Contacts of the helix formed by residues 4 - 22 (chain A) in PDB entry 1BY7
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 LEU 4 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A ASP* 1.3 76.1 + - - +
5A CYS* 1.4 53.5 + - - +
7A ALA* 3.7 4.9 - - + +
8A ASN* 2.7 35.0 + - - +
60A PHE* 4.5 16.1 - - + -
63A VAL* 6.1 1.6 - - + -
103A ILE* 4.7 13.0 - - + +
106A SER* 3.3 22.7 - - - -
107A PHE* 3.3 69.2 - - + +
110A LEU* 3.3 22.9 - - + +
405A CYS* 4.8 0.7 - - - -
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Residues in contact with CYS 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ASP* 2.8 15.7 + - - +
4A LEU* 1.4 75.9 - - - +
6A VAL* 1.3 64.3 + - - +
8A ASN* 3.8 2.3 + - - +
9A THR* 3.2 26.0 + - - -
110A LEU* 3.8 22.2 - - - -
403A THR* 3.6 23.6 - - - +
404A ASN* 3.7 11.5 - - + +
405A CYS* 2.0 52.2 - - - -
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Residues in contact with VAL 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A GLU 5.4 2.2 - - - +
3A ASP* 3.2 33.3 + - + +
5A CYS* 1.3 74.9 - - - +
7A ALA* 1.3 66.9 + - - +
9A THR* 3.1 4.0 + - - -
10A LEU* 3.0 34.6 + - + +
63A VAL* 3.8 19.3 - - + -
288A TYR* 3.7 33.1 - - + +
404A ASN* 6.3 0.7 - - - +
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Residues in contact with ALA 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ASP 3.1 12.8 + - - +
4A LEU* 3.7 9.2 - - - +
6A VAL* 1.3 78.7 - - - +
8A ASN* 1.4 58.2 + - - +
10A LEU* 3.2 3.6 + - - +
11A PHE* 2.9 31.0 + - - +
58A LEU 3.6 13.7 - - - +
59A GLN* 3.5 26.9 - - - +
60A PHE* 4.2 13.7 - - + -
63A VAL* 3.7 14.0 - - + +
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Residues in contact with ASN 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU 2.7 21.9 + - - +
5A CYS* 3.8 7.4 + - - +
6A VAL 3.2 0.2 - - - -
7A ALA* 1.4 73.2 - - - +
9A THR* 1.3 50.8 + - - +
11A PHE* 3.6 1.6 + - - +
12A ALA* 2.7 36.2 + - - +
32A PRO* 3.0 21.7 - - - +
33A TRP* 3.2 12.9 + - - +
36A SER* 2.6 34.1 + - - +
107A PHE* 6.5 0.4 - - + -
405A CYS* 4.3 7.3 - - - -
406A ILE* 3.0 41.6 + - - +
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Residues in contact with THR 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A CYS 3.2 12.8 + - - -
6A VAL 3.1 8.1 + - - -
8A ASN* 1.3 71.6 - - - +
10A LEU* 1.3 67.4 + - - +
12A ALA* 3.2 6.0 + - - +
13A LEU* 3.0 36.6 + - + +
288A TYR* 3.4 29.4 - - + +
291A LEU* 4.7 7.9 - - + -
404A ASN 4.6 3.8 + - - -
406A ILE* 3.3 37.1 + - + +
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Residues in contact with LEU 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A VAL* 3.0 26.6 + - + +
7A ALA* 3.4 5.8 - - - +
9A THR* 1.3 77.5 - - - +
11A PHE* 1.3 61.9 - - - +
13A LEU* 3.5 4.0 + - - +
14A ASN* 3.1 23.7 + - - +
59A GLN* 3.6 19.8 - - + +
62A GLU* 3.2 28.7 - - - +
63A VAL* 3.6 26.0 - - + -
288A TYR* 3.5 37.5 - - + -
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Residues in contact with PHE 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ALA 2.9 19.9 + - - +
8A ASN* 3.7 6.3 - - - +
10A LEU* 1.3 72.9 - - - +
12A ALA* 1.4 67.9 + - - +
14A ASN* 3.1 4.6 + - - -
15A LEU* 2.8 44.3 + - + +
32A PRO* 4.4 3.6 - - + -
35A ILE* 3.7 35.0 - - + -
36A SER* 3.5 22.0 - - - +
39A MET* 5.4 0.2 - - + -
57A VAL* 3.4 21.3 - - + +
58A LEU* 3.9 32.8 - - + +
59A GLN* 3.6 7.5 - - + +
324A LEU* 4.2 17.0 - - + -
327A MET* 3.7 24.2 - - + -
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Residues in contact with ALA 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ASN 2.7 23.3 + - - +
9A THR* 3.2 8.5 + - - +
11A PHE* 1.4 73.9 - - - +
13A LEU* 1.3 60.6 + - + +
15A LEU* 3.5 7.1 + - - +
16A PHE* 2.9 30.5 + - - +
30A LEU* 5.4 1.9 - - - +
32A PRO* 3.4 35.4 - - + +
406A ILE* 5.1 10.1 - - + -
409A PHE* 5.3 7.8 - - + +
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Residues in contact with LEU 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A THR* 3.0 30.1 + - + +
10A LEU* 4.0 3.6 - - - +
