Contacts of the helix formed by residues 105 - 122 (chain D) in PDB entry 4KYI
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 ASN 105 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D ASP* 2.9 12.2 + - + +
103D ILE 3.3 2.0 + - - -
104D THR* 1.3 82.2 - - - +
106D THR* 1.3 59.4 + - - +
107D ASP* 2.9 43.8 + - - +
108D THR* 2.5 45.6 + - + +
109D PHE 3.8 0.7 + - - -
143D ALA* 4.0 3.1 - - - +
144D VAL* 4.5 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 106 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D ASN* 1.3 73.3 + - - +
107D ASP* 1.3 61.0 + - - +
109D PHE* 2.9 26.2 + - + +
110D ALA* 3.0 13.6 + - + +
143D ALA* 3.4 23.7 + - - +
144D VAL* 3.8 18.8 - - + -
148D GLU* 5.7 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 107 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D GLU* 6.1 0.9 - - - -
105D ASN* 2.9 24.7 + - - +
106D THR* 1.3 80.0 - - - +
108D THR* 1.3 55.9 + - + +
110D ALA* 3.2 12.1 + - - +
111D ARG* 3.0 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 108 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D GLU* 4.3 17.3 + - + +
30D SER 5.5 0.2 - - - +
32D VAL* 3.8 23.6 - - + -
100D VAL 5.0 1.5 - - - +
101D TYR* 3.5 10.1 - - - +
102D ASP* 2.8 28.8 + - + +
105D ASN* 2.5 41.0 + - + +
107D ASP* 1.3 75.1 - - + +
109D PHE* 1.3 57.1 + - - +
111D ARG* 3.1 8.8 + - - +
112D ALA* 2.7 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 109 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101D TYR* 4.3 22.7 - + + -
106D THR* 2.9 21.4 + - + +
108D THR* 1.3 82.5 + - - +
110D ALA* 1.3 62.4 + - - +
112D ALA* 3.4 19.7 + - + +
113D LYS* 3.5 44.6 + - - +
131D LEU* 4.8 3.1 - - + -
144D VAL* 4.1 28.7 - - + -
148D GLU* 4.5 20.2 - - + -
149D ALA* 3.7 32.5 - - + -
152D TYR* 4.5 16.4 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 110 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D THR* 3.0 10.2 + - + +
107D ASP* 3.3 16.6 - - - +
108D THR 3.1 0.2 - - - -
109D PHE* 1.3 80.2 - - - +
111D ARG* 1.3 59.3 + - - +
112D ALA 3.3 0.3 + - - -
113D LYS* 3.5 8.7 + - - +
114D ASN* 3.0 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 111 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D GLY* 4.9 0.4 - - - -
29D GLU* 4.1 33.6 + - + +
80D LEU 5.3 1.8 + - - -
81D GLU* 2.8 32.7 + - - +
84D HIS* 3.6 22.8 + - - +
107D ASP 3.0 13.2 + - - +
108D THR* 3.1 11.2 + - - +
110D ALA* 1.3 74.5 - - - +
112D ALA* 1.3 63.4 + - - +
114D ASN* 3.2 32.8 + - - +
115D TRP* 3.0 71.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 112 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D VAL* 3.4 24.6 - - + +
100D VAL 5.3 1.6 - - - -
101D TYR* 4.3 9.4 - - + -
108D THR 2.7 13.1 + - - +
109D PHE* 3.4 18.4 - - + +
110D ALA 3.1 0.2 - - - -
111D ARG* 1.3 74.0 - - - +
113D LYS* 1.3 61.1 + - + +
115D TRP* 3.1 2.9 + - - -
116D VAL* 2.9 32.8 + - - +
131D LEU* 4.2 17.5 - - + -
152D TYR* 5.6 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 113 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D PHE* 3.5 39.9 - - + +
110D ALA* 3.5 9.7 + - - +
112D ALA* 1.3 76.2 - - + +
114D ASN* 1.3 56.3 + - - +
116D VAL* 3.2 1.7 + - - +
117D LYS* 2.6 38.6 + - - +
