Contacts of the helix formed by residues 12 - 34 (chain A) in PDB entry 3KSS
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 ASN 12 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A ARG 3.3 13.5 + - - +
9A SER* 3.0 30.7 - - - +
10A VAL 2.8 2.2 + - - -
11A ALA* 1.3 88.1 + - - +
13A ARG* 1.3 64.9 + - - +
14A PHE* 3.1 30.7 - - + -
15A LEU* 2.9 42.2 + - + +
16A VAL 3.7 2.3 + - - -
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Residues in contact with ARG 13 (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 SER 4.2 5.8 - - - -
10A VAL* 3.2 26.1 + - + +
11A ALA* 4.0 13.6 + - - +
12A ASN* 1.3 71.6 - - - +
14A PHE* 1.3 89.4 + - - +
16A VAL* 3.0 25.9 - - - +
17A LEU* 3.0 8.3 + - - +
498A PRO* 4.7 18.8 - - + +
501A MET* 5.6 8.5 - - + -
502A GLY* 6.1 1.8 - - - +
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Residues in contact with PHE 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ALA 4.3 3.1 - - - -
12A ASN* 3.5 31.2 - - + -
13A ARG* 1.3 99.9 - - - +
15A LEU* 1.3 73.4 + - + +
17A LEU* 3.0 11.5 + - + -
18A MET* 2.7 65.3 + - + +
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Residues in contact with LEU 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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9A SER* 6.0 2.0 - - - -
12A ASN* 2.9 43.6 + - + +
14A PHE* 1.3 89.1 - - + +
16A VAL* 1.3 69.4 + - + +
18A MET* 3.2 11.3 - - - +
19A GLY* 2.6 32.6 + - - -
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Residues in contact with VAL 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A SER* 4.4 19.7 - - - +
12A ASN 3.7 0.2 + - - -
13A ARG* 3.0 21.1 - - - +
15A LEU* 1.3 90.1 - - + +
17A LEU* 1.3 58.6 + - + +
19A GLY* 3.5 2.6 - - - +
20A ALA* 2.7 36.0 + - - +
495A VAL* 4.5 21.1 - - + +
498A PRO* 3.3 40.2 - - + -
499A ILE* 6.0 2.2 - - + -
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Residues in contact with LEU 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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13A ARG 3.0 13.6 + - - +
14A PHE* 3.4 13.9 - - + +
16A VAL* 1.3 78.8 - - + +
18A MET* 1.3 53.5 + - + +
20A ALA* 3.1 5.9 + - + +
21A LEU* 2.7 50.6 + - + +
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Residues in contact with MET 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 PHE* 2.7 59.5 + - + +
15A LEU* 3.2 17.0 - - + +
17A LEU* 1.3 71.1 - - + +
19A GLY* 1.3 62.9 + - - +
20A ALA 2.9 6.0 + - - -
21A LEU* 2.9 33.3 - - + +
22A PHE* 2.7 37.6 + - + -
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Residues in contact with GLY 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 LEU* 2.6 26.3 + - - -
16A VAL* 3.5 4.7 - - - -
18A MET* 1.3 73.1 - - - +
20A ALA* 1.3 55.5 + - - +
22A PHE* 3.2 20.4 - - - +
23A LEU* 3.1 23.0 - - - +
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Residues in contact with ALA 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 VAL 2.7 18.7 + - - +
17A LEU* 3.5 7.4 - - + +
18A MET 2.9 0.2 - - - -
19A GLY* 1.3 77.7 - - - +
21A LEU* 1.3 56.2 + - - +
22A PHE 2.9 5.2 - - - -
23A LEU* 2.7 26.2 + - + +
24A SER* 2.9 12.0 + - - -
368A ILE* 5.7 1.6 - - + -
372A LEU* 4.1 26.3 - - + +
495A VAL* 5.3 6.7 - - + -
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Residues in contact with LEU 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 LEU* 2.7 45.1 + - + +
18A MET* 2.9 41.2 + - + +
20A ALA* 1.3 69.4 - - - +
22A PHE* 1.3 75.2 + - + +
23A LEU 3.3 0.2 - - - -
24A SER* 3.9 12.1 - - - +
25A ILE* 3.4 27.0 + - + +
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Residues in contact with PHE 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 MET* 2.7 43.2 + - + -
19A GLY* 3.2 21.5 - - - +
20A ALA 2.9 0.2 - - - -
21A LEU* 1.3 89.8 - - + +
23A LEU* 1.3 58.0 + - + +
25A ILE* 3.9 7.7 - - + +
26A TRP* 2.7 39.2 + - + +
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Residues in contact with LEU 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 GLY 3.1 22.0 - - - +
20A ALA* 2.7 17.4 + - + +
22A PHE* 1.3 81.3 - - + +
24A SER* 1.3 53.9 + - - +
26A TRP* 4.3 4.8 - - + -
27A GLY* 2.6 31.5 + - - -
372A LEU* 4.2 28.3 - - + +
375A CYS* 4.2 17.7 - - + +
