Contacts of the helix formed by residues 19 - 27 (chain B) in PDB entry 4L2A
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11B ILE 4.5 0.9 - - - -
15B GLU* 3.7 15.9 - - - -
16B PRO 5.4 0.6 - - - -
17B HIS 4.2 0.2 - - - -
18B ILE* 1.3 75.7 - - - +
20B LYS* 1.3 65.1 + - - +
21B GLU* 3.4 9.0 + - - +
22B THR* 2.8 28.2 + - - -
23B LEU* 3.1 22.7 + - - +
165B ILE* 4.4 1.2 - - - +
166B ASP* 2.7 34.7 + - - -
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Residues in contact with LYS 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ILE* 3.2 49.2 + - + +
12B ASP* 4.5 4.7 - - + -
15B GLU* 2.8 21.0 + - - +
19B SER* 1.3 72.7 - - - +
21B GLU* 1.3 64.9 + - - +
23B LEU* 3.3 2.1 + - - +
24B GLU* 2.9 54.2 + - - +
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Residues in contact with GLU 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A ARG* 2.7 39.1 + - - -
19B SER* 3.1 9.4 + - - +
20B LYS* 1.3 82.1 - - - +
22B THR* 1.3 64.6 + - - +
24B GLU* 3.0 15.7 + - - +
25B PHE* 3.0 42.1 + - + -
165B ILE* 3.6 18.4 - - + +
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Residues in contact with THR 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ILE* 3.7 15.0 - - + -
19B SER* 2.8 18.4 + - - -
21B GLU* 1.3 72.4 - - - +
23B LEU* 1.3 55.2 + - + +
25B PHE* 3.2 0.5 + - - +
26B HIS* 2.7 48.3 + - + +
161B HIS 4.3 7.3 + - - +
162B ALA 3.4 30.4 + - - +
163B TYR* 5.3 0.2 - - - -
165B ILE* 3.6 23.6 + - - +
166B ASP* 2.7 31.4 + - - +
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Residues in contact with LEU 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B LEU* 4.3 15.6 - - + +
9B TYR* 4.2 11.4 - - + -
10B ALA 4.4 0.7 - - - +
11B ILE* 3.4 33.4 - - + +
14B LEU* 4.0 32.1 - - + -
18B ILE* 3.8 20.2 - - + +
19B SER 3.1 15.9 + - - +
20B LYS 3.7 6.3 - - - +
22B THR* 1.3 77.6 - - + +
24B GLU* 1.3 64.5 + - - +
26B HIS* 4.5 2.0 - - - -
27B HIS* 2.9 30.1 + - - +
28B GLY 3.5 0.2 + - - -
77B TRP* 3.5 31.4 - - + -
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Residues in contact with GLU 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ILE* 4.9 14.4 - - + +
20B LYS* 2.9 50.0 + - + +
21B GLU* 3.0 20.8 + - - +
23B LEU* 1.3 78.8 - - - +
25B PHE* 1.3 63.4 + - + +
28B GLY* 3.0 27.7 + - - +
29B LYS* 3.6 5.1 + - - +
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Residues in contact with PHE 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A TYR* 3.8 15.3 - - - +
168A ARG* 3.7 35.7 - - + -
169A ASN* 3.7 22.0 - - - -
21B GLU* 3.0 56.2 + - + +
22B THR 4.0 2.0 - - - +
24B GLU* 1.3 79.6 - - + +
26B HIS* 1.3 63.7 + - - +
29B LYS* 2.8 32.2 + - + +
30B HIS* 2.8 29.2 + - + -
165B ILE* 4.1 10.8 - - + -
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Residues in contact with HIS 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B THR* 2.7 31.1 + - + +
25B PHE* 1.3 74.4 - - - +
27B HIS* 1.3 57.3 + - - +
30B HIS* 3.2 10.9 - - + +
31B HIS* 2.9 25.5 + - - +
73B HIS* 3.1 14.6 - + - -
76B TYR* 3.7 18.8 + + - -
77B TRP* 3.4 17.1 - + + -
157B ASP* 2.8 17.4 + - - -
161B HIS* 3.5 16.2 - + - +
162B ALA* 3.4 31.2 + - + -
5001B FE 2.2 25.7 - - - -
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Residues in contact with HIS 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B LEU* 3.6 30.1 - - + +
5B PRO 2.8 29.4 + - - -
6B SER* 4.2 2.0 - - - -
7B LEU* 3.3 47.1 + - + +
11B ILE* 6.4 0.4 - - + -
23B LEU 2.9 17.1 + - - +
26B HIS* 1.3 74.5 - - - +
28B GLY* 1.3 72.5 + - - +
31B HIS* 3.2 21.1 - - - +
32B ASN 3.3 7.4 + - - -
77B TRP* 3.5 28.2 + + + -
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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