Contacts of the helix formed by residues 6 - 22 (chain A) in PDB entry 1F9O
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 6 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ALA* 1.3 66.9 - - - +
7A LYS* 1.3 64.3 + - - +
8A VAL* 3.2 26.5 + - - +
9A TYR* 3.3 21.1 + - + -
10A GLN* 3.0 19.2 + - - +
623A TYR* 4.7 2.0 - - - -
624A ALA* 2.8 25.3 + - - +
627A PHE 3.0 27.9 + - - +
628A PRO* 3.7 13.0 - - + +
629A ASP* 3.5 24.4 + - - +
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Residues in contact with LYS 7 (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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5A ALA 2.9 10.1 + - - +
6A ASN* 1.3 72.9 + - - +
8A VAL* 1.3 67.3 + - + +
10A GLN* 4.1 14.1 - - + +
11A ASP* 3.0 54.4 + - - +
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Residues in contact with VAL 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ASN* 3.2 12.8 + - - +
7A LYS* 1.3 83.5 - - + +
9A TYR* 1.3 77.1 + - + +
11A ASP* 3.3 8.7 + - - +
12A ARG* 3.3 48.9 + - - +
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Residues in contact with TYR 9 (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 ASN* 3.3 21.5 + - - +
8A VAL* 1.3 85.1 - - + +
10A GLN* 1.3 64.0 + - - +
12A ARG* 3.3 33.3 + - - +
13A PHE* 3.2 17.8 + - - +
522A GLN* 2.9 34.8 + - + +
525A LEU* 4.6 11.7 - - + -
526A ASP* 2.8 21.2 + - - -
620A ASN* 3.8 40.7 - - - +
623A TYR* 3.5 32.8 - + - -
624A ALA* 3.8 13.9 - - + +
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Residues in contact with GLN 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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5A ALA* 4.0 16.1 + - - +
6A ASN 3.0 16.6 + - - +
7A LYS* 3.7 15.2 - - - +
8A VAL 3.3 0.2 - - - -
9A TYR* 1.3 76.3 - - - +
11A ASP* 1.3 64.5 + - - +
13A PHE* 3.1 8.3 + - - +
14A GLU* 2.9 44.9 + - - +
70A PHE* 3.7 46.3 + - + +
624A ALA* 3.7 11.1 - - + +
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Residues in contact with ASP 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 LYS* 3.0 46.6 + - - +
8A VAL* 3.4 11.6 - - - +
9A TYR 3.2 0.2 - - - -
10A GLN* 1.3 78.5 + - - +
12A ARG* 1.3 57.2 + - + +
14A GLU* 3.2 20.1 + - - +
15A SER* 2.9 29.4 + - - -
529A TRP* 5.5 0.2 - - - -
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Residues in contact with ARG 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 VAL* 3.4 33.9 - - - +
9A TYR* 3.3 27.6 + - - +
10A GLN 3.2 0.6 - - - -
11A ASP* 1.3 77.2 - - + +
13A PHE* 1.3 61.3 + - - +
15A SER* 3.4 2.4 + - - -
16A MET* 3.1 28.5 + - - +
525A LEU 4.4 1.6 + - - -
526A ASP* 2.9 31.9 + - - +
529A TRP* 3.6 74.6 - - + +
530A ASN* 4.8 6.1 + - - +
620A ASN* 4.1 15.7 + - - -
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Residues in contact with PHE 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 TYR 3.2 12.1 + - - +
10A GLN 3.1 9.1 + - - +
12A ARG* 1.3 74.7 - - - +
14A GLU* 1.3 62.4 + - + +
16A MET* 3.2 6.4 + - - +
17A TYR* 2.7 51.7 + + + +
63A LEU* 3.7 12.1 - - + -
66A MET* 3.2 38.4 - - + -
67A HIS* 3.6 28.7 - - + -
70A PHE* 3.7 22.9 - + + -
617A ALA* 3.3 44.6 - - + +
618A VAL* 4.3 1.1 - - - -
620A ASN* 4.2 6.7 - - + +
621A GLY 4.4 4.0 - - - +
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Residues in contact with GLU 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 GLN* 2.9 47.0 + - + +
11A ASP* 3.5 21.9 - - - +
13A PHE* 1.3 88.3 - - + +
15A SER* 1.3 63.0 + - - +
17A TYR* 3.4 6.8 + - - +
18A SER* 3.1 26.5 + - - -
