Contacts of the helix formed by residues 4 - 20 (chain C) in PDB entry 4FBI
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 PHE 4 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C SER* 1.3 73.2 + - - +
5C LEU* 1.3 68.4 + - + +
7C SER 3.2 2.1 + - - -
8C LYS* 3.0 50.0 + - + +
75C ILE* 3.5 56.3 - - + -
77C LYS 6.0 0.4 - - - -
54D GLU* 4.2 3.7 + - - +
64D ASP* 3.6 17.7 - - - -
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Residues in contact with LEU 5 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C SER* 3.4 1.4 + - - -
4C PHE* 1.3 84.2 - - + +
6C LEU* 1.3 65.1 + - - +
8C LYS* 3.1 3.4 + - - -
9C VAL* 2.9 39.1 + - + +
71C LEU* 4.6 1.6 - - + -
75C ILE* 4.2 15.5 - - + -
50D ILE* 4.1 14.8 - - + +
53D LEU* 4.8 8.3 - - + -
54D GLU* 3.8 35.3 + - + +
57D MET* 3.5 26.9 - - + -
64D ASP* 4.5 11.2 - - - +
68D PHE* 3.8 25.4 - - + -
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Residues in contact with LEU 6 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C SER* 3.1 32.6 + - - +
5C LEU* 1.3 77.1 - - + +
7C SER 1.3 61.6 + - - +
10C SER* 3.0 19.2 + - - -
44C ASN* 3.8 8.1 - - - +
45C SER* 2.9 32.1 + - - +
46C ALA* 3.5 35.9 - - + +
50D ILE* 3.6 23.8 - - + +
51D LYS* 4.0 19.7 - - + -
54D GLU* 3.9 15.9 - - + +
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Residues in contact with SER 7 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C SER 3.0 16.4 + - - -
4C PHE 3.2 1.3 + - - -
6C LEU* 1.3 76.8 + - - +
8C LYS* 1.3 57.3 - - - +
10C SER* 3.4 4.5 - - - -
11C PHE* 2.9 28.9 - - - -
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Residues in contact with LYS 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C PHE* 3.0 49.3 + - + +
5C LEU 3.1 3.6 + - - +
7C SER 1.3 76.7 - - - +
9C VAL* 1.4 59.8 + - - +
11C PHE* 3.3 5.9 + - + +
12C VAL* 2.9 33.4 + - - +
71C LEU* 3.8 15.5 - - + -
74C GLU* 2.5 51.9 + - + +
75C ILE* 4.1 16.4 - - + -
77C LYS* 4.6 10.7 + - - +
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Residues in contact with VAL 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C LEU* 2.9 36.7 + - + +
6C LEU 3.8 3.4 - - - +
8C LYS* 1.4 73.8 - - - +
10C SER* 1.3 64.4 + - - +
12C VAL* 3.3 3.2 + - - +
13C ILE* 3.0 42.4 + - + +
45C SER* 4.0 10.5 - - - +
48C LEU* 4.0 16.2 - - + -
53C LEU* 5.3 1.1 - - + -
67C PHE* 4.5 10.3 - - + -
71C LEU* 3.8 20.8 - - + +
50D ILE* 4.2 22.4 - - + -
68D PHE* 5.6 1.1 - - + -
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Residues in contact with SER 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C LEU 3.0 18.5 + - - -
7C SER 3.6 4.7 - - - -
9C VAL* 1.3 77.7 - - - +
11C PHE* 1.3 64.2 + - - +
13C ILE* 3.4 6.3 + - - +
14C LYS* 3.0 24.6 + - - +
41C ILE 2.7 24.5 + - - -
42C GLU* 3.4 26.6 + - - +
43C ARG 4.4 2.1 + - - -
44C ASN* 4.2 1.9 + - - -
45C SER* 3.3 13.1 + - - -
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Residues in contact with PHE 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C SER 2.9 18.8 - - - -
8C LYS* 3.6 9.9 - - + +
9C VAL 3.2 0.2 - - - -
10C SER* 1.3 78.7 - - - +
12C VAL* 1.3 59.3 + - - +
14C LYS* 3.3 7.8 + - + +
15C LYS* 2.8 52.7 + - + +
74C GLU* 3.6 44.2 - - + -
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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 LYS 2.9 21.1 + - - +
