Contacts of the helix formed by residues 18 - 37 (chain G) in PDB entry 1KYO
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 SER 18 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G TYR* 3.3 16.8 + - - -
15G ILE 3.3 2.8 - - - +
17G LYS* 1.3 77.6 - - - +
19G PRO* 1.4 56.9 - - - +
20G VAL* 2.8 27.5 + - - +
21G LEU* 2.9 38.5 + - - +
22G SER* 3.0 9.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 19 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17G LYS 2.9 11.6 - - - +
18G SER* 1.4 83.8 - - - +
20G VAL* 1.3 63.4 + - + +
22G SER* 3.8 11.9 - - - -
23G LYS* 3.3 38.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 20 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G SER* 2.8 19.3 + - - +
19G PRO* 1.3 77.7 - - + +
21G LEU* 1.3 72.3 + - + +
23G LYS* 4.4 2.9 - - - +
24G LEU* 3.5 22.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 21 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G TYR* 4.4 21.1 - - + +
15G ILE* 3.7 28.3 - - + +
18G SER* 2.9 32.7 + - - +
20G VAL* 1.3 83.8 - - + +
22G SER* 1.3 60.6 + - - +
24G LEU* 3.3 13.0 + - + +
25G CYS* 2.8 40.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 22 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15G ILE* 3.5 15.6 + - - -
16G LEU* 3.8 15.9 + - - +
18G SER 3.0 16.6 + - - -
19G PRO* 3.8 11.2 - - - -
21G LEU* 1.3 76.5 - - - +
23G LYS* 1.3 64.2 + - - +
24G LEU 3.1 1.2 + - - -
26G VAL* 3.2 45.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 23 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G PRO* 3.3 27.8 + - + +
20G VAL* 4.4 2.5 - - - +
22G SER* 1.3 79.4 - - - +
24G LEU* 1.3 56.7 + - - +
26G VAL* 5.6 0.2 - - - -
27G PRO* 3.4 20.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 24 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20G VAL* 3.5 18.9 + - + +
21G LEU* 3.3 12.1 + - + +
22G SER 3.1 0.8 - - - -
23G LYS* 1.3 81.0 - - - +
25G CYS* 1.3 71.5 + - - +
27G PRO* 3.7 5.9 - - - +
28G VAL* 3.6 18.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 25 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377C LEU* 5.5 3.5 - - + +
380C ILE* 3.9 19.9 - - + +
15G ILE* 4.1 18.8 - - + -
21G LEU* 2.8 29.9 + - - +
24G LEU* 1.3 83.1 - - - +
26G VAL* 1.3 66.8 + - - +
27G PRO* 3.1 3.4 - - - -
28G VAL* 2.8 21.0 + - + +
29G ALA* 2.8 13.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 26 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380C ILE* 4.3 11.2 - - + +
15G ILE* 6.1 0.9 - - + -
16G LEU* 3.6 31.0 - - + -
22G SER* 3.2 24.8 + - - +
23G LYS* 5.6 0.2 - - - -
25G CYS* 1.3 74.3 - - + +
27G PRO* 1.3 61.8 - - + +
29G ALA* 4.2 7.6 - - - -
30G ASN* 2.9 46.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 27 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22G SER 4.0 0.4 - - - +
23G LYS* 3.4 27.1 - - - +
24G LEU 3.7 5.4 - - - +
25G CYS 3.1 5.4 - - - -
26G VAL* 1.3 94.0 - - + +
28G VAL* 1.3 67.4 + - + +
30G ASN* 3.1 8.8 + - + +
31G GLN* 3.0 24.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 28 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377C LEU* 4.8 20.2 - - + -
24G LEU* 3.6 22.2 - - + +
25G CYS* 2.8 10.9 + - - +
27G PRO* 1.3 73.5 - - + +
29G ALA* 1.3 54.7 + - - +
31G GLN* 3.1 6.3 + - - +
