Contacts of the helix formed by residues 9 - 28 (chain C) in PDB entry 5FFO
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 9 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C ASP* 1.3 80.3 - - - +
10C GLU* 1.3 59.9 + - + +
11C LEU 3.4 0.2 - - - -
12C VAL* 4.0 15.0 + - + +
13C LYS* 3.4 38.2 + - - +
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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
----------------------------------------------------------
8C ASP 4.2 2.7 - - - +
9C MET* 1.3 78.1 - - + +
11C LEU* 1.3 67.6 + - + +
12C VAL 3.3 0.4 - - - -
13C LYS* 3.7 27.3 + - - +
14C ARG* 3.4 30.0 + - + +
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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
----------------------------------------------------------
8C ASP* 3.8 34.7 + - - +
9C MET 3.4 0.4 - - - -
10C GLU* 1.3 80.5 - - + +
12C VAL* 1.3 66.0 + - + +
13C LYS 3.5 0.2 + - - -
14C ARG* 3.6 14.4 + - + +
15C LYS* 3.9 10.7 + - - +
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Residues in contact with VAL 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ASP 3.1 20.2 + - - +
9C MET* 4.1 16.6 - - - +
10C GLU 3.3 0.6 - - - -
11C LEU* 1.3 80.2 - - + +
13C LYS* 1.3 63.6 + - + +
14C ARG 3.5 0.3 + - - -
15C LYS* 3.6 13.5 + - - +
16C ARG* 4.1 5.5 + - - +
323C ALA* 6.1 5.2 - - + -
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Residues in contact with LYS 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 MET* 3.4 36.6 - - - +
10C GLU* 3.7 29.0 + - - +
11C LEU 3.3 0.6 - - - -
12C VAL* 1.3 80.2 - - + +
14C ARG* 1.3 65.1 + - + +
15C LYS 3.4 0.5 + - - -
16C ARG* 3.6 11.4 + - - +
17C ILE* 3.4 21.7 + - + +
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Residues in contact with ARG 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* 3.4 21.5 + - - +
11C LEU* 3.6 11.1 + - + +
12C VAL 3.3 1.0 - - - -
13C LYS* 1.3 79.8 - - + +
15C LYS* 1.3 60.6 + - - +
17C ILE* 3.7 41.7 + - - +
18C GLU* 3.8 27.1 + - - +
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Residues in contact with LYS 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C LEU 3.9 7.4 + - - +
12C VAL* 3.6 10.4 + - - +
13C LYS 3.3 0.8 - - - -
14C ARG* 1.3 77.2 - - - +
16C ARG* 1.3 65.6 + - - +
17C ILE 3.4 0.3 + - - -
18C GLU* 3.5 12.3 + - - +
19C ALA* 3.5 10.6 + - - +
299C TYR* 5.9 3.1 - - - +
323C ALA* 4.6 25.1 - - + +
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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 VAL 4.1 5.8 + - - +
13C LYS* 3.6 10.2 + - - +
15C LYS* 1.3 76.7 - - - +
17C ILE* 1.3 61.5 + - + +
19C ALA* 3.0 8.3 + - - +
20C ILE* 2.9 56.5 + - + +
320C GLY* 4.7 5.9 - - - -
321C ALA* 3.1 46.4 - - - +
322C SER 6.0 1.3 - - - +
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Residues in contact with ILE 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 LYS* 3.4 20.4 - - + +
14C ARG* 3.7 43.3 - - - +
15C LYS 3.3 1.0 - - - -
16C ARG* 1.3 78.7 - - + +
18C GLU* 1.3 62.9 + - + +
20C ILE* 3.0 12.5 + - + +
21C ARG* 2.9 28.6 + - + +
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Residues in contact with GLU 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C ARG* 3.8 20.8 + - - +
15C LYS* 3.5 10.1 + - - +
16C ARG 3.3 0.6 - - - -
17C ILE* 1.3 82.1 - - + +
19C ALA* 1.3 58.8 + - - +
21C ARG* 3.5 38.3 + - - +
22C GLY* 3.4 16.1 + - - -
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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
----------------------------------------------------------
15C LYS* 3.5 9.5 + - + +
16C ARG* 3.0 13.5 + - - +
18C GLU* 1.3 77.1 - - - +
20C ILE* 1.3 60.1 + - - +
