Contacts of the helix formed by residues 2 - 34 (chain J) in PDB entry 5KHU
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 ASN 2 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3J LEU* 3.8 29.4 - - - +
5J ARG* 4.5 17.5 - - - +
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Residues in contact with LEU 3 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2J ASN* 3.8 25.4 - - - +
4J GLU* 3.8 28.9 - - - +
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Residues in contact with GLU 4 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3J LEU* 3.8 29.2 - - - +
5J ARG* 3.8 25.8 - - - +
7J ARG* 4.4 17.5 - - - +
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Residues in contact with ARG 5 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2J ASN* 4.5 16.4 - - - +
4J GLU* 3.8 24.2 - - - +
6J LEU* 3.8 29.6 - - - +
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Residues in contact with LEU 6 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5J ARG* 3.8 29.2 - - - +
7J ARG* 3.8 27.4 - - - +
9J ARG* 4.1 21.1 - - - +
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Residues in contact with ARG 7 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4J GLU* 4.4 16.6 - - - +
6J LEU* 3.8 29.4 - - - +
8J LYS* 3.8 22.7 - - - +
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Residues in contact with LYS 8 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7J ARG* 3.8 29.6 - - - +
9J ARG* 3.8 25.8 - - - +
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Residues in contact with ARG 9 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6J LEU* 4.1 18.4 - - - +
8J LYS* 3.8 23.8 - - - +
10J VAL* 3.8 29.6 - - - +
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Residues in contact with VAL 10 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9J ARG* 3.8 26.9 - - - +
11J ARG* 3.8 29.4 - - - +
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Residues in contact with ARG 11 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10J VAL* 3.8 29.6 - - - +
12J GLN* 3.8 28.9 - - - +
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Residues in contact with GLN 12 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11J ARG* 3.8 25.6 - - - +
13J TYR* 3.8 28.9 - - - +
15J ASP* 4.3 17.9 - - - +
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Residues in contact with TYR 13 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12J GLN* 3.8 30.1 - - - +
14J LEU* 3.8 25.8 - - - +
16J GLN* 4.7 14.4 - - - +
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Residues in contact with LEU 14 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13J TYR* 3.8 24.0 - - - +
15J ASP* 3.8 29.4 - - - +
17J GLN* 4.6 12.6 - - - +
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Residues in contact with ASP 15 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12J GLN* 4.3 16.6 - - - +
14J LEU* 3.8 29.6 - - - +
16J GLN* 3.8 27.8 - - - +
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Residues in contact with GLN 16 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13J TYR* 4.7 11.7 - - - +
15J ASP* 3.8 29.6 - - - +
17J GLN* 3.8 25.1 - - - +
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Residues in contact with GLN 17 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14J LEU* 4.6 18.2 - - - +
16J GLN* 3.8 29.6 - - - +
18J GLN* 3.8 29.2 - - - +
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Residues in contact with GLN 18 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17J GLN* 3.8 26.2 - - - +
19J TYR* 3.7 29.4 - - - +
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Residues in contact with TYR 19 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18J GLN* 3.7 29.6 - - - +
20J GLN* 3.8 29.4 - - - +
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Residues in contact with GLN 20 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19J TYR* 3.8 28.3 - - - +
21J SER* 3.8 26.7 - - - +
23J LEU* 4.5 15.3 - - - +
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Residues in contact with SER 21 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20J GLN* 3.8 26.7 - - - +
22J ALA* 3.8 29.2 - - - +
24J PHE* 4.4 15.7 - - - +
164K PHE* 4.6 21.5 - - - +
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Residues in contact with ALA 22 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21J SER* 3.8 24.9 - - - +
23J LEU* 3.8 29.4 - - - +
25J TRP* 4.4 17.3 - - - +
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Residues in contact with LEU 23 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20J GLN* 4.5 15.9 - - - +
22J ALA* 3.8 29.2 - - - +
24J PHE* 3.8 25.1 - - - +
26J ALA* 4.5 15.5 - - - +
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Residues in contact with PHE 24 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21J SER* 4.4 15.5 - - - +
23J LEU* 3.8 28.7 - - - +
25J TRP* 3.8 26.0 - - - +
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Residues in contact with TRP 25 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22J ALA* 4.4 14.8 - - - +
24J PHE* 3.8 29.4 - - - +
26J ALA* 3.8 25.6 - - - +
28J LYS* 4.6 16.6 - - - +
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Residues in contact with ALA 26 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23J LEU* 4.5 17.3 - - - +
25J TRP* 3.8 24.7 - - - +
27J ASP* 3.7 29.8 - - - +
29J VAL* 4.5 15.9 - - - +
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Residues in contact with ASP 27 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26J ALA* 3.7 29.2 - - - +
28J LYS* 3.8 25.8 - - - +
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Residues in contact with LYS 28 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25J TRP* 4.6 14.4 - - - +
27J ASP* 3.8 24.0 - - - +
29J VAL* 3.8 29.4 - - - +
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Residues in contact with VAL 29 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26J ALA* 4.5 18.8 - - - +
28J LYS* 3.8 28.5 - - - +
30J ALA* 3.8 27.4 - - - +
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Residues in contact with ALA 30 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29J VAL* 3.8 25.4 - - - +
31J SER* 3.8 29.2 - - - +
33J SER* 4.3 15.3 - - - +
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Residues in contact with SER 31 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30J ALA* 3.8 29.2 - - - +
32J LEU* 3.8 26.5 - - - +
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Residues in contact with LEU 32 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31J SER* 3.8 24.2 - - - +
33J SER* 3.8 29.4 - - - +
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Residues in contact with SER 33 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30J ALA* 4.3 17.9 - - - +
32J LEU* 3.8 25.8 - - - +
34J ARG* 3.8 29.8 - - - +
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Residues in contact with ARG 34 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33J SER* 3.8 29.6 - - - +
35J GLU* 3.8 23.3 - - - +
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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