Contacts of the helix formed by residues 9 - 22 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7C PRO 3.7 1.2 + - - -
8C SER* 1.3 71.9 - - - +
10C GLU* 1.3 70.8 + - - +
12C GLN* 3.3 13.9 + - + +
13C ASP* 2.9 57.5 + - - +
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Residues in contact with GLU 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C SER* 3.1 18.9 - - - +
9C LYS* 1.3 94.6 + - - +
11C LEU* 1.3 61.9 + - - +
13C ASP* 3.6 6.1 + - - +
14C GLU* 3.1 24.3 + - - +
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Residues in contact with LEU 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C PRO* 4.0 12.6 - - + -
8C SER* 3.0 20.8 + - - +
10C GLU* 1.3 76.8 - - - +
12C GLN* 1.3 66.5 + - - +
14C GLU* 3.2 7.6 + - - +
15C LEU* 2.9 45.1 + - + +
178C GLN 3.7 21.8 - - - +
179C SER* 4.9 4.5 - - - +
181C ARG* 3.9 26.9 - - + -
116D PHE* 3.7 31.4 - - + -
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Residues in contact with GLN 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258B ARG* 4.9 4.2 + - - -
6C TYR* 4.2 16.1 - - - +
7C PRO* 2.7 36.3 + - + +
8C SER 2.9 15.2 + - - +
9C LYS* 3.5 12.4 - - + +
11C LEU* 1.3 78.5 - - - +
13C ASP* 1.3 57.8 + - - +
15C LEU* 4.9 0.7 - - - -
16C ARG* 2.9 38.9 + - - +
222C TYR* 3.5 47.8 + - + +
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Residues in contact with ASP 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C LYS* 2.9 50.7 + - - +
10C GLU* 3.9 6.0 + - - +
12C GLN* 1.3 77.7 - - - +
14C GLU* 1.3 58.2 + - - +
16C ARG* 2.7 38.4 + - - +
17C GLU* 2.9 34.3 + - - +
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Residues in contact with GLU 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C GLU 3.1 17.8 + - - +
11C LEU* 3.7 7.8 - - + +
13C ASP* 1.3 78.6 - - - +
15C LEU* 1.3 63.6 + - + +
17C GLU* 3.3 5.9 + - - +
18C ILE* 3.0 41.9 + - + +
138C LYS* 3.0 25.6 + - - -
181C ARG* 3.1 46.0 + - - +
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Residues in contact with LEU 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C PRO* 5.9 2.0 - - + -
11C LEU* 2.9 35.1 + - + +
12C GLN 4.0 2.0 - - - +
14C GLU* 1.3 74.6 - - + +
16C ARG* 1.3 66.4 + - - +
18C ILE* 3.3 1.6 + - + -
19C ALA* 3.1 21.7 + - - +
178C GLN* 3.7 41.3 - - + +
181C ARG* 3.7 20.6 - - - +
182C ILE 3.7 31.2 - - - +
183C VAL* 3.4 18.7 - - + +
222C TYR* 4.6 9.4 - - + -
225C GLY* 3.8 14.3 - - - -
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Residues in contact with ARG 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C GLN* 2.9 27.9 + - - +
13C ASP* 2.7 40.1 + - - +
15C LEU* 1.3 76.4 - - - +
17C GLU* 1.3 57.5 + - - +
19C ALA* 3.3 2.6 + - - +
20C GLN* 2.9 60.9 + - + +
222C TYR* 2.9 34.9 + - + +
224C GLU* 3.9 33.4 - - + +
225C GLY* 4.4 0.8 - - - -
265C THR* 4.6 2.0 - - - +
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Residues in contact with GLU 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C ASP* 2.9 20.2 + - - +
14C GLU* 3.6 7.1 - - - +
15C LEU 3.2 0.2 - - - -
16C ARG* 1.3 78.5 - - - +
18C ILE* 1.3 64.6 + - + +
20C GLN* 3.5 12.1 + - - +
21C LYS* 3.0 55.5 + - + +
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Residues in contact with ILE 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C GLU* 3.0 39.7 + - + +
15C LEU* 4.5 0.9 - - - -
16C ARG 3.3 0.4 - - - -
17C GLU* 1.3 78.7 - - + +
19C ALA* 1.3 62.8 + - - +
21C LYS* 3.2 12.1 + - + +
22C ILE* 3.1 43.3 + - + +
103C ILE* 4.5 6.2 - - + +
138C LYS* 3.9 18.6 - - - +
143C ASP* 3.8 36.8 - - + +
181C ARG 4.2 4.5 - - - +
183C VAL* 3.7 20.9 - - + -
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Residues in contact with ALA 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C LEU 3.1 16.8 + - - +
16C ARG 3.7 2.7 - - - +
18C ILE* 1.3 76.6 - - - +
20C GLN* 1.3 61.1 + - - +
22C ILE* 3.3 22.1 + - - +
23C VAL* 3.3 17.0 + - - +
183C VAL* 4.1 9.6 - - + +
224C GLU 4.0 7.0 - - - +
226C THR 4.3 4.3 - - - +
227C LEU* 4.1 17.9 - - + +
265C THR* 3.6 24.2 - - + +
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Residues in contact with GLN 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C ARG* 2.9 52.9 + - + +
17C GLU* 3.7 11.9 - - - +
19C ALA* 1.3 76.0 - - - +
21C LYS* 1.3 62.6 + - - +
23C VAL* 3.3 7.2 + - - +
24C ALA* 3.2 19.9 + - - +
265C THR* 3.8 19.2 + - + +
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Residues in contact with LYS 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C GLU* 3.0 46.1 + - + +
18C ILE* 3.2 12.9 + - + +
20C GLN* 1.3 77.0 - - - +
22C ILE* 1.3 62.5 + - - +
24C ALA* 3.4 19.8 + - - +
27C LYS* 5.0 1.4 + - - +
74C SER* 3.8 7.6 - - - -
103C ILE* 3.7 23.3 - - + +
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Residues in contact with ILE 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C ILE* 3.1 30.2 + - + +
19C ALA* 3.3 8.2 + - - +
21C LYS* 1.3 75.7 - - - +
23C VAL* 1.3 61.3 + - + +
24C ALA 3.6 1.4 + - - -
27C LYS* 4.3 6.6 - - - +
28C GLY* 4.7 1.7 - - - -
29C ILE* 3.6 34.7 - - + +
74C SER* 2.6 33.2 + - - +
75C GLY 5.5 0.7 - - - +
103C ILE* 4.1 15.3 - - + -
144C PHE* 3.7 39.3 - - + -
183C VAL* 4.8 1.6 - - + -
227C LEU* 3.8 22.9 - - + -
268C THR* 4.9 0.7 - - + -
298C THR* 5.2 0.3 - - - +
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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