Contacts of the helix formed by residues 9 - 30 (chain A) in PDB entry 3CFV
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 ASP 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 PHE* 3.3 6.2 - - + +
8A GLU* 1.3 77.5 - - - +
10A THR* 1.3 59.5 + - - +
11A VAL* 3.0 24.8 + - - +
12A GLU* 3.2 33.2 + - + +
13A GLU* 2.9 29.0 + - - +
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Residues in contact with THR 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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7A PHE 4.9 5.8 - - - +
8A GLU 3.6 7.7 + - - +
9A ASP* 1.3 72.5 + - - +
11A VAL* 1.3 69.8 + - - +
13A GLU* 3.8 16.0 - - - +
14A ARG* 3.1 41.7 + - - +
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Residues in contact with VAL 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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9A ASP* 3.0 11.1 + - - +
10A THR* 1.3 83.8 - - - +
12A GLU* 1.3 63.2 + - + +
14A ARG* 3.4 21.5 + - - +
15A VAL* 3.4 20.5 + - + +
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Residues in contact with GLU 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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7A PHE* 6.3 0.7 - - + -
9A ASP* 3.2 31.4 + - + +
11A VAL* 1.3 77.6 - - - +
13A GLU* 1.3 66.2 + - - +
15A VAL* 3.2 11.2 + - + +
16A ILE* 2.9 47.5 + - + +
339A ARG* 4.8 10.8 + - - +
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Residues in contact with GLU 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A PHE* 3.2 52.5 + - + +
9A ASP 2.9 19.6 + - - +
10A THR* 3.8 16.6 - - - +
12A GLU* 1.3 76.5 - - - +
14A ARG* 1.3 59.4 + - + +
16A ILE* 3.5 4.0 + - - +
17A ASN* 2.9 50.6 + - - +
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Residues in contact with ARG 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 THR* 3.1 37.0 + - - +
11A VAL* 3.4 14.6 + - - +
12A GLU 3.3 0.2 - - - -
13A GLU* 1.3 81.3 - - + +
15A VAL* 1.3 63.8 + - + +
17A ASN* 3.2 5.9 + - - +
18A GLU* 3.0 32.8 + - + +
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Residues in contact with VAL 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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11A VAL* 3.5 20.6 - - + +
12A GLU* 3.2 14.3 + - + +
14A ARG* 1.3 77.6 - - + +
16A ILE* 1.3 65.8 + - + +
18A GLU* 3.4 4.2 + - - +
19A GLU* 3.2 42.9 + - + +
339A ARG* 6.0 1.8 - - - +
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Residues in contact with ILE 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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7A PHE* 4.8 13.5 - - + -
12A GLU* 2.9 37.5 + - + +
13A GLU* 3.7 4.9 - - - +
15A VAL* 1.3 79.1 - - + +
17A ASN* 1.3 60.6 + - - +
19A GLU* 3.5 9.5 + - - +
20A TYR* 3.0 25.8 + - - +
339A ARG* 3.6 37.9 - - - +
340A ARG* 5.8 2.6 + - - +
372A HIS 5.1 0.4 - - - +
373A THR* 3.5 52.3 - - + +
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Residues in contact with ASN 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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7A PHE* 4.1 15.4 - - - -
13A GLU* 2.9 39.8 + - - +
14A ARG* 3.7 6.4 - - - +
16A ILE* 1.3 82.4 - - - +
18A GLU* 1.3 58.3 + - + +
20A TYR* 3.3 8.6 + - - +
21A LYS* 3.0 38.6 + - - +
373A THR* 4.5 6.6 - - - +
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Residues in contact with GLU 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 ARG* 3.0 23.3 + - + +
15A VAL* 4.0 4.3 - - - +
17A ASN* 1.3 73.4 - - + +
19A GLU* 1.3 66.1 + - + +
21A LYS* 3.1 50.2 + - - +
22A ILE* 3.2 20.6 + - + +
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Residues in contact with GLU 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 VAL* 3.2 35.0 + - + +
16A ILE* 3.7 6.9 - - - +
18A GLU* 1.3 76.6 - - + +
20A TYR* 1.3 58.3 + - - +
22A ILE* 3.2 13.9 + - + +
23A TRP* 2.9 27.8 + - - +
339A ARG* 4.3 10.0 + - - -
340A ARG* 3.5 29.6 + - - +
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Residues in contact with TYR 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 ILE 3.0 14.3 + - - +
17A ASN* 3.4 11.4 - - - +
18A GLU 3.2 0.2 - - - -
19A GLU* 1.3 76.3 - - - +
21A LYS* 1.3 63.7 + - + +
23A TRP* 3.0 33.5 + + - +
24A LYS* 2.8 54.7 + - + +
36A THR* 5.0 7.8 + - - +
370A GLY 4.7 3.8 - - - -
371A GLY 3.3 28.7 - - - -
372A HIS 5.4 0.2 - - - -
373A THR* 3.8 24.0 - - + -
399A GLN* 4.8 4.1 + - - -