9C VAL 3.9 3.1 - - - +
11C PHE* 1.3 73.5 - - + +
13C ILE* 1.3 65.1 + - - +
15C LYS* 3.6 7.7 - - + +
16C ILE* 2.9 45.2 + - + +
67C PHE* 3.6 22.9 - - + +
70C MET* 4.0 20.0 - - + +
71C LEU* 3.9 20.0 - - + -
74C GLU* 3.6 27.1 - - + -
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Residues in contact with ILE 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C VAL* 3.0 25.3 + - + +
10C SER* 3.7 7.0 - - - +
12C VAL* 1.3 77.9 - - - +
14C LYS* 1.3 57.6 + - - +
16C ILE* 3.4 1.4 + - - +
17C ARG* 2.9 27.0 + - - +
27C LEU* 4.9 6.7 - - + -
38C ILE* 5.7 0.7 - - + -
41C ILE* 4.2 21.3 - - + +
42C GLU* 3.9 19.5 - - + +
48C LEU* 3.7 29.4 - - + -
53C LEU* 4.4 7.9 - - + -
56C ILE* 4.3 22.4 - - + -
60C LEU* 4.3 6.8 - - + +
67C PHE* 3.8 20.6 - - + -
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Residues in contact with LYS 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C SER 3.0 17.2 + - - +
11C PHE* 3.8 8.3 - - + +
13C ILE* 1.3 75.4 - - - +
15C LYS* 1.3 58.3 - - - +
17C ARG* 3.3 19.3 + - - +
18C LEU* 2.8 53.4 + - + +
24C GLN* 5.7 1.2 - - - +
42C GLU* 3.4 31.5 + - + +
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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 PHE* 2.8 43.0 + - + +
12C VAL* 3.2 8.3 + - + +
14C LYS* 1.3 78.8 - - - +
16C ILE* 1.3 56.9 + - - +
18C LEU* 3.4 6.8 + - - +
19C GLU* 2.9 67.7 + - - +
70C MET* 3.5 28.7 - - + -
74C GLU* 5.0 7.2 - - + +
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Residues in contact with ILE 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C VAL* 2.9 39.3 + - + +
13C ILE 4.0 2.2 - - - +
15C LYS* 1.3 75.2 - - - +
17C ARG* 1.3 63.9 + - - +
19C GLU* 3.1 8.2 + - + +
20C LYS* 2.9 39.1 + - - +
60C LEU* 3.9 29.6 - - + -
62C VAL* 4.1 15.9 - - + -
67C PHE* 3.6 20.9 - - + -
70C MET* 3.5 32.5 - - + -
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Residues in contact with ARG 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 ILE 2.9 18.9 + - - +
14C LYS* 3.6 21.1 - - - +
16C ILE* 1.3 76.9 - - - +
18C LEU* 1.3 84.0 + - - +
20C LYS* 3.2 8.4 + - - +
22C MET* 2.7 70.1 + - + +
23C THR* 3.6 17.6 - - - +
24C GLN* 3.5 31.1 - - - +
27C LEU* 4.1 15.5 - - + -
38C ILE* 4.4 0.2 - - - -
42C GLU* 2.7 42.2 + - - +
60C LEU* 3.5 20.6 - - + +
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Residues in contact with LEU 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 LYS* 2.8 52.5 + - + +
15C LYS* 3.8 6.3 - - - +
17C ARG* 1.3 98.6 - - - +
19C GLU* 1.3 59.8 + - + +
21C GLY* 2.9 21.1 + - - -
22C MET 4.5 4.0 - - - +
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Residues in contact with GLU 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C LYS* 2.9 60.2 + - + +
16C ILE* 3.1 7.6 + - + +
18C LEU* 1.3 77.5 - - + +
20C LYS* 1.3 63.1 + - + +
21C GLY 3.1 1.2 + - - -
70C MET* 4.7 6.4 - - - +
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Residues in contact with LYS 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C ILE* 2.9 31.7 + - + +
17C ARG 3.2 6.0 + - - +
19C GLU* 1.3 79.0 - - - +
21C GLY* 1.3 60.2 + - - +
22C MET* 3.5 27.3 + - + +
60C LEU* 2.7 35.3 + - + +
61C GLU* 3.3 23.5 + - + +
62C VAL* 4.2 5.5 - - - +
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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