Contacts of the helix formed by residues 21 - 29 (chain A) in PDB entry 1DWQ
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 21 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A ILE 4.5 1.2 + - - -
19A TRP 3.1 0.4 - - - -
20A HIS* 1.3 96.4 + - + +
22A LEU* 1.3 66.8 + - - +
23A LYS 3.4 0.4 - - - -
24A PRO* 3.3 14.5 - - - +
25A ALA* 3.4 6.2 + - - +
28A ARG* 5.2 1.2 + - - -
166A GLU* 4.2 13.4 + - + +
239A GLN 3.9 4.9 - - - +
240A LEU* 3.8 30.3 - - + +
243A THR* 3.4 33.1 - - + +
163B THR* 6.0 3.0 - - - +
165B GLY* 4.9 7.2 - - - -
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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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8A LEU* 4.4 5.6 - - + -
19A TRP* 3.4 37.8 + - + +
21A LYS* 1.3 79.2 - - - +
23A LYS* 1.4 61.8 + - - +
25A ALA* 3.0 3.3 + - - +
26A LEU* 3.0 35.2 + - + +
77A VAL* 5.1 1.1 - - + -
239A GLN* 4.0 18.6 + - + +
243A THR* 3.6 30.0 - - + +
246A VAL* 4.0 15.0 - - + -
247A ALA* 3.8 23.1 - - + +
250A LEU* 4.0 20.0 - - + -
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Residues in contact with LYS 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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8A LEU* 4.4 5.2 - - + +
19A TRP 2.9 23.9 + - - +
22A LEU* 1.4 71.0 - - - +
24A PRO* 1.3 68.6 - - + +
26A LEU* 3.2 3.2 + - - +
27A GLU* 2.8 53.8 + - - +
33A VAL* 3.5 45.4 - - + +
35A ALA* 4.3 11.4 - - + +
168B GLU* 3.1 36.4 + - + +
171B LYS* 4.0 9.3 - - - +
172B MET* 4.0 12.8 - - + -
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Residues in contact with PRO 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 HIS 3.1 28.0 - - - +
21A LYS* 3.3 14.6 - - - +
23A LYS* 1.3 92.7 - - + +
25A ALA* 1.3 54.4 + - - -
27A GLU* 3.3 14.6 + - + +
28A ARG* 2.8 45.6 + - + +
164B ASP* 4.3 25.1 - - + +
165B GLY* 4.5 4.5 - - - +
168B GLU* 3.8 12.3 - - + +
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Residues in contact with ALA 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 LYS 3.4 11.7 + - - +
22A LEU* 3.0 9.7 + - - +
24A PRO* 1.3 77.0 - - - +
26A LEU* 1.3 62.6 + - - +
28A ARG* 3.2 39.7 + - - +
29A ALA* 3.4 10.4 + - - +
243A THR* 4.1 11.0 - - + -
244A GLU* 3.9 12.9 - - - +
247A ALA* 4.1 19.8 - - + +
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Residues in contact with LEU 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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6A PHE* 4.1 21.1 - - + -
8A LEU* 4.2 14.6 - - + -
22A LEU* 3.0 34.4 + - + +
23A LYS 3.7 1.6 - - - +
25A ALA* 1.3 74.2 - - - +
27A GLU* 1.3 65.6 + - - +
29A ALA* 3.2 7.9 + - + -
31A HIS* 3.1 39.5 + - + -
33A VAL* 3.6 27.4 - - + -
247A ALA* 4.1 17.9 - - + +
250A LEU* 4.0 37.0 - - + -
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Residues in contact with GLU 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 LYS* 2.8 56.2 + - - +
24A PRO* 3.6 14.6 - - + +
26A LEU* 1.3 73.9 - - - +
28A ARG* 1.3 63.5 + - - +
29A ALA 3.0 2.0 - - - -
30A GLY* 2.8 14.2 + - - -
31A HIS 3.8 13.5 - - - +
33A VAL* 3.8 18.3 + - + +
168B GLU* 4.0 5.5 - - - +
171B LYS* 5.5 1.0 + - - -
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Residues in contact with ARG 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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21A LYS 5.2 1.2 + - - -
24A PRO* 2.8 35.8 + - + +
25A ALA* 3.2 24.3 + - - +
27A GLU* 1.3 74.9 - - - +
29A ALA* 1.3 61.1 + - - +
30A GLY 3.4 0.9 + - - -
243A THR* 5.8 0.4 - - - +
244A GLU* 2.7 33.1 + - - -
164B ASP* 4.4 18.5 + - - +
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Residues in contact with ALA 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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3A THR* 4.3 10.0 - - - +
25A ALA 3.4 5.9 + - - +
26A LEU* 3.2 15.0 + - + +
27A GLU 3.0 0.4 - - - -
28A ARG* 1.3 80.0 - - - +
30A GLY* 1.3 56.9 + - - +
31A HIS* 3.4 22.3 + - + +
247A ALA* 6.5 0.4 - - + -
251A GLN* 4.1 12.0 + - + +
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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