Contacts of the helix formed by residues 19 - 37 (chain A) in PDB entry 1K89
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 PRO 19 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A ALA 3.6 11.4 - - - +
17A ASP* 3.1 11.4 - - - +
18A GLU* 1.3 90.4 - - - +
20A GLU* 1.3 78.5 + - - +
22A VAL* 3.3 7.9 + - + +
23A GLN* 3.0 33.0 + - + +
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Residues in contact with GLU 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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19A PRO* 1.3 90.0 - - - +
21A PHE* 1.3 60.6 + - - +
23A GLN* 3.6 10.1 + - - +
24A THR* 3.0 27.9 + - - -
99A ASN* 5.2 2.7 + - - -
101A SER* 2.6 33.0 + - - +
102A ILE* 4.0 26.2 - - + +
105A PHE* 3.5 26.3 - - + +
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Residues in contact with PHE 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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11A VAL* 4.4 4.5 - - + -
15A TYR* 3.9 26.2 - + + -
18A GLU* 3.1 28.6 + - + +
20A GLU* 1.3 78.6 - - - +
22A VAL* 1.3 67.9 + - - +
24A THR* 3.1 3.4 + - - -
25A VAL* 3.0 54.3 + - + +
52A VAL* 3.3 26.7 - - + -
81A PHE* 3.8 21.3 - + - -
101A SER* 3.6 14.8 + - - +
104A LYS* 3.7 40.2 - - + -
105A PHE* 3.7 9.2 - - - +
108A PHE* 4.4 5.8 - + + -
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Residues in contact with VAL 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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8A ILE* 5.7 1.4 - - + +
11A VAL* 4.2 19.6 - - + +
12A GLU* 3.9 33.7 - - + +
15A TYR* 3.3 40.8 - - + +
16A ALA* 4.5 2.7 - - - +
18A GLU 3.0 11.0 + - - +
19A PRO* 3.6 9.6 - - + +
21A PHE* 1.3 76.8 - - - +
23A GLN* 1.3 69.2 + - + +
25A VAL* 3.3 2.3 + - - +
26A GLU* 3.0 25.6 + - + +
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Residues in contact with GLN 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 PRO* 3.0 23.7 + - - +
20A GLU* 3.9 8.0 - - - +
21A PHE 3.2 0.2 - - - -
22A VAL* 1.3 81.2 - - + +
24A THR* 1.3 64.2 + - - +
26A GLU* 3.3 6.2 + - - +
27A GLU* 3.0 27.8 + - - +
348A MET* 4.5 10.1 - - - +
352A ASN* 3.4 37.4 + - - +
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Residues in contact with THR 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 GLU 3.0 14.0 + - - -
21A PHE* 3.1 8.8 + - - -
23A GLN* 1.3 80.2 - - - +
25A VAL* 1.3 56.9 + - - +
27A GLU* 3.2 12.6 + - - +
28A VAL* 2.8 31.1 + - + +
105A PHE* 3.1 28.9 - - - +
108A PHE* 4.0 16.4 - - + -
109A GLU* 3.5 37.2 - - + +
348A MET* 5.9 0.7 - - - -
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Residues in contact with VAL 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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8A ILE* 4.9 5.2 - - + -
11A VAL* 4.2 22.0 - - + -
21A PHE* 3.0 55.1 + - + +
22A VAL 3.8 3.8 - - - +
24A THR* 1.3 77.5 - - - +
26A GLU* 1.3 59.1 + - - +
29A LEU* 2.7 58.6 + - + +
52A VAL* 4.1 13.2 - - + -
108A PHE* 4.2 21.1 - - + -
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Residues in contact with GLU 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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8A ILE* 3.8 38.6 - - + +
12A GLU* 4.3 11.4 - - - +
22A VAL* 3.0 20.8 + - + +
23A GLN* 3.7 5.9 - - - +
25A VAL* 1.3 76.8 - - - +
27A GLU* 1.3 56.1 + - - +
30A SER* 2.6 44.1 + - - -
356A ARG* 5.0 9.7 + - - -
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Residues in contact with GLU 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 GLN* 3.0 16.1 + - - +
24A THR* 3.8 17.6 + - - +
26A GLU* 1.3 79.2 - - - +
28A VAL* 1.3 64.8 + - + +
30A SER* 2.7 18.4 + - - -
31A SER* 3.8 7.3 + - - -
109A GLU* 3.4 22.8 - - - +
348A MET* 5.7 4.2 - - - +
352A ASN* 4.2 17.2 - - - +
355A LEU* 5.9 9.2 - - + -
370A LYS* 4.1 5.4 + - - -
427A VAL* 6.2 3.4 - - + -
431A ASN* 4.3 5.4 + - - +
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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 THR* 2.8 22.4 + - + +
27A GLU* 1.3 82.0 - - - +
29A LEU* 1.3 65.0 + - - +
31A SER* 3.0 19.4 + - - -
32A LEU* 3.5 12.6 - - + +
108A PHE* 3.8 18.6 - - + -
109A GLU* 3.7 23.3 - - - +
112A PHE* 3.9 36.8 - - + -
370A LYS* 4.1 10.5 - - - +
431A ASN* 4.0 17.5 - - + +