12A ALA* 1.3 75.5 - - + +
14A ASN* 1.3 66.9 + - - +
16A PHE* 3.9 6.2 - - + +
17A LYS* 3.1 24.8 + - - +
286A ILE* 4.0 36.3 - - + +
287A THR* 3.6 10.5 - - - +
288A TYR* 3.4 37.5 - - + +
291A LEU* 4.6 8.3 - - + -
406A ILE* 5.9 1.1 - - + -
409A PHE* 4.0 23.8 - - + -
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Residues in contact with ASN 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A LEU 3.1 18.0 + - - +
11A PHE* 3.8 4.9 - - - +
13A LEU* 1.3 78.1 - - - +
15A LEU* 1.3 58.8 + - - +
17A LYS* 3.4 10.9 + - - +
18A HIS* 2.9 49.3 + - - -
57A VAL* 5.6 1.8 - - - +
59A GLN* 5.0 12.0 + - - +
327A MET* 3.7 23.8 - - + +
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Residues in contact with LEU 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A PHE* 2.8 40.1 + - + +
12A ALA* 3.7 4.9 - - - +
14A ASN* 1.3 69.5 - - - +
16A PHE* 1.3 63.2 + - - +
18A HIS* 3.8 0.6 - - - +
19A LEU* 2.8 34.4 + - + +
30A LEU* 3.9 25.8 - - + -
32A PRO* 5.3 0.9 - - + -
35A ILE* 3.8 28.7 - - + -
320A LEU* 4.7 15.3 - - + -
323A ILE* 3.7 24.2 - - + -
324A LEU* 4.8 6.1 - - + -
327A MET* 3.7 20.8 - - + +
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Residues in contact with PHE 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ALA 2.9 18.4 + - - +
13A LEU* 3.9 7.6 - - + +
14A ASN 3.4 0.2 - - - -
15A LEU* 1.3 78.6 - - - +
17A LYS* 1.3 59.0 + - - +
19A LEU* 3.2 7.2 + - - +
20A ALA* 2.8 34.2 + - + +
28A LEU* 3.4 39.5 - - + -
30A LEU* 5.2 5.1 - - + +
283A GLU* 3.7 46.4 - - + -
286A ILE* 5.5 8.1 - - + -
395A LEU* 3.7 20.6 - - + -
409A PHE* 3.6 37.7 - + + -
411A ARG* 4.0 12.6 - - + -
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Residues in contact with LYS 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LEU 3.1 17.8 + - - +
14A ASN* 3.6 15.0 - - - +
16A PHE* 1.3 82.5 - - - +
18A HIS* 1.3 70.3 + - + +
20A ALA* 3.6 6.9 + - - +
21A LYS* 3.4 28.8 + - - +
283A GLU 3.7 21.4 + - - -
284A SER* 4.4 11.5 + - - +
286A ILE* 5.0 9.3 + - - +
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Residues in contact with HIS 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ASN* 2.9 48.6 + - - +
15A LEU 3.9 0.7 - - - +
17A LYS* 1.3 85.5 - - + +
19A LEU* 1.3 64.8 + - - +
21A LYS* 3.1 25.1 + - + +
22A ALA 3.8 1.7 + - - -
323A ILE* 3.8 26.6 - - + +
326A SER* 3.4 41.6 + - - +
327A MET* 3.5 17.5 - - + +
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Residues in contact with LEU 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A LEU* 2.8 19.8 + - + +
16A PHE 3.5 4.3 - - - +
18A HIS* 1.3 78.5 - - - +
20A ALA* 1.3 56.9 + - - +
22A ALA* 2.9 14.5 + - + +
23A SER* 2.8 26.5 + - - -
28A LEU* 3.8 17.7 - - + -
30A LEU* 3.2 34.8 - - + -
318A TYR* 3.8 37.9 - - + -
320A LEU* 4.7 8.3 - - + -
323A ILE* 3.9 28.9 - - + +
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Residues in contact with ALA 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A PHE* 2.8 21.6 + - + +
17A LYS* 3.9 9.9 - - - +
18A HIS 3.2 0.2 - - - -
19A LEU* 1.3 74.8 - - - +
21A LYS* 1.3 64.1 + - - +
23A SER 3.4 9.2 - - - -
24A PRO* 3.0 29.0 - - + +
28A LEU* 4.3 2.0 - - + +
283A GLU* 3.9 10.5 - - - +
411A ARG* 3.5 23.1 - - - +
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Residues in contact with LYS 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LYS* 3.4 22.6 + - - +
18A HIS* 3.1 16.6 + - + +
20A ALA* 1.3 78.0 - - - +
22A ALA* 1.3 61.8 + - - +
24A PRO* 3.9 9.3 - - - +
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Residues in contact with ALA 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A HIS 3.8 0.2 + - - -
19A LEU* 2.9 14.8 + - + +
21A LYS* 1.3 79.8 - - - +
23A SER* 1.3 61.6 + - - +
24A PRO* 3.5 5.7 - - - +
323A ILE* 4.2 20.4 - - + -
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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
------------------------------------------------------------
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