Contacts of the helix formed by residues 15 - 32 (chain A) in PDB entry 6RKU
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 15 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A ILE* 3.2 24.0 - - + +
14A GLU* 1.3 80.1 + - - +
16A GLU* 1.3 63.1 + - - +
17A LEU* 2.9 4.7 + - - -
18A LYS* 3.0 49.7 + - + +
19A SER* 3.9 9.3 + - - -
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Residues in contact with GLU 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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12A ASN* 3.7 31.8 + - - +
13A ILE* 3.7 10.3 + - - +
14A GLU 2.8 3.1 + - - +
15A GLU* 1.3 80.0 + - - +
17A LEU* 1.3 62.8 + - - +
18A LYS 3.2 0.4 + - - -
19A SER* 3.4 21.3 + - - +
20A SER* 3.4 28.8 + - - +
507B ARG* 5.5 7.8 + - - +
511B LEU* 5.8 7.4 - - + -
529B ILE* 6.3 4.7 - - + -
763B LEU* 5.6 3.8 - - + -
765B VAL* 6.5 0.2 - - + -
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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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14A GLU* 3.3 26.6 + - - +
15A GLU* 2.9 1.5 + - - +
16A GLU* 1.3 79.8 - - - +
18A LYS* 1.3 66.5 + - + +
20A SER* 3.6 1.3 + - - -
21A TYR* 3.3 24.5 + - + +
508B THR* 3.8 35.6 + - + +
511B LEU* 4.3 30.5 - - + +
512B THR* 4.5 8.1 - - - +
515B TYR* 6.5 0.2 - - + -
773B ALA* 5.8 8.1 - - + +
774B ASP* 4.0 23.3 - - - +
777B PHE* 5.4 8.3 - - + -
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Residues in contact with LYS 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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15A GLU* 3.0 35.5 + - + +
17A LEU* 1.3 85.1 - - + +
19A SER* 1.3 64.9 + - - +
21A TYR* 4.3 2.1 - - - +
22A LEU* 3.1 27.6 + - + +
786B GLU* 4.6 15.9 - - + +
789B ARG* 3.3 28.0 - - - +
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Residues in contact with SER 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 GLU* 3.9 11.6 + - - -
16A GLU* 3.4 22.1 + - - -
17A LEU 3.3 0.4 - - - -
18A LYS* 1.3 83.1 - - - +
20A SER* 1.3 61.7 + - - +
22A LEU* 4.0 4.2 - - - +
23A ASP* 3.2 22.3 + - - +
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Residues in contact with SER 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A GLU* 3.4 28.2 + - - +
17A LEU* 4.2 1.8 - - - -
18A LYS 3.3 0.4 - - - -
19A SER* 1.3 76.9 - - - +
21A TYR* 1.3 64.9 + - - +
23A ASP* 3.1 9.3 + - - +
24A TYR 3.0 17.3 + - - -
504B SER* 3.6 31.9 + - - -
507B ARG* 4.6 16.8 + - - -
508B THR* 4.1 10.8 - - - -
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Residues in contact with TYR 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* 3.3 19.9 + - + +
18A LYS* 4.3 2.7 - - - +
20A SER* 1.3 78.3 - - - +
22A LEU* 1.3 67.9 + - + +
24A TYR* 3.1 13.5 + + + +
25A ALA* 2.9 25.7 + - + +
176A VAL* 3.5 29.6 - - + +
504B SER 5.5 0.9 - - - -
505B HIS* 4.5 25.8 - + - +
508B THR* 3.9 28.6 + - + +
509B LEU* 5.9 0.4 - - + -
777B PHE* 4.1 28.8 + + - -
783B ASP* 4.3 15.6 + - - -
22G C 4.7 10.3 + - - -
23G G 5.6 0.3 + - - -
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Residues in contact with LEU 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 LYS* 3.1 22.4 + - + +
19A SER* 4.0 4.3 - - - +
21A TYR* 1.3 80.2 - - + +
23A ASP* 1.3 61.0 + - - +
25A ALA* 3.4 8.9 + - + +
26A MET* 2.9 41.4 + - + +
786B GLU* 5.4 11.2 - - + +
787B PRO* 5.1 16.2 - - + -
789B ARG* 3.9 48.0 - - + +
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Residues in contact with ASP 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 SER 3.2 13.8 + - - +
20A SER* 3.1 13.3 + - - +
22A LEU* 1.3 80.4 - - - +
24A TYR* 1.3 61.8 + - - +
26A MET* 3.4 3.9 + - - +
27A SER* 2.9 27.3 + - - -
501B VAL* 4.7 10.1 - - - +
504B SER* 5.2 4.0 - - - +
