Contacts of the helix formed by residues 1 - 13 (chain B) in PDB entry 3D9L
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 MET 1 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2B GLU* 1.3 66.3 + - - +
4B VAL* 3.1 36.4 + - + +
5B LYS* 3.0 40.3 + - - +
39B PHE* 3.7 36.1 - - + -
42B HIS* 3.4 41.3 - - + +
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Residues in contact with GLU 2 (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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18A LYS* 3.0 42.6 + - - +
1B MET* 1.3 68.9 - - - +
3B ALA* 1.3 54.8 + - - +
5B LYS* 3.1 7.9 + - - +
6B THR* 2.8 45.0 + - - +
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Residues in contact with ALA 3 (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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1B MET* 3.3 0.8 - - - +
2B GLU* 1.3 79.4 - - - +
4B VAL* 1.3 57.5 + - - +
6B THR* 3.7 6.7 - - - +
7B PHE* 3.1 25.6 + - - +
32B ALA 4.4 2.3 - - - +
35B LYS* 4.2 9.6 - - + +
36B ALA* 3.7 30.7 - - + +
39B PHE* 4.5 15.2 - - + -
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Residues in contact with VAL 4 (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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1B MET* 3.1 43.3 + - + +
3B ALA* 1.3 75.3 - - - +
5B LYS* 1.3 60.7 + - + +
7B PHE* 3.2 7.4 + - + +
8B ASN* 2.8 45.9 + - - +
36B ALA* 4.7 3.6 - - + -
39B PHE* 3.5 27.1 - - + +
42B HIS* 3.9 23.3 - - + -
43B VAL* 5.0 2.7 - - - +
46B SER* 4.7 4.3 - - - +
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Residues in contact with LYS 5 (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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15A ASN* 3.0 26.5 + - - +
16A ASP* 3.5 17.5 - - - +
17A TYR 4.4 1.6 - - - +
18A LYS* 3.0 36.4 + - + +
55A LYS* 3.8 24.0 - - - +
57A GLU* 5.4 2.2 + - - -
58A TYR* 3.1 20.2 + - - +
1B MET 3.0 28.2 + - - +
2B GLU* 3.7 8.1 - - - +
4B VAL* 1.3 74.4 - - + +
6B THR* 1.3 61.5 + - - +
8B ASN* 3.8 2.9 - - - +
9B SER* 3.0 22.5 + - - -
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Residues in contact with THR 6 (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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18A LYS* 3.6 23.1 - - + +
2B GLU* 2.8 27.0 + - - +
3B ALA* 3.7 8.5 - - - +
5B LYS* 1.3 76.5 - - - +
7B PHE* 1.3 62.4 + - - +
9B SER* 3.3 6.1 + - - -
10B GLU* 3.1 26.2 + - + +
32B ALA* 4.4 14.6 - - + -
35B LYS* 6.5 1.1 - - + -
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Residues in contact with PHE 7 (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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3B ALA 3.1 15.0 + - - +
4B VAL* 3.2 10.3 + - + +
6B THR* 1.3 73.2 - - - +
8B ASN* 1.3 75.7 + - - +
10B GLU* 3.0 2.8 + - + +
11B LEU* 2.9 41.4 + - + +
29B ILE* 3.7 31.6 - - + -
32B ALA* 3.9 15.2 - - + +
33B ALA* 3.7 28.3 - - + -
43B VAL* 3.6 39.0 - - + -
46B SER* 3.8 13.5 - - - -
47B VAL* 3.4 23.8 - - + -
69B ILE* 4.1 2.2 - - + -
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Residues in contact with ASN 8 (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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16A ASP* 3.0 37.9 + - - +
17A TYR* 3.5 13.3 - - + -
4B VAL* 2.8 34.0 + - - +
5B LYS* 3.8 1.9 - - - +
6B THR 3.4 0.2 - - - -
7B PHE* 1.3 75.9 - - - +
9B SER* 1.3 56.9 + - - +
11B LEU* 4.0 4.5 - - - +
12B TYR* 2.9 33.4 + - - +
46B SER* 2.7 32.8 + - - -
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Residues in contact with SER 9 (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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17A TYR* 3.5 13.7 - - - +
18A LYS* 2.6 43.1 + - - -
20A PRO 4.3 1.9 + - - -
21A ILE* 5.7 0.3 - - - -
22A SER* 5.3 1.0 - - - -
5B LYS 3.0 6.3 + - - -
6B THR* 3.4 10.8 - - - -
7B PHE 3.2 0.2 - - - -
8B ASN* 1.3 73.7 - - - +
10B GLU* 1.3 65.4 + - - +
12B TYR* 4.0 1.1 - - - +
13B SER* 3.1 27.7 + - - -
0Y BTN 3.5 19.0 - - - +
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Residues in contact with GLU 10 (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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6B THR* 3.1 19.4 + - + +
7B PHE 3.0 7.7 + - - +
9B SER* 1.3 75.6 - - - +
11B LEU* 1.3 63.0 + - - +
13B SER* 3.0 16.5 + - - -
14B LEU 3.8 0.7 + - - -
25B LYS* 3.0 32.1 + - - -
28B GLN* 3.0 35.4 - - - +
29B ILE* 3.4 22.7 + - + +
32B ALA* 3.8 19.7 - - + -
0Y BTN 2.7 31.0 + - - +
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Residues in contact with LEU 11 (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 PHE* 2.9 37.6 + - + +
8B ASN* 4.0 3.8 - - - +
10B GLU* 1.3 77.4 - - - +
12B TYR* 1.3 61.7 - - - +
14B LEU* 3.2 33.0 + - + +
29B ILE* 4.1 6.9 - - + +
46B SER* 3.4 36.6 - - - +
47B VAL* 3.8 5.6 - - + -
50B PHE* 3.7 28.9 - - + -
65B VAL* 4.0 38.6 - - + -
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Residues in contact with TYR 12 (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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10A GLU* 5.1 0.3 + - - -
17A TYR* 3.4 32.1 - + + -
22A SER* 3.5 13.2 - - - -
24A ALA* 3.8 8.8 + - + +
25A LYS* 3.5 45.2 + - + -
28A GLN* 3.5 27.5 - - - +
8B ASN 2.9 20.0 + - - +
9B SER 4.4 1.3 - - - +
11B LEU* 1.3 77.3 - - - +
13B SER* 1.3 57.6 + - - +
14B LEU 3.0 0.4 - - - -
15B ASN* 2.8 47.6 + - - +
49B LYS* 6.3 1.3 - - - -
50B PHE* 4.4 11.0 - + + -
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Residues in contact with SER 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A SER* 3.9 12.3 - - - -
9B SER 3.1 12.7 + - - -
10B GLU 3.0 4.5 + - - -
11B LEU 3.2 0.4 - - - -
12B TYR* 1.3 72.9 - - - +
14B LEU* 1.3 59.6 + - - +
15B ASN 3.0 2.0 - - - +
16B ASP* 2.9 33.0 + - - +
17B TYR* 3.0 18.7 - - - -
25B LYS* 2.8 30.7 + - - -
0Y BTN 3.1 26.2 - - - +
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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