Contacts of the strand formed by residues 164 - 177 (chain B) in PDB entry 3IML
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 164 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B GLN* 3.3 39.5 - - + +
155B LEU* 4.2 2.7 - - + -
156B ARG* 3.7 26.1 - - + +
161B LEU* 3.2 42.3 + - + +
162B PRO 3.7 7.6 - - - +
163B TRP* 1.3 107.4 - - + +
165B ARG* 1.3 62.2 - - - +
191B THR* 3.4 31.4 - - + +
192B GLN 4.0 1.8 - - - +
206B VAL* 4.9 5.2 - - + -
210B VAL* 5.4 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 165 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B GLN* 3.7 12.6 + - - -
156B ARG* 3.4 12.4 + - - +
163B TRP 4.1 0.2 - - - +
164B LEU* 1.3 78.4 - - - +
166B PRO* 1.4 79.9 - - + +
167B ASP 3.5 3.0 + - - +
192B GLN* 3.2 39.9 + - + +
193B HIS 3.5 20.0 + - - -
194B ALA* 3.8 17.9 - - + +
195B PRO* 3.9 14.8 - - - +
235B VAL* 3.0 37.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 166 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B SER* 2.6 28.9 + - - -
15B GLY* 3.7 9.5 + - - -
77B ILE 3.7 22.7 - - - +
78B GLY* 3.8 21.1 - - - +
79B TYR* 3.5 32.8 - - + +
152B GLN* 4.0 5.9 - - - +
156B ARG* 3.6 18.6 + - - +
165B ARG* 1.4 92.8 - - + +
167B ASP* 1.3 52.6 + - - +
168B ALA 3.5 0.2 + - - -
192B GLN* 3.7 6.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 167 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B SER* 3.6 2.9 - - - -
15B GLY 3.9 8.5 - - - -
16B HIS* 3.4 24.1 - - - +
17B PRO* 3.6 9.7 - - - +
79B TYR* 3.4 13.0 - - - +
165B ARG 4.0 0.2 - - - +
166B PRO* 1.3 76.7 - - - +
168B ALA* 1.3 72.2 + - - +
169B LYS* 5.8 0.3 - - - +
191B THR* 4.0 1.6 + - - -
192B GLN* 2.8 41.7 + - - +
234B PHE* 3.7 24.0 - - + -
237B GLY* 3.8 1.3 - - - -
238B GLY 3.0 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 168 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B VAL* 3.3 6.9 - - - +
13B SER* 2.9 36.9 + - - -
16B HIS* 5.1 0.3 - - - -
149B VAL* 4.1 5.8 - - + -
152B GLN* 3.7 37.2 - - + +
167B ASP* 1.3 85.4 + - - +
169B LYS* 1.3 62.8 + - - +
189B LEU* 5.0 2.5 - - + -
190B SER 3.3 12.8 - - - +
191B THR* 4.1 3.4 - - - -
234B PHE* 5.0 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 169 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ASP* 3.1 36.3 + - - +
123A GLN* 3.6 33.6 + - - +
306A ILE* 5.8 4.5 - - + -
10B GLU* 4.8 8.7 - - - -
11B SER 3.6 10.5 - - - +
12B VAL* 4.1 16.4 - - + -
16B HIS* 4.4 18.0 + - + -
149B VAL* 4.1 2.9 - - - -
167B ASP* 5.8 0.4 - - - +
168B ALA* 1.3 75.5 - - - +
170B SER* 1.3 60.8 + - - +
188B VAL* 3.9 0.5 - - - +
189B LEU* 3.3 6.2 - - - +
190B SER* 2.8 43.5 + - - +
234B PHE* 6.0 2.0 - - + -
249B LYS* 5.6 4.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 170 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A GLN* 3.2 12.4 + - - -
10B GLU* 3.3 1.1 - - - -
11B SER* 3.0 33.1 + - - +
145B SER* 2.7 36.5 + - - -
148B LEU* 4.0 21.5 - - - -
149B VAL* 3.8 10.6 - - - +
169B LYS* 1.3 76.2 - - - +
171B GLN* 1.3 60.4 + - - +