152D TYR* 3.4 56.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 114 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110D ALA* 3.0 23.7 + - - +
111D ARG* 3.4 37.4 + - - +
112D ALA 3.2 0.6 - - - -
113D LYS* 1.3 81.0 - - - +
115D TRP* 1.3 59.8 + - - +
117D LYS* 3.8 10.3 - - - +
118D GLU* 3.4 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 115 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D LEU* 3.6 34.1 - - + -
28D GLY* 3.5 40.6 + - - +
79D GLY* 6.4 0.7 - - - -
80D LEU 5.8 2.9 - - - -
83D TYR 5.3 1.6 - - - -
84D HIS* 3.8 22.9 - + - -
87D ALA* 3.7 25.6 - - + -
91D TYR* 4.9 0.7 - + - -
99D VAL* 4.0 16.8 - - + -
111D ARG* 3.0 60.4 + - + +
112D ALA 3.5 6.3 - - - +
114D ASN* 1.3 76.1 - - - +
116D VAL* 1.3 59.1 + - - +
117D LYS 3.2 0.2 - - - -
118D GLU* 3.2 32.2 + - - +
119D LEU* 2.9 35.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 116 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D VAL* 3.7 21.5 - - + -
112D ALA 2.9 19.0 + - - +
113D LYS 3.6 6.5 - - - +
115D TRP* 1.3 75.8 - - - +
117D LYS* 1.3 52.7 + - - +
119D LEU* 3.1 9.7 + - - +
120D GLN* 2.7 61.2 + - + +
129D ILE* 4.2 5.8 - - + -
131D LEU* 5.3 2.9 - - + -
152D TYR* 3.7 21.1 - - + +
158D LEU* 3.8 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 117 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113D LYS 2.6 21.6 + - - +
114D ASN* 3.8 10.5 - - - +
116D VAL* 1.3 72.7 - - - +
118D GLU* 1.3 58.3 + - - +
120D GLN* 3.0 27.8 + - - +
121D ARG* 3.1 40.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 118 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D HIS* 3.7 20.7 + - - +
87D ALA* 4.3 5.9 - - - +
88D PRO* 4.5 3.6 - - - +
91D TYR* 2.6 37.7 + - + +
111D ARG* 5.8 0.2 + - - -
114D ASN 3.4 10.7 + - - +
115D TRP* 3.2 35.1 + - + +
117D LYS* 1.3 79.0 - - - +
119D LEU* 1.3 57.8 + - + +
121D ARG* 4.0 14.8 - - - +
122D GLN* 2.8 50.8 + - - +
123D ALA* 3.4 4.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 119 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D LEU* 4.3 13.0 - - + -
91D TYR* 3.7 33.7 - - + -
97D ALA* 4.0 19.5 - - + -
99D VAL* 3.9 25.6 - - + -
115D TRP* 2.9 21.5 + - + +
116D VAL* 3.4 5.2 - - - +
118D GLU* 1.3 78.0 - - + +
120D GLN* 1.3 62.5 + - - +
121D ARG 3.3 0.2 - - - -
123D ALA* 3.2 37.5 + - + +
124D SER 4.3 5.9 - - - +
127D ILE* 4.2 11.4 - - + +
129D ILE* 3.7 23.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 120 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D VAL* 2.7 44.7 + - + +
117D LYS* 3.0 14.0 + - - +
119D LEU* 1.3 74.9 - - - +
121D ARG* 1.3 63.3 + - + +
123D ALA 5.6 0.4 - - - -
129D ILE* 4.5 7.9 - - + -
156D ASN* 3.0 39.6 + - - +
158D LEU* 4.6 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 121 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D LYS* 3.1 40.4 + - + +
118D GLU* 4.0 12.7 - - - +
119D LEU 3.3 0.2 - - - -
120D GLN* 1.3 84.6 - - + +
122D GLN* 1.3 104.2 + - - +
123D ALA 3.4 7.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 122 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D PRO* 4.6 8.1 - - - +
91D TYR* 3.0 27.2 + - + +
118D GLU* 2.8 26.3 + - - +
121D ARG* 1.3 113.5 + - - +
123D ALA* 1.3 67.1 + - - +
----------------------------------------------------------
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