Contacts of the helix formed by residues 118 - 131 (chain F) in PDB entry 6IY6
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 118 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66F GLY 5.5 0.4 - - - -
67F LEU* 3.4 18.2 - - - +
69F GLY* 5.2 2.7 - - - -
78F ILE* 3.9 15.9 - - - -
113F VAL* 3.6 25.6 + - - +
116F SER* 4.2 3.8 - - - -
117F LEU* 1.3 74.1 - - - +
119F LEU* 1.3 66.6 + - - +
120F ALA* 3.6 10.4 - - - +
121F ASP* 2.8 34.4 + - - +
122F LEU* 3.4 11.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 119 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F ALA* 4.5 5.4 - - + -
55F LEU* 3.3 52.2 - - + +
56F ARG* 3.9 6.7 - - - +
59F ALA* 3.4 27.8 - - + +
67F LEU* 2.9 28.1 + - + +
68F TYR* 4.0 12.8 - - + -
78F ILE* 3.9 15.5 - - + +
82F LEU* 4.5 11.2 - - + -
118F SER* 1.3 68.0 - - - +
120F ALA* 1.3 56.2 + - - +
122F LEU* 3.1 14.1 + - + +
123F CYS* 2.7 38.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 120 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78F ILE* 4.2 11.4 - - + +
81F TRP* 3.7 36.1 - - + -
112F LEU* 3.7 12.6 - - + -
113F VAL* 4.0 7.2 - - + -
118F SER* 3.6 13.2 + - - +
119F LEU* 1.3 75.5 - - - +
121F ASP* 1.3 62.9 + - - +
123F CYS* 3.9 8.5 - - - -
124F VAL* 3.0 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 121 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111F TYR* 3.5 15.2 - - - +
112F LEU* 2.8 26.7 + - - +
116F SER 3.5 9.5 - - - +
117F LEU* 3.6 14.8 - - + -
118F SER* 2.8 39.2 + - - +
120F ALA* 1.3 78.8 - - - +
122F LEU* 1.3 57.7 + - - +
125F TRP* 3.1 32.7 + - - +
150F TRP* 3.3 24.5 + - - -
154F LEU* 3.9 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 122 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16F GLY* 4.5 10.5 - - - +
19F LEU* 4.2 11.6 - - + +
20F ALA* 3.8 36.1 - - + +
23F HIS* 4.9 4.3 - - + +
55F LEU* 5.8 1.6 - - + -
67F LEU* 4.4 18.6 - - + -
117F LEU* 3.8 26.7 - - + -
118F SER 3.7 10.3 - - - +
119F LEU* 3.1 13.8 + - + +
121F ASP* 1.3 73.1 - - - +
123F CYS* 1.3 58.1 + - - +
125F TRP* 3.2 4.5 + - - +
126F ALA* 2.8 37.8 + - - +
154F LEU* 5.8 0.2 - - + -
158F LEU* 4.3 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 123 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16F GLY* 5.0 3.4 - - - -
52F ASN* 5.4 0.4 - - - +
55F LEU* 4.1 17.0 - - + +
81F TRP 3.6 16.8 - - - -
82F LEU* 3.7 26.5 - - + -
85F SER* 3.4 20.9 - - - +
119F LEU 2.7 18.9 + - - +
120F ALA* 3.4 15.9 - - - -
122F LEU* 1.3 71.5 - - - +
124F VAL* 1.3 63.1 + - - +
126F ALA* 4.0 4.9 - - - +
127F THR* 2.7 32.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 124 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81F TRP* 4.0 26.2 - - + +
84F PHE* 4.6 2.9 - - + -
85F SER* 4.0 8.7 - - - -
89F LEU* 3.7 8.0 - - + +
102F LEU* 3.3 30.5 - - + -
112F LEU* 3.7 12.8 - - + -
120F ALA 3.0 17.8 + - - +
123F CYS* 1.3 88.9 - - - +
125F TRP* 1.3 52.5 + - - +
127F THR* 3.3 3.6 + - - -
