Contacts of the helix formed by residues 14 - 29 (chain J) in PDB entry 6AHU
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 ASP 14 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13J SER* 1.3 86.4 + - - +
15J LEU* 1.3 83.1 + - - +
16J LYS* 3.2 23.4 + - + +
17J ALA* 3.6 8.1 + - + +
18J LEU* 3.3 23.5 + - - +
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Residues in contact with LEU 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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14J ASP* 1.3 82.9 + - - +
16J LYS* 1.3 64.4 + - + +
17J ALA 3.4 0.2 - - - -
18J LEU* 3.9 23.3 - - + -
19J ARG* 3.2 48.6 + - + +
52J VAL 5.5 0.9 - - - +
57J LEU* 3.8 57.0 - - + +
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Residues in contact with LYS 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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14J ASP* 3.2 20.0 - - + +
15J LEU* 1.3 82.1 - - + +
17J ALA* 1.3 59.7 + - - +
19J ARG* 4.6 1.7 - - - +
20J GLY* 3.6 14.9 + - - -
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Residues in contact with ALA 17 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13J SER* 5.0 10.5 - - - +
14J ASP* 3.6 10.6 + - + +
15J LEU 3.4 0.2 - - - -
16J LYS* 1.3 78.1 - - - +
18J LEU* 1.3 63.3 + - - +
19J ARG 3.5 0.2 - - - -
20J GLY* 3.6 2.2 + - - +
21J LEU* 3.4 29.7 + - + +
192J GLU 4.9 12.8 - - - +
194J PRO* 6.1 4.2 - - + +
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Residues in contact with LEU 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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9J LEU* 6.3 2.2 - - + -
11J ALA 3.6 23.8 - - - +
12J GLY* 5.3 5.4 - - - -
14J ASP 3.3 17.6 + - - +
15J LEU* 4.3 22.2 - - + -
16J LYS 3.5 0.2 - - - -
17J ALA* 1.3 75.9 - - - +
19J ARG* 1.3 65.7 + - + +
21J LEU* 3.4 18.5 + - + +
22J VAL* 3.4 20.0 + - + +
35J ILE* 3.8 34.5 - - + -
52J VAL* 5.0 12.6 - - + -
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Residues in contact with ARG 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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15J LEU* 3.2 36.9 + - + +
16J LYS* 4.8 2.5 - - - +
18J LEU* 1.3 76.5 - - + +
20J GLY* 1.3 64.3 + - - +
22J VAL* 3.3 8.9 + - - +
23J GLU* 3.2 34.6 + - - +
56J GLU 5.2 0.2 + - - -
57J LEU* 2.8 43.3 + - - +
58J PHE* 3.9 23.9 - - + +
59J THR* 3.8 27.5 - - - +
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Residues in contact with GLY 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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16J LYS 3.6 12.2 + - - -
17J ALA* 3.6 6.2 + - - -
18J LEU 3.2 1.0 - - - -
19J ARG* 1.3 79.3 - - - +
21J LEU* 1.3 55.9 + - - +
23J GLU* 3.7 8.3 + - - +
24J THR* 2.6 36.6 + - - -
194J PRO* 5.6 7.4 - - - -
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Residues in contact with LEU 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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9J LEU* 4.2 27.6 - - + +
11J ALA* 4.0 15.7 - - + -
17J ALA* 3.4 17.4 + - + +
18J LEU* 3.4 15.6 + - + +
19J ARG 3.3 0.6 - - - -
20J GLY* 1.3 74.1 - - - +
22J VAL* 1.3 61.5 + - + +
24J THR* 4.1 3.2 - - - -
25J ALA* 3.1 29.8 + - - +
33J VAL* 5.4 0.2 - - - +
191J ALA* 3.3 32.8 - - + +
192J GLU 4.8 4.7 - - - +
193J ARG 3.4 25.6 - - - +
194J PRO* 4.1 13.9 - - + +
197J ILE* 5.5 7.9 - - + +
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Residues in contact with VAL 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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9J LEU* 6.2 0.9 - - + -
18J LEU* 3.4 20.9 - - + +
19J ARG* 3.3 9.8 + - - +
20J GLY 3.3 0.4 - - - -
