Contacts of the helix formed by residues 156 - 168 (chain D) in PDB entry 3RIK
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 LEU 156 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ILE* 4.1 19.5 - - + +
131A ARG* 4.0 25.4 - - + -
87D ASP* 5.0 4.5 - - + +
90D ALA* 3.8 18.8 - - + +
91D LEU* 4.5 18.8 - - + +
94D LEU* 3.5 27.8 - - + +
151D GLU 3.3 7.5 + - - +
152D GLU* 3.3 30.7 - - + +
154D THR 3.7 0.2 - - - -
155D LYS* 1.3 84.8 - - + +
157D LYS* 1.3 67.4 + - + +
158D ILE 3.5 1.1 - - - -
159D PRO* 3.6 2.3 - - - +
160D LEU* 3.2 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 157 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85D MET* 3.6 36.1 - - + +
86D THR 4.4 0.4 - - - +
87D ASP* 3.4 25.8 + - - +
90D ALA* 4.2 11.2 - - + -
121D VAL* 3.7 14.4 - - - -
122D PRO* 2.7 32.2 + - + +
124D ALA 4.4 5.7 + - - +
133D TYR* 5.0 1.4 + - - -
135D TYR* 4.0 2.0 + - - -
152D GLU 3.0 19.0 + - - +
153D ASP* 3.3 19.5 + - - +
156D LEU* 1.3 74.3 - - - +
158D ILE* 1.3 61.1 - - - +
160D LEU* 3.1 3.6 + - - +
161D ILE* 2.9 36.7 + - + +
220D TYR* 3.6 17.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 158 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149D LEU* 3.9 17.0 - - + -
153D ASP 2.9 24.4 + - - +
154D THR* 4.5 3.1 - - - +
157D LYS* 1.3 75.5 - - - +
159D PRO* 1.4 71.1 - - + +
160D LEU 3.1 0.2 + - - -
161D ILE* 3.1 6.4 + - - +
162D HIS* 3.0 41.1 + - + +
220D TYR* 3.5 48.0 - - + +
223D HIS* 3.9 38.8 - - + +
225D LEU* 4.0 6.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 159 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D LEU* 5.9 2.7 - - + -
153D ASP 3.7 0.2 - - - +
154D THR 3.3 27.6 - - - +
155D LYS* 3.6 15.7 - - + +
156D LEU 3.6 14.6 - - - +
158D ILE* 1.4 92.8 - - + +
160D LEU* 1.3 61.8 + - + +
162D HIS* 3.3 9.1 + - + +
163D ARG* 3.1 35.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 160 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85D MET* 3.7 22.2 - - + +
90D ALA* 3.4 47.8 - - + +
93D ILE* 3.7 28.7 - - + -
94D LEU* 3.9 13.0 - - + -
105D LEU* 4.2 17.3 - - + +
156D LEU 3.2 13.8 + - - +
157D LYS 3.1 4.1 + - - +
158D ILE 3.1 1.0 - - - -
159D PRO* 1.3 78.2 - - + +
161D ILE* 1.3 58.7 + - - +
163D ARG* 3.2 28.2 + - - +
164D ALA* 2.9 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 161 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85D MET* 4.1 22.4 - - + -
119D ILE* 4.1 11.4 - - + -
121D VAL* 4.0 26.5 - - + -
157D LYS* 2.9 30.7 + - + +
158D ILE* 3.7 7.9 - - - +
160D LEU* 1.3 74.1 - - - +
162D HIS* 1.3 59.2 + - - +
164D ALA* 3.1 7.8 + - - +
165D LEU* 2.8 32.0 + - + +
174D LEU* 3.8 26.5 - - + -
220D TYR* 4.6 6.5 - - + -
225D LEU* 4.1 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 162 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158D ILE* 3.0 34.8 + - + +
159D PRO* 3.7 10.1 - - + +
161D ILE* 1.3 76.2 - - - +
163D ARG* 1.3 66.0 + - + +
165D LEU* 3.2 10.4 + - + +
166D GLN* 3.0 30.0 + - + +
223D HIS* 2.7 29.4 + - - +
224D LYS* 4.0 14.1 - - + -
225D LEU* 3.5 23.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 163 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D LEU* 3.7 17.6 - - - +
98D PRO* 4.2 3.4 + - - +
101D GLN* 2.9 41.2 + - - +
102D ASN* 3.0 32.3 + - - +
105D LEU* 3.9 18.0 - - + +
159D PRO* 3.1 21.4 + - - +
160D LEU* 3.6 14.5 - - - +
161D ILE 3.2 0.2 - - - -
162D HIS* 1.3 78.9 - - + +
164D ALA* 1.3 61.0 + - - +
166D GLN* 3.4 8.5 + - + +
167D LEU* 3.1 31.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 164 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85D MET* 5.5 1.1 - - + -
105D LEU* 4.8 3.7 - - + +
109D PHE* 3.5 50.6 - - + +
119D ILE* 4.0 12.8 - - + -
160D LEU 2.9 13.9 + - - +
161D ILE* 3.1 8.0 + - - +
163D ARG* 1.3 77.0 - - - +
165D LEU* 1.3 60.5 + - - +
167D LEU* 3.3 5.0 + - - -
168D ALA* 3.2 23.1 + - - +
172D VAL* 5.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 165 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119D ILE* 4.9 1.8 - - + -
161D ILE* 2.8 25.3 + - + +
162D HIS* 3.2 9.4 + - + +
164D ALA* 1.3 73.2 - - - +
166D GLN* 1.3 64.0 + - + +
168D ALA* 3.4 21.3 + - - +
172D VAL* 3.3 44.4 - - + +
174D LEU* 4.6 14.6 - - + -
224D LYS 5.7 1.6 - - - +
225D LEU* 4.0 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 166 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162D HIS* 3.0 19.5 + - + +
163D ARG* 3.6 11.4 - - - +
165D LEU* 1.3 77.9 - - - +
167D LEU* 1.3 64.3 + - + +
168D ALA 3.5 4.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 167 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D ASN* 4.4 12.3 - - - +
105D LEU* 3.6 34.5 - - + -
106D LYS* 3.9 39.7 - - + +
109D PHE* 4.2 8.1 - - + -
110D SER* 3.7 26.0 - - - -
111D GLU 5.0 0.5 + - - -
163D ARG* 3.1 19.5 + - + +
164D ALA* 3.3 4.9 + - - +
166D GLN* 1.3 79.9 - - + +
168D ALA* 1.3 62.4 + - - +
169D GLN* 3.6 6.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 168 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D PHE* 3.3 19.3 + - + +
116D TYR 5.0 2.9 - - - +
164D ALA 3.2 16.5 + - - +
165D LEU 3.5 13.3 - - - +
166D GLN 3.3 3.9 - - - +
167D LEU* 1.3 77.7 - - - +
169D GLN* 1.3 60.3 + - - +
170D ARG* 3.6 8.5 - - + +
172D VAL* 3.5 28.5 - - + -
----------------------------------------------------------
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