Contacts of the helix formed by residues 18 - 36 (chain I) in PDB entry 1K9O
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 ILE 18 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14I ASP* 2.9 41.3 - - + +
15I LEU* 4.3 3.8 - - - +
17I LYS* 1.3 87.8 - - + +
19I LEU* 1.3 56.9 + - - +
20I ARG 3.2 4.2 + - - -
21I GLU* 3.6 26.1 + - - +
22I SER* 3.2 19.2 + - - +
74I ALA 5.6 2.7 - - - +
75I LEU* 5.4 10.4 - - + +
76I PRO* 6.0 6.5 - - + -
84I VAL* 5.6 5.4 - - + -
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Residues in contact with LEU 19 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15I LEU 3.1 19.3 + - - +
16I GLN* 3.2 17.9 + - + +
18I ILE* 1.3 80.0 - - - +
20I ARG* 1.3 59.2 + - - +
21I GLU 3.5 0.4 - - - -
22I SER* 4.2 7.3 - - - -
23I ASN* 3.6 18.9 + - - +
48I PHE* 4.9 11.6 - - + -
51I LEU* 5.5 9.0 - - + -
75I LEU* 6.2 1.3 - - - -
84I VAL* 3.5 38.8 - - + +
85I PHE* 4.6 8.5 - - + -
87I ASP* 6.0 1.1 - - + -
88I LEU* 3.8 39.3 - - + -
376I ILE* 6.0 0.7 - - - +
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Residues in contact with ARG 20 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16I GLN 3.0 14.2 + - - +
17I LYS* 2.7 70.8 + - - +
18I ILE 3.2 0.2 - - - -
19I LEU* 1.3 78.6 - - - +
21I GLU* 1.3 86.7 + - - +
22I SER 3.3 0.2 - - - -
23I ASN* 3.6 6.5 + - - +
24I ASP* 3.2 38.3 + - - +
375I GLY 5.0 16.6 - - - +
376I ILE* 5.4 10.1 - - + -
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Residues in contact with GLU 21 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17I LYS 3.2 14.5 - - - +
18I ILE* 3.6 23.8 + - - +
20I ARG* 1.3 107.6 + - - +
22I SER* 1.3 64.9 + - - +
24I ASP* 3.7 7.0 + - - +
25I GLN* 3.5 27.0 + - - +
74I ALA* 5.1 1.2 - - - +
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Residues in contact with SER 22 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18I ILE 3.2 15.0 + - - -
19I LEU* 4.3 9.4 - - - -
20I ARG 3.3 0.2 - - - -
21I GLU* 1.3 75.5 - - - +
23I ASN* 1.3 64.9 + - - +
25I GLN* 3.0 6.2 + - - +
26I PHE* 2.9 25.4 + - - +
51I LEU* 4.7 8.1 - - - -
72I ALA 5.3 0.5 - - - +
73I LEU 3.1 27.4 + - - -
74I ALA* 3.2 27.5 + - - +
75I LEU* 4.1 7.3 - - - +
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Residues in contact with ASN 23 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19I LEU* 3.6 17.5 + - + +
20I ARG* 3.6 6.9 - - - +
22I SER* 1.3 79.3 - - - +
24I ASP* 1.3 52.8 + - - +
26I PHE* 3.2 1.2 + - - +
27I THR* 2.6 61.0 + - - +
47I ALA 4.5 0.4 - - - -
48I PHE* 3.6 40.6 - - + +
51I LEU* 4.1 15.5 - - + +
376I ILE* 3.4 16.0 - - + +
377I PRO* 3.3 27.8 + - - +
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Residues in contact with ASP 24 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20I ARG* 3.2 28.0 + - - +
21I GLU* 4.0 7.9 - - - +
22I SER 3.3 0.2 - - - -
23I ASN* 1.3 76.6 - - - +
25I GLN* 1.3 60.2 + - - +
27I THR* 4.2 4.4 - - - -
28I ALA* 3.4 23.7 + - - +
262I PRO* 3.5 30.1 - - + +
265I LEU* 5.6 3.8 - - - +
266I SER* 4.8 7.9 + - - -
375I GLY 5.5 1.6 - - - +
377I PRO* 3.8 27.5 - - - +
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Residues in contact with GLN 25 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21I GLU* 3.5 16.1 + - - +
22I SER* 3.0 11.5 + - - +
24I ASP* 1.3 80.0 - - - +
26I PHE* 1.3 61.5 + - - +
28I ALA* 3.7 2.3 + - - +
29I GLN* 3.2 46.7 + - - +
72I ALA 5.6 2.5 - - - +
74I ALA* 5.1 9.2 - - + +
262I PRO* 3.0 34.8 - - + +
263I LYS* 5.3 3.6 - - - +
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Residues in contact with PHE 26 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22I SER 2.9 14.2 + - - +
23I ASN* 3.7 3.4 - - - +
25I GLN* 1.3 76.2 - - - +
27I THR* 1.3 54.0 + - - +
29I GLN* 3.5 6.1 - - - +
30I MET* 2.7 67.6 + - + +
47I ALA* 4.2 3.4 - - + -
50I VAL* 4.8 0.9 - - + -
51I LEU* 3.3 34.1 - - + -
54I LEU* 3.4 28.5 - - + -
72I ALA* 3.1 43.7 + - + -
73I LEU* 4.4 2.5 - - - -
296I LEU* 3.8 11.2 - - + -
299I MET* 3.8 23.1 - - + -
301I ILE* 4.2 2.9 - - + -
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Residues in contact with THR 27 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23I ASN* 2.6 50.4 + - - -
24I ASP* 4.2 5.4 - - - -
26I PHE* 1.3 73.3 - - - +