32G PHE* 2.7 37.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 29 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377C LEU* 3.4 29.1 - - + +
380C ILE* 3.5 24.9 - - + -
381C GLY* 3.6 9.2 - - - -
25G CYS 2.8 12.6 + - - +
26G VAL* 3.7 4.5 - - - +
28G VAL* 1.3 78.0 - - - +
30G ASN* 1.3 60.1 + - - +
32G PHE* 3.4 7.0 + - - +
33G ILE* 3.0 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 30 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381C GLY* 3.0 31.5 + - - -
26G VAL* 2.9 36.7 + - - +
27G PRO* 3.1 6.8 + - + +
29G ALA* 1.3 75.3 - - - +
31G GLN* 1.3 57.9 + - - +
33G ILE* 3.4 6.5 + - - +
34G ASN* 3.0 39.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 31 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27G PRO 3.0 15.8 + - - +
28G VAL* 3.5 6.3 - - - +
30G ASN* 1.3 77.3 + - - +
32G PHE* 1.3 59.4 + - - +
33G ILE 3.1 0.2 - - - -
34G ASN* 3.2 12.5 + - - +
35G LEU* 2.8 57.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 32 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318C PHE 4.6 1.6 - - - -
319C LYS* 4.4 1.1 - - - -
320C VAL* 3.7 31.4 - - + +
321C LEU* 4.3 9.0 - - + -
374C GLU* 3.6 40.8 - - + -
377C LEU* 3.7 35.4 - - + -
378C PHE* 3.7 39.5 - + - -
28G VAL* 2.7 22.2 + - + +
29G ALA* 3.5 7.4 - - - +
31G GLN* 1.3 72.2 - - - +
33G ILE* 1.3 68.1 + - + +
35G LEU* 3.3 9.3 + - - +
36G ALA* 2.9 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 33 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377C LEU 4.1 2.7 - - - +
378C PHE* 3.9 22.9 - - + +
381C GLY* 3.4 43.1 - - - +
382C ARG* 4.3 4.5 - - + +
29G ALA 3.0 11.4 + - - +
30G ASN* 3.7 4.9 - - - +
32G PHE* 1.3 84.4 - - + +
34G ASN* 1.3 64.6 + - - +
35G LEU 3.1 1.8 - - - -
36G ALA* 3.0 22.7 + - - +
37G GLY 3.6 3.1 + - - -
38G TYR* 3.4 27.3 + - + +
39G LYS* 3.3 32.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 34 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30G ASN* 3.0 31.7 + - - +
31G GLN* 3.2 15.7 + - - +
33G ILE* 1.3 76.0 - - - +
35G LEU* 1.3 60.9 + - - +
36G ALA 3.3 0.2 - - - -
37G GLY* 3.8 3.5 + - - -
39G LYS* 3.2 27.9 - - - +
40G LYS* 3.5 22.5 + - - -
96G ALA* 5.7 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 35 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320C VAL* 3.9 23.4 - - + +
323C LYS* 5.6 2.9 + - - -
31G GLN* 2.8 45.1 + - + +
32G PHE* 3.5 8.1 - - - +
34G ASN* 1.3 78.9 - - - +
36G ALA* 1.3 65.2 + - - +
37G GLY* 3.2 1.9 + - - -
40G LYS* 5.5 1.1 + - - +
58H TYR* 4.5 15.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 36 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317C THR 4.0 4.3 - - - +
318C PHE* 3.2 46.1 - - - +
320C VAL* 4.5 4.7 - - + -
323C LYS* 5.0 3.5 + - - +
378C PHE* 4.4 5.8 - - + -
32G PHE* 2.9 13.9 + - + +
33G ILE* 3.0 15.7 + - - +
35G LEU* 1.3 79.0 - - - +
37G GLY* 1.3 61.1 + - - +
38G TYR* 3.4 20.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 37 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318C PHE* 4.5 4.1 - - - -
33G ILE 3.6 5.7 + - - -
34G ASN 3.8 1.7 + - - -
35G LEU 3.2 4.2 - - - -
36G ALA* 1.3 79.7 - - - +
38G TYR* 1.3 64.0 - - - +
39G LYS* 3.3 3.8 - - - -
40G LYS* 3.1 42.2 + - - +
41G LEU* 4.0 7.1 + - - +
87G LEU* 5.2 0.7 - - - +
----------------------------------------------------------
Back to top of page
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