22C GLY* 3.6 1.7 + - - +
23C GLN* 3.0 27.5 + - - +
299C TYR* 4.3 27.4 - - + +
319C PRO* 3.8 20.9 - - - +
320C GLY* 4.9 4.7 - - - -
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Residues in contact with ILE 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 58.5 + - + +
17C ILE* 3.0 12.3 + - + +
19C ALA* 1.3 76.5 - - - +
21C ARG* 1.3 60.4 + - - +
23C GLN* 3.3 22.4 - - - +
24C ILE* 2.8 54.9 + - + +
319C PRO 4.8 4.9 - - - +
320C GLY* 5.2 1.1 - - - -
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Residues in contact with ARG 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C ILE* 2.9 17.0 + - + +
18C GLU* 3.5 35.8 + - - +
19C ALA 3.3 0.2 - - - -
20C ILE* 1.3 78.9 - - - +
22C GLY* 1.3 62.9 + - - +
24C ILE* 4.3 4.0 - - - +
25C LEU* 3.2 44.7 + - + +
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Residues in contact with GLY 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C GLU 3.4 11.0 + - - -
19C ALA* 3.6 3.8 + - - -
20C ILE 3.3 0.2 - - - -
21C ARG* 1.3 80.3 - - - +
23C GLN* 1.3 57.8 + - - +
25C LEU* 4.5 5.6 - - - +
26C SER* 3.0 25.4 + - - -
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Residues in contact with GLN 23 (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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19C ALA 3.0 17.2 + - - +
20C ILE* 3.0 30.2 + - - +
22C GLY* 1.3 75.2 - - - +
24C ILE* 1.3 57.6 + - - +
26C SER* 2.5 22.7 + - - +
27C LYS* 2.7 53.5 + - + +
74C TYR* 5.8 4.8 - - - -
319C PRO* 4.0 34.7 + - + +
320C GLY* 5.5 0.2 - - - -
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Residues in contact with ILE 24 (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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20C ILE* 2.8 42.6 + - + +
21C ARG* 4.3 3.8 - - - +
23C GLN* 1.3 74.8 - - + +
25C LEU* 1.3 62.9 + - + +
27C LYS* 3.2 10.2 + - + +
28C LEU* 2.8 52.5 + - + +
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Residues in contact with LEU 25 (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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21C ARG* 3.2 36.9 + - + +
22C GLY* 4.5 4.7 - - - +
23C GLN 3.3 0.4 - - - -
24C ILE* 1.3 82.3 - - + +
26C SER* 1.3 58.2 + - - +
28C LEU* 5.9 0.9 - - + -
29C ARG* 3.0 5.2 + - - -
30C LEU* 2.7 65.6 + - + +
31C ALA 3.9 20.4 - - - +
32C SER* 4.9 1.1 - - - -
33C PRO* 4.7 16.8 - - + -
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Residues in contact with SER 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C GLY 3.0 17.2 + - - -
23C GLN* 2.5 23.6 + - - +
25C LEU* 1.3 77.7 - - - +
27C LYS* 1.3 65.5 + - - +
29C ARG* 3.5 7.8 + - - +
75C TYR* 3.3 25.5 - - - -
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Residues in contact with LYS 27 (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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23C GLN* 2.7 55.7 + - + +
24C ILE* 3.8 9.4 - - + +
26C SER* 1.3 76.8 - - - +
28C LEU* 1.3 63.9 + - + +
29C ARG* 3.6 1.2 + - - +
74C TYR* 2.3 50.7 + - + +
75C TYR* 3.7 15.9 + - - +
76C ALA* 3.0 31.9 + - + +
238C ARG* 5.1 1.7 + - - -
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Residues in contact with LEU 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C ILE* 2.8 38.7 + - + +
25C LEU* 5.5 1.8 - - + -
27C LYS* 1.3 77.0 - - + +
29C ARG* 1.3 70.3 + - - +
30C LEU* 3.3 32.8 + - + +
76C ALA* 3.7 22.9 - - + -
238C ARG* 3.6 26.3 + - - +
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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
------------------------------------------------------------
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