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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 ASN* 3.0 22.5 + - - +
18A GLU* 3.1 43.9 + - - +
20A TYR* 1.3 82.8 - - + +
22A ILE* 1.3 62.1 + - + +
24A LYS* 3.6 7.1 + - - +
25A LYS* 3.4 39.8 + - - +
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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 GLU* 3.7 15.0 - - + +
19A GLU* 3.2 13.1 + - + +
20A TYR 3.1 0.6 - - - -
21A LYS* 1.3 77.1 - - + +
23A TRP* 1.3 66.9 + - - +
25A LYS* 3.2 15.3 + - + +
26A ASN* 3.2 33.6 + - - +
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Residues in contact with TRP 23 (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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19A GLU 2.9 14.2 + - - +
20A TYR* 3.0 44.4 + + - +
22A ILE* 1.3 77.9 - - - +
24A LYS* 1.3 81.2 + - + +
26A ASN* 3.1 8.1 + - - +
27A THR* 3.1 44.4 + - + +
30A LEU* 5.2 4.3 - - + -
31A TYR* 2.9 37.4 + + - -
34A VAL* 4.4 11.0 - - + -
36A THR* 5.2 3.8 - - + -
368A ILE 5.7 0.4 - - - -
369A HIS* 3.9 6.1 - + - -
370A GLY* 3.6 23.3 - - - +
371A GLY* 3.4 23.9 - - - +
399A GLN* 3.9 11.7 - - - -
41F GLY 3.7 23.6 - - - +
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Residues in contact with LYS 24 (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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20A TYR* 2.8 47.1 + - + +
21A LYS* 3.8 8.3 - - - +
22A ILE 3.2 0.2 - - - -
23A TRP* 1.3 88.3 - - + +
25A LYS* 1.3 59.3 + - + +
27A THR* 2.6 26.5 + - + +
28A PRO* 3.9 2.1 - - - +
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Residues in contact with LYS 25 (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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21A LYS* 3.4 29.0 + - - +
22A ILE* 3.2 15.6 + - - +
24A LYS* 1.3 79.1 - - + +
26A ASN* 1.3 62.4 + - - +
27A THR 3.4 0.2 - - - -
28A PRO* 3.3 15.6 - - - +
29A PHE* 4.2 1.6 - - - -
304B ASN* 4.2 33.5 - - - +
306B LYS* 3.6 40.7 - - + +
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Residues in contact with ASN 26 (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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22A ILE* 3.2 25.1 + - - +
23A TRP* 3.1 11.7 + - - +
25A LYS* 1.3 80.2 + - - +
27A THR* 1.3 65.0 + - - +
28A PRO* 3.2 4.7 - - - -
29A PHE* 2.8 30.5 + - - +
30A LEU* 3.2 20.1 + - + +
304B ASN* 5.4 2.4 + - - -
307B LEU* 5.6 6.9 - - - +
37F LEU* 3.5 41.6 - - + +
41F GLY 5.3 4.2 - - - +
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Residues in contact with THR 27 (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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23A TRP* 3.1 57.2 + - + +
24A LYS* 2.6 23.7 + - + +
26A ASN* 1.3 76.3 - - - +
28A PRO* 1.3 64.6 - - - +
30A LEU 3.0 0.3 + - - -
31A TYR* 2.9 50.9 + - + +
34A VAL* 4.3 16.7 - - + +
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Residues in contact with PRO 28 (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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24A LYS 3.9 1.3 - - - +
25A LYS 3.3 15.7 - - - +
26A ASN 3.2 5.6 - - - -
27A THR* 1.3 99.1 - - - +
29A PHE* 1.3 57.0 + - + +
31A TYR 4.2 9.1 - - - +
303B ARG* 3.4 55.1 + - + +
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Residues in contact with PHE 29 (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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25A LYS 4.2 5.2 - - - -
26A ASN* 2.8 32.5 + - - +
28A PRO* 1.3 78.3 - - + +
30A LEU* 1.3 61.8 + - - +
31A TYR 3.6 0.4 - - - -
404A ALA* 3.9 9.9 - - - +
406A ASN* 4.8 0.3 + - - -
301B ASP* 3.3 37.5 - - + -
303B ARG* 3.5 35.0 + - + +
304B ASN* 3.7 29.6 - - + -
307B LEU* 5.6 7.6 - - + -
309B LEU* 5.2 6.7 - - + -
34F ILE* 3.5 42.4 - - + +
37F LEU* 4.4 14.8 - - + -
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Residues in contact with LEU 30 (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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23A TRP* 5.2 3.8 - - + -
26A ASN* 3.2 19.7 + - + +
27A THR 3.0 1.8 + - - -
29A PHE* 1.3 85.5 - - - +
31A TYR* 1.3 81.6 + - + +
367A PHE* 3.8 17.2 - - + -
368A ILE 5.6 0.7 - - - +
403A MSE 3.3 7.4 - - - +
404A ALA* 2.9 19.6 + - - +
407A ILE* 4.0 5.5 - - + +
34F ILE* 3.8 9.6 - - + +
37F LEU* 4.2 22.0 - - + +
38F ALA* 3.7 36.6 - - + +
41F GLY* 4.2 26.7 - - - +
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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