Contacts of the helix formed by residues 9 - 28 (chain B) in PDB entry 3KSA
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 LEU 9 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B SER* 1.3 75.5 + - - +
10B GLU* 1.3 67.8 + - - +
11B ASP 3.4 0.2 - - - -
12B ILE* 5.3 0.2 - - + -
13B MET* 3.0 44.7 + - + +
519D LEU* 4.0 31.4 - - + +
523D TYR* 4.2 19.3 - - + -
530D VAL* 4.8 8.3 - - + -
606D VAL* 3.6 22.0 - - + -
607D THR 2.9 14.1 + - - +
608D ILE* 4.2 14.7 - - + +
614D ALA* 4.2 15.9 - - + -
618D VAL* 4.1 19.5 - - + -
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Residues in contact with GLU 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B SER* 2.9 5.5 + - - +
9B LEU* 1.3 84.9 - - - +
11B ASP* 1.3 57.3 + - - +
13B MET* 3.6 0.8 - - - +
14B GLY 2.8 23.9 + - - -
608D ILE* 5.6 3.7 - - + +
613D ARG* 5.0 11.7 - - + +
614D ALA* 5.0 14.1 - - + +
617D ARG* 3.4 35.2 + - + +
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Residues in contact with ASP 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B MET* 6.1 2.7 - - + -
8B SER* 2.9 19.9 + - - +
10B GLU* 1.3 75.2 - - - +
12B ILE* 1.3 65.6 + - + +
14B GLY* 3.1 2.6 + - - -
15B GLU* 3.0 23.7 + - - +
617D ARG* 4.6 5.8 - - - +
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Residues in contact with ILE 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B MET* 3.4 39.0 - - + +
8B SER 3.0 24.9 + - - +
9B LEU* 4.1 2.5 - - - +
10B GLU 3.5 0.2 - - - -
11B ASP* 1.3 77.8 - - - +
13B MET* 1.3 63.3 - - - +
15B GLU* 3.6 2.4 + - - -
16B ARG* 3.0 41.8 + - + +
519D LEU* 3.6 26.5 - - + -
537D ILE* 3.7 12.1 - - + -
604D ILE* 3.5 21.3 - - + -
606D VAL* 3.7 17.5 - - + -
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Residues in contact with MET 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B LEU* 3.0 45.8 + - + +
10B GLU* 3.6 4.9 - - - +
12B ILE* 1.3 77.6 - - - +
14B GLY* 1.3 56.3 + - - +
16B ARG* 4.3 3.7 - - - +
17B PHE* 3.0 33.4 + - - +
516D THR* 3.7 36.7 + - + +
519D LEU* 4.5 8.1 - - + -
520D THR* 3.8 7.6 - - - -
617D ARG* 4.8 2.5 - - + -
618D VAL* 3.9 20.0 - - + +
621D LEU* 3.6 30.3 - - + +
622D MET* 3.6 25.6 - - + -
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Residues in contact with GLY 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B GLU 2.8 15.8 + - - -
11B ASP* 3.1 5.3 + - - -
13B MET* 1.3 75.0 - - - +
15B GLU* 1.3 64.4 + - - -
17B PHE* 3.8 1.2 - - - +
18B GLY* 3.0 20.1 + - - -
617D ARG* 4.2 18.6 - - - +
621D LEU* 4.7 3.8 - - - -
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Residues in contact with GLU 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ASP 3.0 15.8 + - - +
12B ILE* 4.2 3.8 - - - +
14B GLY* 1.3 68.6 - - - +
16B ARG* 1.3 77.1 + - - +
18B GLY* 3.0 4.0 + - - -
19B ARG* 2.9 32.0 + - + +
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Residues in contact with ARG 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B MET* 5.4 2.4 - - - +
12B ILE* 3.0 43.6 + - + +
13B MET* 4.3 1.6 - - - +
15B GLU* 1.3 89.2 - - - +
17B PHE* 1.3 62.9 + - - +
19B ARG* 3.7 27.3 + - - +
20B TYR* 3.5 18.2 + - - +
512D ALA* 3.7 28.2 - - + +
515D GLN* 2.8 42.5 + - + +
516D THR* 3.7 11.4 + - - +
519D LEU* 6.4 0.2 - - + -
537D ILE* 4.1 11.4 - - - +
538D ALA 5.6 1.0 + - - -
539D LEU* 5.8 5.3 - - - +
604D ILE* 4.4 20.4 - - - +
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Residues in contact with PHE 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B MET 3.0 20.8 + - - +
14B GLY 3.8 2.2 - - - +
16B ARG* 1.3 77.0 - - - +
18B GLY* 1.3 54.6 + - - +
20B TYR* 3.0 13.5 + + + +
21B SER* 2.7 50.9 + - - -
172B ALA* 4.8 13.9 - - + -
513D HIS* 5.0 12.3 - + - +
516D THR* 3.8 21.7 + - + +
621D LEU* 3.8 44.4 - - + -
622D MET* 4.1 19.3 - - + -
629D ARG* 4.2 24.9 - - + -
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Residues in contact with GLY 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B GLY 3.0 11.2 + - - -
15B GLU* 3.0 6.9 + - - -
17B PHE* 1.3 76.1 - - - +
19B ARG* 1.3 63.2 + - - +
21B SER* 2.8 18.3 + - - -
22B LYS* 3.1 15.6 + - - +
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Residues in contact with ARG 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B GLU* 2.9 21.2 + - + +