188B VAL 3.3 7.9 - - - -
189B LEU* 4.5 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 171 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A GLN* 3.5 26.7 - - - +
124A GLY* 3.8 20.2 + - - +
303A SER* 4.9 1.6 - - - -
304A TYR 3.1 28.6 + - - +
305A ALA* 4.4 7.6 - - - +
312A THR* 5.0 3.2 + - - -
8B THR* 3.4 34.1 - - + +
9B SER 3.3 8.7 - - - +
10B GLU* 4.5 2.2 + - + -
170B SER* 1.3 74.6 - - - +
172B VAL* 1.3 62.8 + - - +
173B THR* 4.2 6.9 + - - -
186B THR* 3.9 1.8 - - - +
187B VAL* 3.4 4.7 - - - +
188B VAL* 2.7 59.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 172 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B PHE 3.8 1.4 - - - +
8B THR* 3.4 2.3 - - - -
9B SER 3.0 30.8 + - - -
141B PRO* 4.1 8.7 - - - +
144B LEU* 4.2 17.3 - - + -
145B SER* 3.4 27.1 - - - +
148B LEU* 3.4 33.0 - - + -
171B GLN* 1.3 75.7 - - - +
173B THR* 1.3 62.3 + - - +
174B VAL* 4.0 20.3 + - + -
184B ILE* 4.1 19.1 - - + -
186B THR 3.7 2.2 - - - +
187B VAL* 4.2 4.5 - - + +
215B LEU* 5.2 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 173 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A THR* 4.3 14.9 - - + +
6B LEU* 3.8 27.8 - - + -
7B PHE 3.3 4.5 - - - +
8B THR* 2.8 27.3 + - - +
171B GLN* 4.5 7.4 + - - -
172B VAL* 1.3 72.4 - - - +
174B VAL* 1.3 61.4 + - - +
184B ILE* 3.7 4.7 - - - +
185B ASP* 2.9 39.0 + - + +
186B THR* 2.8 32.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 174 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B LEU* 3.5 3.6 - - - -
7B PHE 2.7 35.5 + - - +
140B LEU* 4.3 15.7 - - + -
141B PRO* 4.0 21.8 - - + -
144B LEU* 4.7 1.6 - - + -
172B VAL* 4.0 18.6 - - + -
173B THR* 1.3 76.5 - - - +
175B ARG* 1.3 72.4 + - - +
176B TYR* 3.5 26.0 - - + -
181B PRO* 4.0 17.3 - - + -
183B SER 3.4 13.2 - - - +
184B ILE* 4.6 9.6 - - + -
219B LEU* 5.5 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 175 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B TYR 3.4 8.9 - - - +
6B LEU* 3.8 23.4 - - + +
173B THR 4.2 1.2 + - - -
174B VAL* 1.3 71.1 - - - +
176B TYR* 1.3 66.9 + - - +
177B VAL* 4.1 19.2 - - + +
181B PRO* 3.6 3.8 - - - +
182B HIS* 2.8 44.2 + - + -
183B SER* 2.9 32.9 + - - +
185B ASP* 4.6 4.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 176 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B TYR* 2.7 79.0 + + + +
7B PHE* 4.0 16.4 - + + -
133B GLU* 2.8 41.9 + - - -
139B PRO* 5.2 0.7 - - - +
140B LEU* 4.3 0.7 - - - +
141B PRO* 3.3 19.8 - - + +
174B VAL* 3.5 30.7 - - + -
175B ARG* 1.3 73.8 - - - +
177B VAL* 1.3 67.4 + - - +
179B GLY 4.0 4.9 - - - -
180B LYS* 3.4 28.0 - - - +
181B PRO* 3.9 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 177 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B ARG* 4.1 23.8 + - - +
176B TYR* 1.3 80.5 - - - +
178B ASP* 1.3 78.5 + - + +
179B GLY 3.1 0.9 - - - -
180B LYS* 2.9 21.1 + - - +
182B HIS* 3.7 35.6 - - + +
----------------------------------------------------------
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