376A ILE* 5.1 3.8 - - + +
379A ILE* 3.8 28.0 - - + -
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Residues in contact with SER 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 ALA 2.9 12.3 + - - -
21A LEU* 4.2 11.4 - - - -
22A PHE 3.4 0.2 - - - -
23A LEU* 1.3 76.8 - - - +
25A ILE* 1.3 59.8 + - - +
28A THR* 3.1 30.3 + - - +
372A LEU* 5.1 5.6 - - - +
375A CYS* 5.4 4.9 - - - -
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Residues in contact with ILE 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 LEU* 3.4 18.5 + - + +
22A PHE* 3.9 10.3 - - + +
24A SER* 1.3 76.6 - - - +
26A TRP* 1.3 70.9 + - + +
28A THR* 3.4 17.8 - - + +
29A TRP* 3.9 8.7 - - - +
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Residues in contact with TRP 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 PHE 2.7 26.6 + - - +
23A LEU* 4.0 3.8 - - + +
25A ILE* 1.3 76.4 - - + +
27A GLY* 1.3 74.2 + - - +
29A TRP* 3.2 14.9 + + - +
30A THR* 3.0 35.6 + - + -
379A ILE* 2.9 56.6 - - + +
382A HIS* 6.0 1.6 - + - -
383A PHE* 3.7 28.3 - + - -
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Residues in contact with GLY 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 LEU 2.6 24.4 + - - -
25A ILE 3.4 0.2 - - - -
26A TRP* 1.3 79.7 - - - +
28A THR* 1.3 53.7 + - - +
29A TRP 2.6 14.0 + - - -
30A THR* 2.7 15.6 + - - -
31A ILE* 2.8 17.5 + - - +
375A CYS* 4.1 20.0 - - - -
378A PHE* 6.3 1.3 - - - -
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Residues in contact with THR 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 SER 3.1 22.8 + - - +
25A ILE* 3.4 15.5 - - + +
27A GLY* 1.3 68.7 - - - +
29A TRP* 1.3 59.9 + - + +
31A ILE* 3.2 10.7 - - - +
32A ILE* 3.0 35.0 + - - +
375A CYS* 5.0 2.2 - - - -
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Residues in contact with TRP 29 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A ILE 3.9 9.0 - - - +
26A TRP* 3.2 18.4 + + - +
27A GLY 2.6 5.3 + - - -
28A THR* 1.3 76.7 - - + +
30A THR* 1.3 88.8 + - - +
32A ILE* 4.3 0.9 - - - -
33A ASN* 2.6 81.7 + - + +
382A HIS* 5.2 12.8 - + - -
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Residues in contact with THR 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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26A TRP* 3.0 31.7 + - + +
27A GLY* 2.7 10.5 + - - -
29A TRP* 1.3 97.8 + - - +
31A ILE* 1.3 55.7 + - - -
33A ASN* 4.9 1.8 - - - -
34A THR* 3.0 27.3 + - + +
378A PHE* 3.1 32.7 - - - +
379A ILE* 4.4 0.9 - - - -
382A HIS* 3.5 28.9 + - + +
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Residues in contact with ILE 31 (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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27A GLY* 2.8 22.7 + - - +
28A THR* 3.2 17.7 - - - +
30A THR* 1.3 76.9 - - - +
32A ILE* 1.3 71.3 + - + +
34A THR* 2.8 20.7 + - - +
374A LEU* 5.3 6.1 - - + -
375A CYS* 5.6 4.0 - - - -
378A PHE* 3.4 44.7 - - + +
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Residues in contact with ILE 32 (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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28A THR* 3.0 23.6 + - - +
29A TRP* 4.3 0.9 - - - -
31A ILE* 1.3 87.4 - - + +
33A ASN* 1.3 82.0 + - - +
34A THR 4.2 3.3 - - - +
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Residues in contact with ASN 33 (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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29A TRP* 2.6 71.2 + - + +
30A THR* 4.6 2.0 - - - +
32A ILE* 1.3 94.6 - - - +
34A THR* 1.3 69.5 + - - +
35A PRO* 3.6 0.9 - - - +
296A ASN* 4.7 8.5 + - - -
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Residues in contact with THR 34 (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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30A THR* 3.0 29.0 + - + +
31A ILE* 2.8 22.2 + - - +
32A ILE 4.2 4.5 - - - +
33A ASN* 1.3 83.5 - - - +
35A PRO* 1.3 75.8 - - + +
36A VAL* 3.9 5.4 + - - +
296A ASN* 4.8 3.3 + - - +
381A MET* 4.1 26.5 - - + +
382A HIS* 4.6 19.5 - - + +
387A ASN 5.8 0.2 - - - +
388A ALA* 5.6 1.5 - - - +
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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