128F LEU* 2.7 38.1 + - + +
150F TRP* 3.5 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 125 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15F LEU* 6.2 1.3 - - + -
19F LEU* 3.7 24.5 - - + -
121F ASP 3.1 22.2 + - - +
122F LEU* 3.8 2.7 - - - +
124F VAL* 1.3 75.4 - - - +
126F ALA* 1.3 59.9 + - - +
128F LEU* 3.3 4.4 + - - +
129F LYS* 2.8 68.6 + - + +
150F TRP* 3.8 10.1 - + + -
151F PHE* 3.3 55.2 + + - -
154F LEU* 3.5 24.9 - - + +
155F GLU* 3.8 30.1 - - + -
158F LEU* 3.7 24.7 - - + -
159F GLU 5.5 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 126 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15F LEU* 3.6 21.4 - - + +
16F GLY* 3.3 35.9 - - - +
19F LEU* 4.3 3.8 - - + -
122F LEU 2.8 21.4 + - - +
123F CYS* 4.0 4.5 - - - +
125F TRP* 1.3 83.5 - - - +
127F THR* 1.3 57.7 + - - +
129F LYS* 3.4 3.3 + - - +
130F GLY 3.0 22.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 127 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15F LEU* 5.8 0.4 - - - -
85F SER* 3.3 33.6 + - - +
89F LEU* 3.7 8.7 - - + +
90F SER* 3.6 26.6 + - - +
123F CYS 2.7 22.1 + - - -
124F VAL 3.3 3.9 + - - -
126F ALA* 1.3 76.2 - - - +
128F LEU* 1.3 56.8 + - - +
130F GLY* 3.3 2.8 + - - +
131F ASN* 2.9 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 128 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89F LEU* 3.6 31.8 - - + +
95F PHE* 4.0 6.3 - - + -
99F ILE* 3.8 17.7 - - + -
102F LEU* 4.9 2.0 - - + -
124F VAL* 2.7 25.0 + - + +
125F TRP 3.5 5.4 - - - +
127F THR* 1.3 70.2 - - - +
129F LYS* 1.3 63.4 + - - +
131F ASN* 3.3 14.4 + - - +
134F TRP* 3.0 43.4 - - + +
147F VAL* 3.9 18.8 - - + -
150F TRP* 3.8 27.6 - - + -
151F PHE* 3.8 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 129 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15F LEU* 5.1 8.7 - - + -
125F TRP* 2.8 53.7 + - + +
126F ALA* 3.6 5.2 - - - +
128F LEU* 1.3 71.1 - - - +
130F GLY* 1.3 61.7 + - - +
131F ASN 3.4 5.2 + - - +
134F TRP* 4.4 1.8 - - - -
135F GLN* 3.2 35.9 + - - +
151F PHE* 3.9 21.6 - - + -
155F GLU* 4.2 20.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 130 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15F LEU* 4.3 13.4 - - - +
126F ALA 3.0 14.4 + - - -
127F THR* 3.6 6.1 - - - -
128F LEU 3.3 0.2 - - - -
129F LYS* 1.3 72.2 - - - +
131F ASN* 1.3 62.5 + - - +
132F ALA 3.9 0.7 + - - -
135F GLN* 5.8 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 131 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89F LEU* 3.0 24.9 + - + +
90F SER 5.1 1.4 + - - -
91F SER 3.9 5.9 + - - -
92F CYS* 4.1 10.0 - - - +
95F PHE* 3.3 26.8 - - + -
127F THR 2.9 13.1 + - - +
128F LEU* 3.4 18.8 - - - +
129F LYS 3.2 10.3 - - - +
130F GLY* 1.3 78.6 - - - +
132F ALA* 1.3 62.1 + - - +
133F ALA* 2.7 33.6 + - - +
134F TRP* 2.9 12.3 + - + -
135F GLN* 3.7 12.6 + - - +
----------------------------------------------------------
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