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Residues in contact with TYR 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 SER 3.0 8.4 + - - +
21A TYR* 3.1 17.9 + + - +
23A ASP* 1.3 77.2 - - - +
25A ALA* 1.3 60.9 + - - +
27A SER* 3.3 1.9 + - - -
28A VAL* 2.9 55.2 + - + +
32A ARG* 4.0 13.3 + - - -
176A VAL* 4.5 12.8 - - + -
449B LYS* 4.2 13.5 + - - -
501B VAL* 3.2 35.2 - - + -
502B ASP* 3.2 26.9 + - - -
504B SER* 3.9 13.2 + - - +
505B HIS* 3.2 43.1 - + + +
21G A 5.9 0.3 + - - -
22G C 5.7 2.7 - - - -
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Residues in contact with ALA 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 TYR* 2.9 23.2 + - + +
22A LEU* 3.8 11.0 - - + +
24A TYR* 1.3 77.7 - - + +
26A MET* 1.3 59.6 + - - +
28A VAL* 3.9 0.2 - - - -
29A ILE* 3.0 43.0 + - + +
176A VAL* 4.1 34.3 - - + -
787B PRO* 5.9 5.4 - - + -
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Residues in contact with MET 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 LEU* 2.9 29.7 + - + +
23A ASP* 3.9 5.6 - - - +
25A ALA* 1.3 75.8 - - - +
27A SER* 1.3 62.1 + - - +
29A ILE* 4.5 7.6 - - - +
30A VAL* 3.2 42.3 + - + +
787B PRO* 5.6 8.1 - - + -
789B ARG* 3.8 36.1 - - + +
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Residues in contact with SER 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 ASP* 2.9 21.2 + - - -
24A TYR 3.7 2.2 - - - -
26A MET* 1.3 75.6 - - - +
28A VAL* 1.3 65.8 + - - +
30A VAL* 3.4 2.6 + - - +
31A GLY* 2.9 23.2 + - - -
501B VAL* 3.5 33.2 - - - +
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Residues in contact with VAL 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 TYR* 2.9 55.7 + - + +
25A ALA 3.9 2.7 - - - +
27A SER* 1.3 77.1 - - - +
29A ILE* 1.3 66.0 + - - +
30A VAL 3.0 0.2 + - - -
32A ARG* 2.9 59.7 + - + +
33A ALA* 3.9 6.2 + - + +
174A ILE 5.7 0.9 - - - +
175A ALA* 5.0 11.9 - - + -
176A VAL* 4.5 15.3 - - + -
501B VAL* 5.2 2.5 - - + -
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Residues in contact with ILE 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 ALA* 3.0 28.7 + - + +
26A MET* 4.5 8.1 - - - +
28A VAL* 1.3 75.9 - - - +
30A VAL* 1.3 66.2 + - + +
33A ALA 5.6 0.9 - - - +
34A LEU* 4.0 31.0 + - + +
175A ALA* 4.0 21.8 - - + -
176A VAL* 4.4 10.3 - - + +
177A GLY* 4.5 16.2 - - - +
178A MET* 5.6 5.8 - - + +
337A LEU* 4.3 4.9 - - + +
342A PRO* 3.9 30.1 - - + -
787B PRO* 5.3 14.4 - - + -
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Residues in contact with VAL 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 MET* 3.2 34.2 + - + +
27A SER* 3.4 3.4 + - - +
28A VAL 3.1 0.4 - - - -
29A ILE* 1.3 86.1 - - + +
31A GLY* 1.3 59.8 + - - +
32A ARG 3.8 0.2 - - - -
34A LEU 5.1 2.5 - - - +
43A PRO* 5.5 1.9 - - - +
337A LEU* 4.0 22.3 - - + +
340A GLY* 4.3 24.2 - - - +
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Residues in contact with GLY 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 SER 2.9 14.8 + - - -
30A VAL* 1.3 82.1 - - - +
32A ARG* 1.3 59.2 + - - +
34A LEU 6.0 0.7 - - - -
43A PRO* 3.2 28.5 - - - +
13E A 5.5 0.9 + - - -
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Residues in contact with ARG 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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24A TYR* 4.0 17.2 + - - -
28A VAL* 2.9 40.9 + - + +
30A VAL 3.8 0.6 - - - -
31A GLY* 1.3 80.2 - - - +
33A ALA* 1.3 65.6 + - + +
34A LEU 4.0 1.1 + - - -
42A LYS* 4.3 9.4 - - - +
43A PRO* 4.1 13.7 - - - +
44A VAL* 5.8 2.1 - - - +
80A HIS* 5.1 8.5 + - - -
449B LYS* 5.7 2.4 - - - +
501B VAL* 5.0 7.3 - - - +
502B ASP* 4.0 24.2 + - - -
12E T 4.0 36.1 + - - +
13E A 3.7 47.8 + - - +
21G A 5.7 3.8 - - - -
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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