16B ARG* 3.7 36.8 - - - +
18B GLY* 1.3 77.7 - - - +
20B TYR* 1.3 62.6 + - - +
22B LYS* 3.5 5.1 - - - +
23B TYR* 3.0 23.2 + - - +
507D ALA 3.6 11.9 + - - -
508D ASP* 3.6 24.9 + - - +
509D THR* 4.0 19.5 - - + +
512D ALA* 4.0 13.7 - - + +
559D TRP 5.0 7.0 + - - -
560D THR* 5.4 9.6 - - - -
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Residues in contact with TYR 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ARG 3.5 10.4 + - - +
17B PHE* 3.0 16.7 + + + +
19B ARG* 1.3 76.7 - - - +
21B SER* 1.3 72.1 + - - +
22B LYS 3.1 0.3 + - - -
23B TYR* 3.1 7.7 + + + +
24B ILE* 2.9 47.9 + - + +
28B ARG* 3.7 11.9 + - - -
172B ALA* 5.2 6.7 - - + -
458D LYS* 3.2 13.3 + - - +
509D THR* 3.4 24.9 - - - +
510D ASP* 3.5 20.0 - - - -
513D HIS* 3.0 64.7 + + + +
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Residues in contact with SER 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B PHE* 2.7 36.1 + - - -
18B GLY* 2.8 20.3 + - - -
20B TYR* 1.3 75.0 - - - +
22B LYS* 1.3 58.2 + - - +
24B ILE* 3.5 2.6 + - - +
25B ILE* 3.0 36.0 + - - +
172B ALA* 4.0 25.0 - - - +
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Residues in contact with LYS 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B GLY 3.1 16.1 + - - +
19B ARG* 3.5 4.9 - - - +
20B TYR 3.1 0.2 - - - -
21B SER* 1.3 78.6 + - - +
23B TYR* 1.3 66.6 + - - +
25B ILE* 3.0 18.9 + - - +
26B GLN* 3.1 47.7 + - + +
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Residues in contact with TYR 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B ARG 3.0 16.6 + - - +
20B TYR* 3.1 5.1 + + - +
22B LYS* 1.3 76.0 - - - +
24B ILE* 1.3 60.4 + - + +
26B GLN* 5.2 3.1 - - - -
27B ASP* 2.8 73.8 + - + +
28B ARG* 3.3 31.7 + - + -
43B ARG* 5.5 3.5 + - - -
75B PRO* 5.6 1.2 - - - +
76B HIS* 3.7 25.8 + + - -
509D THR* 3.3 35.9 - - + +
510D ASP* 4.6 3.8 - - - -
579D ARG* 5.9 1.0 + - - -
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Residues in contact with ILE 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B TYR* 2.9 48.8 + - + +
21B SER* 3.6 5.2 - - - +
23B TYR* 1.3 79.6 - - + +
25B ILE* 1.3 61.8 + - - +
28B ARG* 3.0 53.5 + - + +
29B ALA* 3.0 31.5 + - + +
170B ILE 4.8 1.1 - - - +
171B SER* 3.3 30.3 - - - -
172B ALA* 3.4 13.5 - - + +
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Residues in contact with ILE 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B SER* 3.0 21.5 - - - +
22B LYS* 3.0 9.3 + - - +
24B ILE* 1.3 80.5 - - - +
26B GLN* 1.3 70.3 + - + +
30B LEU* 3.3 35.9 + - + +
171B SER* 4.3 7.4 - - - +
172B ALA 3.9 21.8 - - - +
174B TYR* 4.0 11.4 - - + -
332B ILE* 3.7 12.8 - - + +
337B PRO* 3.3 37.5 - - + -
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Residues in contact with GLN 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B LYS* 3.1 49.8 + - + +
23B TYR* 5.1 2.4 + - - -
25B ILE* 1.3 90.5 - - + +
27B ASP* 1.3 72.3 + - - +
28B ARG 3.6 0.5 + - - -
30B LEU 3.7 13.0 - - - +
39B PRO* 4.1 6.9 - - - +
332B ILE* 4.4 12.9 - - + +
335B PHE* 2.7 47.6 + - - +
337B PRO* 5.9 0.4 - - + -
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Residues in contact with ASP 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B TYR* 2.8 59.3 + - + +
26B GLN* 1.3 84.5 - - - +
28B ARG* 1.3 58.4 + - - +
39B PRO* 2.9 31.7 - - - +
40B VAL* 5.6 0.9 - - - +
43B ARG* 4.5 15.0 + - - -
74B HIS* 5.9 1.6 - - - -
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Residues in contact with ARG 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B TYR* 3.7 9.5 + - - -
23B TYR* 3.3 13.6 + - + +
24B ILE* 3.0 51.4 + - + +
26B GLN 3.5 0.8 - - - -
27B ASP* 1.3 81.0 - - - +
29B ALA* 1.3 64.5 + - + +
30B LEU 3.7 0.7 - - - -
38B LYS* 3.7 21.0 - - - +
39B PRO* 4.2 2.7 - - - +
40B VAL* 5.0 12.4 - - + +
74B HIS* 6.5 1.3 - - + -
76B HIS* 4.2 20.3 + - + -
458D LYS* 4.4 2.2 - - - +
510D ASP* 2.5 42.6 + - - -
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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
------------------------------------------------------------
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