Contacts of the helix formed by residues 19 - 27 (chain D) in PDB entry 4L2D
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 19 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11D ILE 4.6 0.4 - - - -
15D GLU* 3.5 15.9 - - - -
16D PRO 5.2 0.8 + - - -
18D ILE* 1.3 75.5 - - - +
20D LYS* 1.3 65.6 + - - +
21D GLU* 3.5 9.3 + - - +
22D THR* 3.1 18.0 + - - -
23D LEU* 3.2 20.0 + - - +
165D ILE* 4.5 1.4 - - - +
166D ASP* 2.7 32.9 + - - -
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Residues in contact with LYS 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A LYS* 5.9 9.7 - - + +
50A LYS* 5.9 3.0 - - - +
11D ILE* 3.3 46.3 + - + +
12D ASP* 4.5 7.9 - - + -
15D GLU* 2.7 23.0 + - - +
18D ILE 3.9 0.2 + - - -
19D SER* 1.3 72.6 - - - +
21D GLU* 1.3 63.7 + - - +
23D LEU* 3.3 2.9 + - - +
24D GLU* 3.0 50.6 + - - +
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Residues in contact with GLU 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C ARG* 2.7 36.5 + - - -
19D SER* 3.1 9.1 + - - +
20D LYS* 1.3 78.7 - - - +
22D THR* 1.3 64.4 + - - +
24D GLU* 3.1 15.0 + - - +
25D PHE* 3.0 41.4 + - + -
165D ILE* 3.8 16.9 - - + +
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Residues in contact with THR 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D ILE* 3.8 15.5 - - + -
19D SER* 3.1 13.4 + - - -
21D GLU* 1.3 76.1 - - - +
23D LEU* 1.3 54.7 + - + +
25D PHE* 3.2 1.4 + - - +
26D HIS* 2.5 52.5 + - + +
161D HIS 4.4 7.9 - - - +
162D ALA 3.6 23.8 - - - +
163D TYR* 5.4 0.7 - - - -
165D ILE* 3.6 23.8 + - + +
166D ASP* 2.8 29.6 + - - +
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Residues in contact with LEU 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D LEU* 4.1 16.8 - - + -
9D TYR* 4.4 3.1 - - + -
10D ALA 4.3 3.1 - - - +
11D ILE* 3.2 42.2 - - + +
14D LEU* 4.2 29.6 - - + -
18D ILE* 3.9 18.6 - - + +
19D SER 3.2 13.4 + - - +
20D LYS 3.3 3.6 + - - +
22D THR* 1.3 78.9 - - + +
24D GLU* 1.3 58.7 + - - +
26D HIS* 4.4 1.1 - - - -
27D HIS* 2.7 37.4 + - - +
28D GLY 3.3 0.5 + - - -
77D TRP* 3.4 33.9 - - + -
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Residues in contact with GLU 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D ILE* 3.8 18.1 - - + +
20D LYS* 3.0 49.0 + - - +
21D GLU* 3.1 21.3 + - - +
23D LEU* 1.3 76.2 - - - +
25D PHE* 1.3 63.4 + - + +
28D GLY* 2.9 29.3 + - - +
29D LYS* 3.3 4.6 + - - +
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Residues in contact with PHE 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164C TYR* 3.6 17.7 - - - +
168C ARG* 3.4 37.0 - - + -
169C ASN* 3.7 21.1 - - - -
21D GLU* 3.0 46.6 + - + +
22D THR 4.0 3.1 - - - +
24D GLU* 1.3 81.4 - - + +
26D HIS* 1.3 59.7 + - - +
29D LYS* 2.8 31.4 + - + +
30D HIS* 2.8 29.0 + - + -
165D ILE* 4.2 10.1 - - + -
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Residues in contact with HIS 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164C TYR* 5.5 0.2 - - - -
22D THR* 2.5 31.6 + - + +
25D PHE* 1.3 74.8 - - - +
27D HIS* 1.3 56.4 + - - +
30D HIS* 3.5 8.4 + - + -
31D HIS* 3.0 27.0 + - - +
73D HIS* 3.3 11.8 + + - -
76D TYR* 3.7 18.3 + + - -
77D TRP* 3.4 17.6 - + + -
157D ASP* 2.8 18.6 + - - -
161D HIS* 3.1 18.8 - + - +
162D ALA* 3.5 31.1 + - + -
201D FE2 2.2 27.0 - - - -
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Residues in contact with HIS 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D LEU* 3.5 29.9 - - + +
5D PRO* 2.9 30.3 + - + -
6D SER* 4.3 1.9 - - - -
7D LEU* 3.5 45.3 + - + +
11D ILE* 5.7 2.0 - - + -
23D LEU 2.7 19.1 + - - +
26D HIS* 1.3 74.9 - - - +
28D GLY* 1.3 68.9 + - - +
29D LYS 3.4 0.7 + - - -
31D HIS* 3.3 24.7 + + - +
32D ASN 3.4 5.2 + - - -
77D TRP* 3.5 29.9 + + + -
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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