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Residues in contact with LEU 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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4A VAL* 3.5 17.6 - - + +
7A VAL* 4.0 26.2 - - + -
8A ILE* 4.0 17.9 - - + -
25A VAL* 2.7 42.4 + - + +
28A VAL* 1.3 74.0 - - + +
30A SER* 1.3 63.4 + - - +
32A LEU* 3.0 39.1 + - + +
33A GLY 3.8 0.2 + - - -
48A LEU* 4.4 24.9 - - + -
51A MET* 5.8 3.1 - - + -
52A VAL* 4.3 7.2 - - + -
108A PHE* 4.5 16.4 - - + -
112A PHE* 5.4 1.6 - - + -
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Residues in contact with SER 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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4A VAL* 4.4 4.9 - - - -
8A ILE* 4.0 12.7 - - - +
26A GLU* 2.6 29.8 + - - +
27A GLU* 2.7 16.3 + - - -
29A LEU* 1.3 76.4 - - - +
31A SER* 1.3 59.6 + - - +
32A LEU 3.5 0.5 + - - -
33A GLY* 3.9 7.6 + - - -
34A PRO* 5.0 1.9 - - - +
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Residues in contact with SER 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 GLU 4.4 3.6 - - - -
28A VAL 3.0 7.9 + - - -
29A LEU 3.1 0.8 + - - -
30A SER* 1.3 83.0 + - - +
32A LEU* 1.3 57.3 + - - +
33A GLY 3.3 2.4 + - - -
34A PRO* 3.9 11.3 - - - +
422A LEU* 5.0 1.9 - - - +
427A VAL* 6.1 1.1 - - - -
428A ALA* 4.0 24.6 - - - +
431A ASN* 2.9 36.5 + - - +
432A ILE* 4.1 16.5 - - - +
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Residues in contact with LEU 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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4A VAL* 4.8 0.7 - - + -
28A VAL* 3.5 25.1 - - + +
29A LEU* 3.0 29.5 + - + +
31A SER* 1.3 76.4 - - - +
33A GLY* 1.3 65.9 + - - +
34A PRO* 3.2 3.1 - - - -
35A VAL* 2.8 20.8 + - + +
36A VAL* 2.9 26.1 + - + +
48A LEU* 5.3 1.8 - - + -
112A PHE* 4.6 1.6 - - + -
431A ASN* 3.9 22.2 - - + +
432A ILE* 4.0 12.6 - - + -
435A PHE* 3.7 51.4 - - + -
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Residues in contact with GLY 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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1A SER* 4.1 21.9 - - - -
4A VAL* 4.2 7.0 - - - -
29A LEU 3.8 5.0 + - - -
30A SER 3.9 5.8 + - - -
31A SER 3.3 0.8 - - - -
32A LEU* 1.3 77.5 - - - +
34A PRO* 1.3 72.2 - - - +
36A VAL* 3.3 1.4 + - - +
37A ASP* 3.0 31.1 + - - +
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Residues in contact with PRO 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 SER 5.0 2.0 - - - +
31A SER 3.9 11.7 - - - +
32A LEU 3.6 2.5 - - - -
33A GLY* 1.3 91.1 - - - +
35A VAL* 1.3 60.7 + - + +
37A ASP* 3.7 7.4 + - + +
38A ALA* 3.4 19.8 + - - +
420A TYR* 3.9 34.5 - - + +
422A LEU* 4.8 19.3 - - + -
432A ILE* 5.8 0.2 - - + -
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Residues in contact with VAL 35 (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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32A LEU* 2.8 16.4 + - + +
34A PRO* 1.3 71.0 - - + +
36A VAL* 1.3 66.6 + - - +
38A ALA* 3.2 4.9 + - - +
39A HIS* 2.9 31.1 - - + -
420A TYR* 3.7 33.4 - - + +
432A ILE* 3.9 32.8 - - + -
435A PHE* 3.8 21.8 - - + -
436A GLN* 3.0 33.7 - - - +
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Residues in contact with VAL 36 (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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1A SER* 3.8 13.0 - - - +
3A TYR* 3.5 33.7 - - + -
4A VAL* 3.9 17.7 - - + -
32A LEU* 2.9 28.0 + - + +
33A GLY 3.8 2.9 - - - +
35A VAL* 1.3 78.5 - - - +
37A ASP* 1.3 56.0 + - - +
39A HIS 2.8 34.6 + - - +
40A PRO* 4.7 0.9 - - - +
42A TYR* 4.4 12.6 - - + -
48A LEU* 4.4 10.3 - - + -
435A PHE* 4.4 19.7 - - + -
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Residues in contact with ASP 37 (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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1A SER* 3.1 37.3 + - - -
2A LYS 4.8 0.5 + - - -
33A GLY 3.0 20.2 + - - +
34A PRO* 4.0 7.4 - - + +
36A VAL* 1.3 79.3 - - - +
38A ALA* 1.3 58.7 + - - +
39A HIS 3.4 0.5 + - - -
40A PRO* 4.3 8.7 - - - +
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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
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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