Contacts of the helix formed by residues 97 - 112 (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 ASP 97 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74M LEU* 3.5 36.4 - - + +
75M GLY 4.4 0.9 - - - +
94M LEU* 3.2 34.1 + - - +
96M ASP* 1.3 76.4 - - - +
98M LEU* 1.3 62.1 + - - +
99M PRO* 3.3 7.4 - - - -
100M TYR* 3.2 11.6 + - + +
101M TYR* 3.1 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 98 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29M SER* 5.7 0.7 - - - +
31M LEU* 3.7 17.5 - - + -
93M PHE* 3.8 20.6 - - + -
95M LYS* 3.6 17.0 + - + +
96M ASP 2.7 10.9 + - - +
97M ASP* 1.3 72.3 - - - +
99M PRO* 1.3 66.2 - - + +
100M TYR 3.3 0.9 + - - -
101M TYR* 3.4 5.0 + - - +
102M VAL* 3.2 32.9 + - + +
192M VAL* 3.3 31.2 - - + -
193M VAL* 4.4 15.9 - - + +
196M ASP* 5.0 7.6 - - + -
197M LEU* 3.8 12.3 - - + +
200M PHE* 5.1 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 99 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96M ASP 3.7 8.5 - - - +
97M ASP* 3.3 4.9 - - - +
98M LEU* 1.3 94.2 - - + +
100M TYR* 1.3 65.3 + - + +
102M VAL* 3.0 15.9 + - + +
103M ASN* 3.1 22.7 + - - +
200M PHE* 3.6 44.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 100 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62M ARG* 3.8 24.5 + - - -
67M LEU* 3.9 9.4 + - + +
70M GLU* 2.6 46.8 + - + +
71M SER* 4.6 4.9 - - - -
74M LEU* 3.4 33.9 - - + -
78M PHE* 4.2 20.6 - + - -
97M ASP* 3.2 14.1 + - + +
99M PRO* 1.3 81.3 - - + +
101M TYR* 1.3 65.0 + + + +
102M VAL 3.0 1.2 + - - -
103M ASN* 3.1 5.3 + - - +
104M ALA* 2.7 35.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 101 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31M LEU* 4.3 3.0 - - + +
71M SER* 3.9 4.3 + - - -
74M LEU* 3.5 16.0 + - + +
75M GLY 3.0 23.6 + - - -
76M GLY* 3.5 17.8 - - - -
77M THR 4.6 0.7 - - - -
78M PHE* 3.6 30.3 - + - -
91M ALA* 4.3 9.9 - - + -
92M THR 4.6 0.7 - - - -
93M PHE* 3.3 56.1 - + + -
97M ASP* 3.1 34.5 - - + -
98M LEU 3.4 3.3 + - - +
99M PRO 3.4 0.6 - - - -
100M TYR* 1.3 86.0 - + + +
102M VAL* 1.3 58.6 + - - +
104M ALA* 3.7 7.6 - - - -
105M LEU* 3.2 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 102 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31M LEU* 4.2 9.0 - - + -
98M LEU* 3.2 36.3 - - + +
99M PRO* 3.0 9.8 + - + +
100M TYR 3.0 1.0 - - - -
101M TYR* 1.3 78.0 - - - +
103M ASN* 1.3 67.1 + - - +
105M LEU* 3.3 6.2 + - - +
106M ALA* 3.0 20.1 + - - +
197M LEU* 3.9 13.7 - - + -
200M PHE* 4.3 17.0 - - + +
201M VAL* 4.3 14.8 - - + +
204M SER* 4.2 21.8 - - - +
206M LEU* 4.2 7.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 103 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62M ARG* 5.0 4.0 - - - +
99M PRO* 3.1 18.1 + - - +
100M TYR* 3.7 7.7 - - - +
102M VAL* 1.3 80.5 - - - +
104M ALA* 1.3 53.6 + - - +
106M ALA* 3.0 6.0 + - - +
107M ASP* 2.8 46.2 + - - +
200M PHE* 6.0 1.0 - - - -
203M GLU 4.6 4.6 + - - -
204M SER* 3.9 25.2 - - - +
205M LEU* 4.4 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 104 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56M PHE* 5.5 0.2 - - - -
62M ARG* 4.0 21.3 + - - +
67M LEU* 4.6 5.0 - - + +
78M PHE* 3.6 35.0 - - + -
100M TYR* 2.7 20.3 + - + +
101M TYR* 3.7 5.4 - - - -
103M ASN* 1.3 79.2 - - - +
105M LEU* 1.3 63.6 + - - +