28I ALA* 1.3 59.6 + - - +
30I MET* 3.9 1.2 - - - +
31I PHE* 2.9 31.5 + - + +
45I LEU* 4.7 0.3 - - - +
47I ALA* 3.5 16.7 - - + +
368I TYR* 5.2 4.7 - - - +
377I PRO* 4.1 21.8 + - + +
379I PHE* 6.0 0.7 - - - -
380I ASN* 3.0 27.4 - - - +
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Residues in contact with ALA 28 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24I ASP 3.4 17.7 + - - +
25I GLN 3.9 3.1 - - - +
26I PHE 3.4 0.2 - - - -
27I THR* 1.3 80.5 - - - +
29I GLN* 1.3 61.8 + - + +
31I PHE* 3.6 5.9 + - - +
32I SER* 3.3 26.7 + - - -
259I LEU 3.9 21.5 - - - +
260I LYS* 4.4 8.5 - - - +
261I ASP 4.9 0.2 - - - +
262I PRO* 4.3 20.0 - - + -
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Residues in contact with GLN 29 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25I GLN* 3.2 44.6 + - - +
26I PHE* 3.5 4.3 - - - +
27I THR 3.2 0.2 - - - -
28I ALA* 1.3 75.4 - - + +
30I MET* 1.3 63.8 + - - +
31I PHE 3.2 1.3 - - - -
32I SER* 3.7 4.4 + - - -
33I GLU* 3.3 29.3 + - - +
72I ALA* 5.3 7.4 + - - +
299I MET* 3.0 46.1 - - + +
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Residues in contact with MET 30 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26I PHE* 2.7 40.6 + - + +
27I THR 3.9 0.2 - - - +
29I GLN* 1.3 72.4 - - - +
31I PHE* 1.3 60.1 + - - +
33I GLU* 3.5 4.4 + - - +
34I VAL* 3.0 35.8 + - + +
45I LEU* 3.3 22.7 - - + -
46I SER 4.4 0.7 - - - +
47I ALA* 3.3 34.1 - - + +
50I VAL* 3.5 31.6 - - + -
290I THR* 5.8 0.7 - - + -
292I LEU* 4.1 13.2 - - - -
295I VAL* 4.0 19.5 - - - -
296I LEU* 4.3 7.0 - - + -
299I MET* 3.9 7.6 - - - +
329I GLN* 5.1 1.6 - - - +
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Residues in contact with PHE 31 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27I THR 2.9 20.6 + - - +
28I ALA* 3.7 7.2 - - - +
29I GLN 3.2 0.2 - - - -
30I MET* 1.3 77.2 - - - +
32I SER* 1.3 70.1 + - - +
34I VAL* 3.1 11.7 - - - +
35I VAL* 3.0 43.6 - - + +
45I LEU* 3.9 8.2 - - + +
256I GLU* 4.2 31.0 - - + -
259I LEU* 4.6 16.2 - - + -
368I TYR* 3.4 37.5 - + + -
380I ASN* 2.9 26.9 - - - +
381I GLY* 3.6 20.0 - - - -
382I LYS* 4.7 4.9 - - + -
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Residues in contact with SER 32 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28I ALA 3.3 15.1 + - - -
29I GLN* 4.2 4.5 - - - -
30I MET 3.5 0.2 - - - -
31I PHE* 1.3 84.5 - - - +
33I GLU* 1.3 59.2 + - - +
35I VAL* 3.3 7.7 + - - +
36I LYS* 2.9 52.1 + - - +
256I GLU* 4.7 2.4 + - - -
259I LEU 5.2 0.2 + - - -
260I LYS* 3.3 32.3 - - - +
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Residues in contact with GLU 33 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29I GLN 3.3 18.7 + - - +
30I MET 3.7 0.7 - - - +
31I PHE 3.3 0.6 - - - -
32I SER* 1.3 80.9 - - - +
34I VAL* 1.3 56.5 + - - +
36I LYS* 3.4 31.6 + - - +
37I ALA* 3.1 25.5 + - - +
295I VAL* 3.7 29.2 - - + +
298I ASN* 3.4 36.4 + - - +
299I MET* 4.0 19.1 - - + -
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Residues in contact with VAL 34 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30I MET* 3.0 20.6 - - + +
31I PHE 3.1 15.3 - - - +
33I GLU* 1.3 73.7 - - - +
35I VAL* 1.3 70.2 + - + +
37I ALA* 4.2 2.9 - - - -
38I ASN* 2.7 45.0 + - - +
43I VAL* 4.3 12.2 - - + +
44I VAL 5.9 0.2 - - - +
45I LEU* 3.2 35.4 - - + -
288I THR* 5.8 1.8 - - + -
290I THR* 4.2 29.2 - - + +
295I VAL* 4.5 5.8 - - + -
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Residues in contact with VAL 35 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31I PHE* 3.0 41.5 - - + +
32I SER* 3.3 10.2 + - - +
34I VAL* 1.3 87.5 - - + +
36I LYS* 1.3 63.6 + - + +
37I ALA 3.3 1.2 + - - -
38I ASN 3.4 11.0 + - - -
39I PRO* 3.5 17.4 - - + +
43I VAL* 4.2 7.4 - - + -
256I GLU* 3.4 31.9 - - + +
382I LYS* 3.9 23.3 - - + +
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Residues in contact with LYS 36 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32I SER* 2.9 35.3 + - - +
33I GLU* 3.6 32.6 + - - +
34I VAL 3.2 0.2 - - - -
35I VAL* 1.3 79.3 - - + +
37I ALA* 1.3 57.5 + - - +
39I PRO* 4.1 11.4 - - - +
260I LYS* 3.4 27.4 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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