Contacts of the helix formed by residues 130 - 146 (chain B) in PDB entry 3ROT
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 130 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ARG* 5.4 8.4 + - - +
126B PHE* 5.5 0.9 - - - -
129B SER* 1.3 72.9 + - - +
131B ASN* 1.3 59.0 + - - +
132B LEU* 3.3 11.1 + - - +
133B LEU* 3.2 45.2 + - + +
134B ALA* 2.9 26.5 + - - +
137B LYS* 5.5 2.2 + - - +
291B ASN* 3.9 21.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ASP 3.8 21.0 + - - -
113B THR* 4.9 3.4 + - - +
114B ARG 5.7 0.2 - - - +
126B PHE* 5.3 1.4 - - - -
129B SER* 3.2 10.7 + - - -
130B ASP* 1.3 72.7 + - - +
132B LEU* 1.3 61.9 + - - +
134B ALA* 3.9 4.5 - - - +
135B GLY 3.2 16.6 + - - -
161B HIS* 5.7 0.2 - - - -
163B GLY* 3.5 39.0 - - - +
166B LYS* 3.8 17.5 - - + +
167B ARG* 2.8 48.4 + - + +
264B GLN* 4.2 5.0 + - - +
317B GOL 5.6 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ASP* 3.2 8.1 + - - +
131B ASN* 1.3 78.7 - - - +
133B LEU* 1.3 67.4 + - + +
135B GLY 3.4 0.3 + - - -
136B LYS* 3.3 50.8 + - - +
166B LYS* 3.6 30.3 - - + +
169B TYR* 4.4 17.7 - - + -
170B GLY* 3.7 14.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ASP* 3.0 35.2 + - + +
132B LEU* 1.3 83.6 - - + +
134B ALA* 1.3 66.0 + - - +
136B LYS* 2.9 23.8 + - + +
137B LYS* 2.8 41.4 + - + +
291B ASN* 5.7 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B SER* 3.8 17.3 - - - +
130B ASP 2.9 19.2 + - - +
131B ASN* 3.9 8.3 - - - +
133B LEU* 1.3 71.7 - - - +
135B GLY* 1.3 58.6 + - - +
137B LYS* 3.2 20.9 + - - +
138B LEU* 2.9 29.3 + - - +
243B PHE* 3.8 21.3 - - + -
262B MSE 3.9 11.5 - - + +
264B GLN* 6.5 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B ASN 3.2 8.7 + - - -
132B LEU 3.4 2.7 + - - -
133B LEU 3.1 0.8 - - - -
134B ALA* 1.3 80.6 - - - +
136B LYS* 1.3 56.4 + - - +
138B LEU* 3.1 1.6 + - - -
139B GLY 2.9 25.1 + - - -
167B ARG* 3.5 21.5 - - - -
171B ILE* 3.3 22.0 + - - +
243B PHE* 4.0 10.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B LEU* 3.3 37.8 + - + +
133B LEU* 2.9 24.5 + - + +
135B GLY* 1.3 75.8 - - - +
137B LYS* 1.3 63.6 + - + +
139B GLY 3.3 0.5 + - - -
140B GLU* 3.0 37.0 + - - +
169B TYR* 5.1 2.0 - - - -
170B GLY* 3.7 11.1 - - - +
173B THR* 2.9 35.4 + - - +
174B ILE* 3.5 20.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B SER* 5.1 1.2 + - - -
130B ASP* 5.5 1.4 + - - +
133B LEU* 2.8 26.9 + - + +
134B ALA* 3.3 31.7 - - - +
136B LYS* 1.3 77.9 - - + +
138B LEU* 1.3 56.8 + - - +
140B GLU* 3.6 11.6 + - - +
141B LYS* 3.0 29.0 + - - +
260B TYR* 5.8 0.2 - - - -
262B MSE 3.5 25.4 - - + +
291B ASN* 5.6 4.4 - - - +
293B ALA* 4.4 19.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B ALA 2.9 15.7 + - - +
135B GLY* 3.1 4.9 + - - +
137B LYS* 1.3 74.5 - - - +