106M ALA 3.2 0.2 + - - -
107M ASP* 3.4 7.8 + - - +
108M VAL* 3.4 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 105 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31M LEU* 3.9 26.5 - - + -
33M VAL* 3.8 26.9 - - + -
56M PHE* 3.6 29.4 - - + -
78M PHE* 4.2 9.0 - - + -
89M LEU* 3.4 35.5 - - + +
91M ALA* 4.3 6.3 - - + -
101M TYR 3.2 20.2 + - - +
102M VAL* 3.3 5.4 + - - +
104M ALA* 1.3 79.2 - - - +
106M ALA* 1.3 63.7 + - - +
108M VAL* 3.6 6.8 + - - +
109M LEU* 3.5 25.4 + - - +
206M LEU* 5.0 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 106 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102M VAL 3.0 13.6 + - - +
103M ASN* 3.1 15.0 - - - +
105M LEU* 1.3 73.4 - - - +
107M ASP* 1.3 57.6 + - - +
108M VAL 3.0 2.0 - - - -
109M LEU* 2.8 27.3 + - - +
110M TYR* 3.0 11.8 + - - +
204M SER* 4.5 1.1 - - - -
205M LEU* 4.0 29.3 - - + +
206M LEU* 3.6 27.5 - - + +
209M LEU* 5.8 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 107 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59M THR* 4.0 10.2 - - + +
61M THR* 2.7 27.8 + - - -
62M ARG* 4.0 21.1 + - - +
103M ASN* 2.8 34.2 + - - +
104M ALA 3.7 5.6 - - - +
106M ALA* 1.3 73.3 - - - +
108M VAL* 1.3 56.9 + - - +
111M LYS* 3.0 54.7 + - - +
205M LEU* 4.7 11.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 108 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55M ASN* 3.6 29.8 - - + +
56M PHE* 3.9 39.9 - - + +
59M THR* 4.4 11.4 - - + -
67M LEU* 5.1 4.9 - - + -
89M LEU* 4.2 11.0 - - + -
104M ALA 3.4 14.6 - - - +
105M LEU* 3.7 9.9 - - - +
106M ALA 2.9 0.8 + - - -
107M ASP* 1.3 79.3 - - + +
109M LEU* 1.3 58.0 + - - +
112M THR* 2.7 41.6 + - + +
180M TYR* 4.9 2.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 109 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33M VAL* 4.1 20.0 - - + -
35M VAL* 4.6 6.3 - - + -
89M LEU* 4.1 16.6 - - + -
105M LEU 3.5 15.5 - - - +
106M ALA 2.8 12.4 + - - +
108M VAL* 1.3 74.8 - - + +
110M TYR* 1.3 59.7 + - - +
112M THR* 4.7 2.3 + - - -
180M TYR* 3.2 65.1 - - + +
185M LEU* 4.3 9.0 - - + -
206M LEU* 3.7 28.9 - - + -
209M LEU* 4.2 15.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 110 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106M ALA 3.0 9.9 + - - +
109M LEU* 1.3 79.8 - - - +
111M LYS* 1.3 66.2 + - + +
112M THR 3.9 1.2 + - - -
205M LEU* 3.3 43.5 - - + +
208M THR* 3.9 29.7 + - + +
209M LEU* 3.8 22.7 - - + -
210M PRO* 4.5 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 111 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59M THR* 3.1 5.9 - - - -
60M ASN* 3.0 44.7 + - - +
61M THR* 3.2 38.2 + - - +
107M ASP* 3.0 39.3 + - - +
110M TYR* 1.3 84.3 - - + +
112M THR* 1.3 60.0 + - - +
205M LEU* 3.6 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 112 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54M PHE* 4.6 16.6 - - + +
55M ASN* 4.9 3.4 - - - +
56M PHE 4.9 1.3 - - - +
57M GLN* 4.7 4.0 - - + +
58M ASN 3.7 12.1 - - - +
59M THR* 4.0 7.0 - - + +
60M ASN* 4.7 0.9 + - - -
108M VAL* 2.7 43.5 + - + +
109M LEU 4.7 3.1 + - - -
110M TYR 3.9 0.8 + - - -
111M LYS* 1.3 72.6 - - - +
113M ALA* 1.3 61.1 + - - +
114M PHE* 2.8 52.5 - - + -
180M TYR* 5.1 3.6 - - - -
----------------------------------------------------------
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