21J LEU* 1.3 78.8 - - + +
23J GLU* 1.3 59.1 + - - +
25J ALA* 3.5 4.2 + - - +
26J ALA* 3.0 28.1 + - - +
33J VAL* 5.2 13.9 - - + -
35J ILE* 5.5 8.7 - - + -
58J PHE* 3.8 32.1 - - + -
62J PRO* 5.0 0.4 - - + -
71J ILE* 3.9 22.7 - - + +
73J ILE* 4.4 19.1 - - + -
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Residues in contact with GLU 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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19J ARG* 3.2 21.6 + - - +
20J GLY* 4.3 6.5 - - - +
22J VAL* 1.3 79.9 - - + +
24J THR* 1.3 60.9 + - - +
26J ALA* 3.6 7.2 + - - +
27J HIS* 3.2 20.6 + - - +
58J PHE* 5.5 9.9 - - + -
59J THR* 5.6 1.7 + - - -
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Residues in contact with THR 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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103H ARG* 3.4 37.2 - - - +
20J GLY 2.6 23.4 + - - -
21J LEU* 4.1 6.1 - - - -
23J GLU* 1.3 76.4 - - - +
25J ALA* 1.3 63.2 + - - +
27J HIS* 3.2 20.1 + - + +
28J LEU* 3.6 10.6 + - - +
194J PRO* 3.9 16.9 + - - +
195J LEU* 4.7 2.5 - - + -
197J ILE* 3.7 13.0 - - + -
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Residues in contact with ALA 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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7J LEU* 4.1 9.9 - - + -
9J LEU* 5.7 0.9 - - + -
21J LEU 3.1 19.2 + - - +
22J VAL 4.0 1.1 - - - +
24J THR* 1.3 76.6 - - - +
26J ALA* 1.3 61.6 + - - +
27J HIS 3.3 0.2 + - - -
28J LEU 3.6 3.3 + - - -
30J TYR* 3.2 51.8 + - + -
33J VAL* 3.9 25.6 - - + -
197J ILE* 5.1 6.0 - - + +
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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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22J VAL 3.0 18.5 + - - +
23J GLU* 3.9 8.7 - - - +
24J THR 3.3 0.2 - - - -
25J ALA* 1.3 75.8 - - - +
27J HIS* 1.3 61.5 + - - +
28J LEU 4.8 1.3 - - - -
29J GLY* 4.9 0.5 + - - -
30J TYR 4.1 2.5 + - - -
62J PRO* 5.7 0.4 - - + -
63J ILE 3.3 23.4 - - - +
64J VAL* 3.4 32.6 - - + +
65J GLN* 3.7 5.5 + - - +
71J ILE* 3.7 19.9 - - + +
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Residues in contact with HIS 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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27H GLU* 4.5 15.0 + - - -
103H ARG* 4.7 4.3 - - - -
119H ARG* 3.3 27.5 + - - -
23J GLU 3.2 12.3 + - - +
24J THR* 3.2 14.5 + - + +
25J ALA 3.2 1.0 - - - -
26J ALA* 1.3 78.7 - - - +
28J LEU* 1.3 74.2 + - + +
65J GLN* 3.1 28.5 + - - +
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Residues in contact with LEU 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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27H GLU* 5.4 0.2 - - - +
103H ARG* 3.6 49.6 - - + +
104H VAL 6.1 0.9 - - - +
119H ARG* 4.7 8.3 - - - +
24J THR 3.6 8.3 + - - +
25J ALA 3.6 2.4 + - - -
26J ALA 3.5 0.6 - - - -
27J HIS* 1.3 92.6 - - + +
29J GLY* 1.3 60.9 + - - +
30J TYR* 4.4 8.7 - - + -
65J GLN* 2.4 29.3 + - - +
197J ILE* 4.3 4.3 - - + +
198J ARG 3.6 7.6 - - - +
199J GLY* 3.5 36.8 - - - +
200J PRO* 4.3 3.1 - - + -
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Residues in contact with GLY 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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4J PHE* 4.5 6.1 - - - +
5J ALA* 3.3 18.1 - - - +
26J ALA 4.9 1.5 + - - -
28J LEU* 1.3 82.0 - - - +
30J TYR* 1.3 64.8 + - - +
31J SER* 3.5 3.6 + - - -
64J VAL* 6.0 2.5 - - - -
65J GLN* 5.4 2.7 - - - -
200J PRO* 3.9 17.1 - - - +
103L GLU* 5.0 7.6 - - - +
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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