.7 + - - -
213A ASN* 2.7 66.9 + - + +
214A SER* 4.8 0.4 - - - -
239A LEU* 2.6 27.6 + - - +
242A ARG* 3.6 23.8 - - + -
243A PHE* 3.5 50.0 - + + -
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Residues in contact with LYS 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 PHE* 2.8 36.5 + - + +
26A GLN* 3.6 21.2 - - - +
27A ILE 3.2 0.6 - - - -
28A TYR* 1.3 73.4 - - - +
30A LYS* 1.3 75.0 + - + +
33A ILE* 3.8 2.3 - - - +
212A ARG* 3.7 16.2 - - + +
213A ASN* 2.9 29.8 + - - +
214A SER* 3.4 30.3 - - - +
1002A G3A 3.2 18.3 + - - -
1004A GOL 4.0 14.9 + - - +
1005A SO4 3.3 25.8 + - - -
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Residues in contact with LYS 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 GLN* 4.0 14.6 + - - +
27A ILE 3.4 6.7 + - - +
28A TYR 3.1 0.4 - - - -
29A LYS* 1.3 96.7 - - + +
31A SER* 1.3 64.0 + - - +
32A GLY 3.1 4.2 + - - -
33A ILE* 3.4 27.1 - - + +
35A GLU* 3.4 26.2 + - - +
212A ARG* 3.9 9.2 - - + +
248A LYS 5.9 0.2 - - - +
249A LYS* 4.6 3.6 - - + -
250A ALA* 3.2 23.4 + - + +
1004A GOL 2.9 39.1 + - - -
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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 ILE* 2.8 29.4 + - - +
28A TYR* 3.2 13.6 + - - -
30A LYS* 1.3 72.6 - - - +
32A GLY* 1.3 63.7 + - - +
213A ASN* 2.8 20.9 + - - +
242A ARG* 3.8 6.3 - - - -
245A MET* 3.0 33.7 + - - +
248A LYS* 3.5 28.3 + - - +
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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