Contacts of the helix formed by residues 8 - 20 (chain C) in PDB entry 4BPU
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 GLU 8 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4C PHE* 5.8 0.2 - - - -
5C ASP* 3.3 35.9 + - - +
7C THR* 1.3 76.4 - - - +
9C LEU* 1.3 63.8 + - - +
10C PRO* 3.5 1.3 - - - -
11C GLU* 3.2 13.2 + - + +
12C LEU* 3.0 40.4 + - + +
351C SER* 4.5 8.8 - - - -
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Residues in contact with LEU 9 (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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4C PHE* 4.0 21.1 - - + -
5C ASP 4.0 2.3 + - - +
6C PRO* 3.5 18.9 + - + +
8C GLU* 1.3 77.2 - - - +
10C PRO* 1.3 66.5 - - + +
11C GLU 3.0 0.3 + - - -
12C LEU* 3.1 5.7 + - - +
13C LEU* 2.8 54.7 + - + +
76C TYR* 3.6 33.0 - - + -
323C VAL* 4.2 8.3 - - + -
324C HIS 5.2 0.7 - - - +
325C PRO* 3.7 32.3 - - + +
350C ILE* 4.2 14.4 - - + -
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Residues in contact with PRO 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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6C PRO 4.4 2.5 - - - +
7C THR* 3.4 17.7 - - - +
8C GLU 3.6 0.2 - - - -
9C LEU* 1.3 95.8 - - + +
11C GLU* 1.3 70.0 + - + +
13C LEU* 3.9 11.1 - - + +
14C LYS* 3.4 28.9 + - - +
50C LYS* 5.4 11.7 - - + +
74C ASN* 5.5 2.1 - - - +
76C TYR* 3.6 24.5 - - + +
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Residues in contact with GLU 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 THR 5.2 1.3 - - - +
8C GLU* 3.2 13.2 + - + +
9C LEU 3.1 0.6 - - - -
10C PRO* 1.3 89.8 - - + +
12C LEU* 1.3 64.8 + - + +
13C LEU 3.2 0.2 - - - -
14C LYS* 3.4 41.9 + - - +
15C LEU* 3.5 7.6 + - - +
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Residues in contact with LEU 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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4C PHE* 4.5 4.7 - - + -
8C GLU* 3.0 40.7 + - + +
9C LEU* 3.6 6.3 - - - +
11C GLU* 1.3 74.3 - - + +
13C LEU* 1.3 59.7 + - - +
15C LEU* 3.3 4.6 + - + -
16C TYR* 2.8 30.3 + - - +
350C ILE* 3.6 24.2 - - + +
351C SER* 3.7 35.2 - - - +
354C CYS* 3.4 35.6 - - + -
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Residues in contact with LEU 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C LEU* 2.8 40.4 + - + +
10C PRO* 3.9 9.6 - - + +
12C LEU* 1.3 74.4 - - - +
14C LYS* 1.3 60.3 + - - +
16C TYR* 4.3 0.9 - - + -
17C TYR* 2.8 58.1 + - + +
74C ASN* 4.1 14.8 - - + +
75C PRO 3.6 22.7 - - - +
76C TYR* 4.2 22.2 - - + +
323C VAL* 4.2 17.3 - - + -
350C ILE* 3.8 20.2 - - + +
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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
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10C PRO* 3.4 19.9 + - - +
11C GLU* 3.4 33.1 + - - +
12C LEU 3.3 0.4 - - - -
13C LEU* 1.3 79.6 - - - +
15C LEU* 1.3 61.7 + - - +
17C TYR* 3.7 2.4 + - - +
18C ARG* 3.3 21.5 + - - +
71C GLN* 5.6 1.0 - - - +
74C ASN* 3.4 32.8 + - - +
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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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11C GLU 3.5 7.0 + - - +
12C LEU* 3.3 9.5 + - + +
14C LYS* 1.3 77.2 - - - +
16C TYR* 1.3 62.9 + - - +
18C ARG* 3.0 6.1 + - + +
19C ARG* 2.8 43.4 + - + +
20C LEU* 5.0 1.0 - - + +
354C CYS* 3.9 33.0 - - + +
357C LEU* 3.8 31.2 - - + -
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Residues in contact with TYR 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 LEU 2.8 18.1 + - - +
13C LEU* 3.7 2.7 - - + +
15C LEU* 1.3 76.7 - - - +
17C TYR* 1.3 75.8 + + - +
20C LEU* 2.9 56.8 + - + -
21C PHE* 3.0 38.0 + + + -
22C PRO* 4.5 1.4 - - - +
321C PHE* 2.7 39.1 + - - +
323C VAL* 3.7 21.3 - - + -
330C ILE* 4.1 14.1 - - + +
350C ILE* 3.5 18.2 - - + -
353C ILE* 3.7 27.6 - - + -
354C CYS* 4.2 1.8 - - - -
388C LEU* 4.5 4.8 - - + +
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Residues in contact with TYR 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 LEU* 2.8 40.7 + - + +
14C LYS 4.1 1.3 - - - +
16C TYR* 1.3 98.3 - + - +
18C ARG* 1.3 57.2 + - - +
21C PHE* 4.4 4.5 - + + -
23C TYR* 2.5 36.5 + - - +
70C MET* 3.8 20.6 - - + -
71C GLN* 3.2 15.0 - - + +
74C ASN* 3.4 28.7 - - - +
75C PRO* 2.5 51.9 + - + +
76C TYR 4.6 3.5 + - - -
78C ILE* 3.7 26.7 - - + +
321C PHE 5.8 0.2 - - - -
322C SER* 5.6 0.8 + - - -
323C VAL* 5.2 6.3 + - + +
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Residues in contact with ARG 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 3.3 16.4 + - - +
15C LEU* 3.0 7.8 + - + +
17C TYR* 1.3 79.2 - - - +
19C ARG* 1.3 73.3 + - + +
20C LEU 3.9 0.4 - - - -
23C TYR* 4.9 5.0 - - - -
67C GLU* 4.9 6.6 + - - +
71C GLN* 2.8 51.7 + - + +
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Residues in contact with ARG 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* 2.8 23.1 + - - +
18C ARG* 1.3 96.4 - - + +
20C LEU* 1.3 66.0 + - - +
21C PHE 5.4 0.4 - - - -
357C LEU* 3.3 58.2 + - + +
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Residues in contact with LEU 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C LEU 5.3 0.2 - - - +
16C TYR* 2.9 29.9 + - + +
18C ARG 3.9 0.4 - - - -
19C ARG* 1.3 87.1 - - - +
21C PHE* 1.3 71.0 + - - +
22C PRO* 3.0 11.0 - - - +
353C ILE* 3.6 43.3 - - + +
354C CYS* 4.1 14.4 - - - -
357C LEU* 4.6 15.3 - - + -
386C THR* 3.8 34.5 - - + +
388C LEU* 3.9 17.6 - - + +
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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