Contacts of the helix formed by residues 63 - 75 (chain M) 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 63 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116G GLU* 2.8 34.9 + - - -
57M GLN 5.0 0.2 - - - -
58M ASN* 3.2 18.4 - - - -
62M ARG* 1.3 75.5 - - - +
64M ALA* 1.3 66.5 + - - +
65M LEU* 2.9 7.9 + - - +
66M LYS* 2.9 28.6 + - - +
67M LEU* 3.0 13.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 64 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296L LEU* 3.7 18.8 - - + -
56M PHE 3.7 24.1 - - - +
57M GLN* 3.8 22.0 - - - +
58M ASN* 2.6 20.4 + - - +
62M ARG 3.9 0.8 + - - -
63M SER* 1.3 70.0 - - - +
65M LEU* 1.3 58.7 - - - +
67M LEU* 3.7 5.8 + - - +
68M VAL* 3.1 30.0 + - - +
118M GLU* 5.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 65 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113G ALA 5.0 2.0 - - - +
116G GLU* 4.5 7.4 - - + +
117G LYS* 3.6 44.6 - - + +
120G LEU* 4.1 10.1 - - + -
296L LEU* 3.6 35.8 - - + +
63M SER* 2.9 7.9 - - - +
64M ALA* 1.3 77.8 - - - +
66M LYS* 1.3 61.6 + - - +
68M VAL* 3.2 5.9 + - - +
69M ARG* 2.9 64.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 66 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116G GLU* 3.8 15.9 - - + +
120G LEU* 3.8 27.9 - - + +
62M ARG* 4.4 11.9 - - + +
63M SER* 2.9 24.2 + - - +
65M LEU* 1.3 76.9 - - - +
67M LEU* 1.3 67.8 + - - +
70M GLU* 2.7 63.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 67 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56M PHE* 3.6 47.8 - - + +
57M GLN 5.5 1.6 - - - +
59M THR* 6.1 3.1 - - + -
62M ARG* 3.9 30.6 - - + +
63M SER 3.0 11.0 + - - +
64M ALA* 3.7 9.9 - - - +
66M LYS* 1.3 74.3 - - - +
68M VAL* 1.3 54.7 + - + +
70M GLU* 3.6 1.9 - - - +
71M SER* 2.8 38.9 + - - -
78M PHE* 3.6 33.0 - - + -
100M TYR* 3.9 14.5 + - - +
104M ALA* 4.6 5.6 - - + +
108M VAL* 5.1 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 68 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293L ALA* 4.3 18.8 - - + +
296L LEU* 4.1 35.7 - - + +
297L GLN* 4.2 2.2 - - + +
56M PHE 5.9 1.3 - - - +
64M ALA 3.1 16.6 - - - +
65M LEU 3.2 6.5 + - - +
66M LYS 3.1 0.4 - - - -
67M LEU* 1.3 78.0 - - + +
69M ARG* 1.3 67.4 + - - +
71M SER* 3.4 6.2 + - - +
72M GLU* 3.0 52.3 + - + +
78M PHE* 6.0 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 69 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117G LYS* 4.6 8.5 - - - +
120G LEU* 3.5 52.5 + - + -
121G ASP* 2.6 31.5 + - - +
123G ILE* 5.4 3.6 - - + -
296L LEU 3.0 29.2 + - - -
297L GLN 3.2 6.3 + - - -
298L GLY* 3.5 30.6 - - - +
299L ILE 4.8 0.6 - - - +
65M LEU* 2.9 41.9 + - + +
66M LYS 3.9 2.0 - - - +
68M VAL* 1.3 74.5 - - - +
70M GLU* 1.3 60.9 + - - +
72M GLU* 3.5 5.3 + - - +
73M LEU* 2.9 35.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 70 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120G LEU* 5.8 1.8 - - + -
62M ARG* 3.2 21.9 + - - -
66M LYS* 2.7 51.3 + - + +
69M ARG* 1.3 71.5 - - + +
71M SER* 1.3 62.6 + - - +
73M LEU* 2.9 10.4 + - - +
74M LEU* 2.8 31.8 + - + +
100M TYR* 2.6 39.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 71 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67M LEU 2.8 28.2 + - - -
68M VAL* 3.4 12.3 + - - -
70M GLU* 1.3 73.8 - - - +
72M GLU* 1.3 52.4 + - - +
74M LEU* 3.5 11.2 - - - +
75M GLY 2.8 28.2 + - - -
76M GLY 3.1 29.1 + - - -
77M THR* 5.1 0.5 - - - -
78M PHE* 3.6 28.0 - - - -
100M TYR* 4.2 3.5 + - - -
101M TYR* 4.4 7.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 72 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297L GLN* 3.3 26.0 - - - +
298L GLY* 3.1 15.4 + - - -
364L ARG* 2.5 50.7 + - + +
367L SER* 3.2 19.2 - - - -
368L LEU* 4.0 26.5 - - + +
68M VAL* 3.0 34.1 + - + +
69M ARG* 3.6 7.1 - - - +
71M SER* 1.3 75.6 - - - +
73M LEU* 1.3 67.5 + - + +
75M GLY* 3.2 3.6 + - - -
76M GLY 4.5 2.0 - - - +
77M THR* 6.3 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 73 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123G ILE* 4.4 22.9 - - + -
125G VAL* 4.3 24.5 - - + -
360L THR* 4.6 6.5 - - - +
363L GLU* 4.6 3.1 - - + -
364L ARG* 4.2 35.7 - - + +
367L SER* 2.7 21.3 + - - -
69M ARG* 2.9 26.5 - - + +
70M GLU* 2.9 9.9 + - - +
72M GLU* 1.3 82.9 - - + +
74M LEU* 1.3 59.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 74 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367L SER* 4.2 1.8 - - - -
70M GLU* 2.8 18.2 + - + +
71M SER* 3.7 2.0 - - - +
73M LEU* 1.3 80.9 - - + +
75M GLY* 1.3 63.9 + - - +
94M LEU* 3.7 8.5 - - - +
97M ASP* 3.5 31.4 - - + +
100M TYR* 3.4 56.3 - - + -
101M TYR* 3.5 17.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 75 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367L SER* 3.6 31.4 - - - -
368L LEU* 4.7 0.9 - - - -
371L LEU* 4.4 7.4 - - - -
71M SER 2.8 6.7 + - - -
72M GLU 3.2 6.8 + - - -
73M LEU 3.3 0.6 + - - -
74M LEU* 1.3 83.1 - - - +
76M GLY* 1.3 57.5 + - - -
94M LEU* 3.6 24.2 + - - +
97M ASP* 4.4 0.3 - - - +
101M TYR* 3.0 8.6 + - - -
----------------------------------------------------------
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