Contacts of the helix formed by residues 9 - 22 (chain A) in PDB entry 1FBA
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 LYS 9 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A PRO 3.7 1.0 + - - -
8A SER* 1.3 72.3 - - - +
10A GLU* 1.3 71.0 + - + +
12A GLN* 3.1 14.8 + - + +
13A ASP* 2.9 60.1 + - - +
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Residues in contact with GLU 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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8A SER* 3.2 20.8 + - - +
9A LYS* 1.3 90.5 + - + +
11A LEU* 1.3 59.8 + - - +
13A ASP* 3.7 7.8 + - - +
14A GLU* 3.2 23.6 + - - +
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Residues in contact with LEU 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 PRO* 3.9 12.1 - - + -
8A SER* 3.0 23.4 + - - +
10A GLU* 1.3 74.1 - - - +
12A GLN* 1.3 68.7 + - - +
14A GLU* 3.4 5.2 + - - +
15A LEU* 3.1 43.7 + - + +
178A GLN 3.4 26.5 - - - +
179A SER* 4.7 4.0 - - - +
181A ARG* 3.7 32.1 - - + -
116B PHE* 3.8 26.0 - - + -
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Residues in contact with GLN 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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6A TYR* 4.1 16.7 - - - +
7A PRO* 2.7 35.2 + - + +
8A SER 2.9 13.4 + - - +
9A LYS* 3.4 13.2 - - + +
11A LEU* 1.3 78.3 - - - +
13A ASP* 1.3 58.6 + - - +
16A ARG* 2.9 39.1 + - - +
222A TYR* 3.6 49.7 + - + +
258D ARG* 4.9 4.4 + - - -
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Residues in contact with ASP 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 LYS* 2.9 54.5 + - - +
10A GLU* 4.0 7.0 - - - +
12A GLN* 1.3 77.2 - - - +
14A GLU* 1.3 57.7 + - - +
16A ARG* 3.0 32.4 + - - +
17A GLU* 2.9 34.3 + - - +
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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 GLU 3.2 16.9 + - - +
11A LEU* 3.9 6.6 - - + +
12A GLN 3.3 0.2 - - - -
13A ASP* 1.3 80.3 - - - +
15A LEU* 1.4 64.2 + - + +
17A GLU* 3.8 8.3 - - - +
18A ILE* 3.1 35.9 + - + +
138A LYS* 2.8 28.3 + - - -
181A ARG* 2.7 47.9 + - - +
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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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7A PRO* 5.8 2.2 - - + -
11A LEU* 3.1 40.0 + - + +
12A GLN 3.9 2.7 - - - +
14A GLU* 1.4 76.6 - - + +
16A ARG* 1.3 65.1 + - - +
18A ILE* 3.4 2.3 + - + -
19A ALA* 3.0 21.5 + - - +
178A GLN* 3.8 37.0 - - + +
181A ARG* 3.8 9.9 - - - +
182A ILE 3.7 39.9 - - - +
183A VAL* 3.3 20.5 - - + +
222A TYR* 4.6 8.3 - - + -
225A GLY* 3.9 14.8 - - - -
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Residues in contact with ARG 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 GLN* 2.9 22.7 + - - +
13A ASP* 3.0 33.4 + - - +
15A LEU* 1.3 76.4 - - - +
17A GLU* 1.3 59.4 + - - +
19A ALA* 3.2 2.6 + - - +
20A GLN* 2.9 64.5 + - + +
222A TYR* 3.1 25.5 + - - +
224A GLU* 3.8 35.2 - - + +
225A GLY* 4.3 0.8 - - - -
265A THR* 4.4 2.0 - - - +
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Residues in contact with GLU 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 ASP 2.9 19.2 + - - +
14A GLU* 3.8 8.5 - - - +
16A ARG* 1.3 78.8 - - - +
18A ILE* 1.3 65.3 + - - +
20A GLN* 3.4 11.9 + - - +
21A LYS* 3.1 54.1 + - + +
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Residues in contact with ILE 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 36.4 + - + +
15A LEU* 3.8 4.5 - - - +
16A ARG 3.3 0.2 - - - -
17A GLU* 1.3 79.1 - - + +
19A ALA* 1.3 64.3 + - - +
21A LYS* 3.2 11.9 + - - +
22A ILE* 3.1 37.2 + - + +
103A ILE* 4.7 7.2 - - + -
138A LYS* 3.8 25.6 - - - +
143A ASP* 3.7 41.7 - - + +
181A ARG 4.3 3.6 - - - +
183A VAL* 3.7 13.0 - - + -
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Residues in contact with ALA 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 3.0 17.0 + - - +
16A ARG 3.7 3.4 - - - +
18A ILE* 1.3 77.7 - - - +
20A GLN* 1.3 61.1 + - - +
22A ILE* 3.3 21.3 + - - +
23A VAL* 3.3 17.2 + - - +
183A VAL* 4.3 11.4 - - + -
224A GLU 4.0 7.9 - - - +
225A GLY 4.6 1.1 - - - -
226A THR 4.2 4.9 - - - +
227A LEU* 4.1 13.1 - - + +
265A THR* 3.6 23.5 - - + +
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Residues in contact with GLN 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 ARG* 2.9 48.5 + - + +
17A GLU* 3.7 11.2 - - - +
19A ALA* 1.3 75.5 - - - +
21A LYS* 1.3 63.4 + - + +
23A VAL* 3.4 6.0 + - - +
24A ALA* 3.2 21.0 + - - +
265A THR* 3.9 18.0 + - + -
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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 GLU* 3.1 45.9 + - + +
18A ILE* 3.5 11.1 - - + +
20A GLN* 1.3 78.4 - - + +
22A ILE* 1.3 61.7 + - - +
24A ALA* 3.4 19.4 + - - +
27A LYS* 4.7 1.7 + - - +
74A SER* 3.7 9.7 - - - -
103A ILE* 3.5 24.4 - - + +
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Residues in contact with ILE 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 ILE* 3.1 24.3 + - + +
19A ALA* 3.3 7.8 + - - +
21A LYS* 1.3 76.8 - - - +
23A VAL* 1.3 61.8 + - + +
24A ALA 3.4 1.3 + - - -
27A LYS 4.2 8.0 - - - +
28A GLY* 4.5 2.1 + - - -
29A ILE* 3.4 35.4 - - + -
74A SER* 2.6 30.4 + - - +
75A GLY* 5.6 0.2 - - - -
103A ILE* 4.2 14.6 - - + -
144A PHE* 3.6 46.0 - - + -
183A VAL* 4.9 1.6 - - + -
227A LEU* 3.7 24.0 - - + -
268A THR* 4.8 0.2 - - + -
298A THR* 5.1 0.2 - - - +
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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