139B GLY* 1.3 61.8 + - - +
141B LYS* 3.3 3.0 + - + +
142B ALA* 2.9 28.4 + - - +
171B ILE* 4.6 2.2 - - + -
212B PHE* 4.0 14.6 - - + -
213B CYS 5.3 0.2 - - - +
241B TYR* 3.8 34.8 - - + +
242B SER 3.7 15.3 - - - +
243B PHE* 3.7 29.4 - - + -
260B TYR* 3.9 33.0 - - + +
262B MSE 4.0 13.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B GLY 2.9 13.8 + - - -
136B LYS 3.8 2.5 - - - -
138B LEU* 1.3 75.2 - - - +
140B GLU* 1.3 61.3 + - - +
142B ALA* 3.2 3.1 + - - +
143B LEU* 3.1 27.9 + - - +
171B ILE* 4.4 7.8 - - - +
174B ILE* 3.6 17.7 - - - -
175B LEU* 5.0 1.6 - - - -
212B PHE* 4.1 17.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B LYS* 3.0 28.8 + - - +
137B LYS* 3.7 10.5 + - - +
139B GLY* 1.3 77.8 - - - +
141B LYS* 1.3 56.8 + - - +
143B LEU* 3.5 4.4 + - - +
144B GLU* 3.0 30.5 + - - +
174B ILE* 3.6 30.2 - - + +
178B LYS* 6.6 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B LYS 3.0 17.9 + - - +
138B LEU* 3.6 10.3 - - + +
139B GLY 3.3 0.2 - - - -
140B GLU* 1.3 76.2 - - - +
142B ALA* 1.3 58.6 + - - +
144B GLU* 3.2 24.4 + - - +
145B LEU* 2.9 49.3 + - + +
241B TYR* 4.3 1.3 - - + -
260B TYR* 3.5 58.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B LEU 2.9 17.3 + - - +
139B GLY 3.2 3.3 + - - +
141B LYS* 1.3 78.2 - - - +
143B LEU* 1.3 57.8 + - + +
146B THR* 2.8 35.8 + - - -
210B ILE* 4.2 6.7 - - + -
212B PHE* 3.5 30.7 - - + -
241B TYR* 3.4 28.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B GLY 3.1 15.6 + - - +
140B GLU* 4.1 4.0 - - - +
142B ALA* 1.3 77.2 - - - +
144B GLU* 1.3 57.7 + - - +
146B THR 4.0 4.0 - - - +
147B PRO* 3.2 31.7 - - + +
149B ALA* 4.5 14.8 - - + -
174B ILE* 3.8 20.2 - - + +
175B LEU* 4.2 13.2 - - + -
178B LYS* 3.3 42.6 - - + -
180B ILE* 3.5 30.7 - - + -
210B ILE* 4.7 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B GLU 3.0 19.3 + - - +
141B LYS* 3.5 33.0 + - - +
143B LEU* 1.3 80.2 - - - +
145B LEU* 1.3 72.8 + - - +
147B PRO* 3.5 14.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 145 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B LYS* 2.9 37.5 + - + +
144B GLU* 1.3 95.4 - - - +
146B THR* 1.3 66.9 + - + +
147B PRO* 3.5 4.2 - - - +
241B TYR* 3.5 27.8 - - + +
259B ASN* 4.2 17.9 + - + +
260B TYR* 4.3 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 146 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B ALA 2.8 19.8 + - - +
143B LEU* 3.6 5.7 - - - +
145B LEU* 1.3 87.2 - - - +
147B PRO* 1.3 59.2 - - - +
148B SER* 3.1 6.5 - - - -
149B ALA* 3.0 24.6 + - - +
209B ASN* 6.3 0.2 - - - -
210B ILE* 3.0 20.4 - - - +
239B GLN* 3.3 39.7 - - + +
241B TYR* 3.3 12.7 + - - +
259B ASN* 3.7 2.5 - - - +
----------------------------------------------------------
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