67A HIS* 6.1 2.7 - - - +
70A PHE* 4.5 10.5 - - + +
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Residues in contact with SER 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 ASP 2.9 14.3 + - - -
12A ARG 3.5 9.2 - - - -
14A GLU* 1.3 76.3 - - - +
16A MET* 1.3 64.4 + - - +
18A SER* 3.0 16.4 + - - -
19A LYS* 3.1 31.6 + - - +
529A TRP* 3.7 24.0 - - - -
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Residues in contact with MET 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 ARG 3.1 14.0 + - - +
13A PHE 3.6 6.7 - - - +
15A SER* 1.3 78.5 - - - +
17A TYR* 1.3 57.2 + - - +
19A LYS* 3.1 10.5 + - - +
20A ILE* 2.8 42.0 + - + +
529A TRP* 4.8 6.1 - - + -
537A GLY* 3.7 26.9 - - - +
538A ILE* 4.6 1.1 - - + -
613A GLN* 3.3 52.0 - - + +
616A PHE* 3.6 38.6 - - + -
617A ALA* 3.9 15.9 - - + -
620A ASN* 4.9 0.2 - - - +
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Residues in contact with TYR 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 PHE* 2.7 31.7 + + + +
14A GLU* 3.5 10.8 - - - +
16A MET* 1.3 73.5 - - - +
18A SER* 1.3 65.8 + - - +
20A ILE* 3.4 4.3 + - - +
21A LYS* 3.0 56.5 + - + +
63A LEU* 3.9 27.8 - - + -
64A GLU* 2.7 37.6 + - - -
67A HIS* 3.2 56.5 + + + -
76A GLY* 5.3 0.9 - - - -
617A ALA* 5.0 0.4 - - - +
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Residues in contact with SER 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 GLU 3.1 13.1 + - - -
15A SER* 3.0 10.9 + - - -
17A TYR* 1.3 82.4 - - - +
19A LYS* 1.3 59.2 + - - +
21A LYS* 3.9 2.6 - - - -
22A ASP* 2.9 31.9 + - - +
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Residues in contact with LYS 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 SER* 3.1 26.4 + - - +
16A MET* 3.1 14.5 + - - +
18A SER* 1.3 77.4 - - - +
20A ILE* 1.3 65.3 + - + +
21A LYS 3.5 0.2 + - - -
22A ASP* 3.5 5.6 + - - -
25A ASN* 2.7 35.0 + - - +
27A TYR* 3.9 3.5 - - - -
529A TRP* 5.7 5.9 - - - -
533A SER* 4.9 8.1 - - - -
534A ASP 3.0 22.8 + - - +
535A SER* 3.6 20.2 - - - +
536A LYS 4.2 8.3 - - - +
537A GLY* 3.7 21.2 + - - +
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Residues in contact with ILE 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 MET* 2.8 32.2 + - + +
17A TYR 3.9 3.4 - - - +
19A LYS* 1.3 75.4 - - + +
21A LYS* 1.3 60.5 + - + +
22A ASP 4.7 1.6 - - - +
27A TYR* 3.4 27.1 - - + +
28A PHE* 3.4 16.2 - - + -
63A LEU* 3.8 35.7 - - + -
536A LYS 5.4 0.9 - - - +
610A PHE* 3.7 29.2 - - + -
613A GLN* 3.8 44.4 - - + +
614A SER* 3.8 6.1 - - - +
617A ALA* 4.6 1.3 - - + -
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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
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17A TYR* 3.0 49.3 + - + +
18A SER* 4.4 2.7 - - - +
20A ILE* 1.3 82.6 - - + +
22A ASP* 1.3 65.1 + - - +
23A PRO* 3.0 10.4 - - - +
28A PHE* 4.0 33.2 - - + -
60A TYR* 4.5 8.9 + - - -
63A LEU* 4.4 2.7 - - + -
64A GLU* 2.7 29.1 + - - +
76A GLY* 5.7 2.2 - - - -
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Residues in contact with ASP 22 (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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18A SER 2.9 21.3 + - - +
19A LYS* 3.7 8.7 - - - +
20A ILE 3.4 2.9 - - - +
21A LYS* 1.3 74.3 - - - +
23A PRO* 1.3 72.0 - - - +
24A ALA* 3.2 25.3 + - - +
25A ASN* 2.8 42.1 + - - +
26A GLY 3.8 3.3 + - - -
27A TYR 5.1 1.0 + - - -
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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