Contacts of the strand formed by residues 162 - 172 (chain B) in PDB entry 3LBF
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 162 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B PRO* 4.2 1.9 - - - +
142B PHE 3.7 7.9 - - - +
145B ILE* 3.5 31.8 - - + +
158B LEU 3.9 5.2 - - - +
159B MET* 3.1 19.3 + - - +
160B THR 3.9 0.7 - - - +
161B GLN* 1.3 78.9 - - - +
163B ASP* 1.3 63.7 + - - +
166B GLY 3.8 15.0 - - - +
167B ILE 3.8 23.1 - - - +
168B LEU* 3.8 20.6 - - + +
182B VAL* 4.1 13.7 - - + +
184B ARG* 2.6 34.8 + - + -
189B PHE* 4.1 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 163 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B PRO* 3.6 26.7 - - + +
142B PHE* 2.9 13.9 + - - +
143B ASP* 2.7 48.8 + - - +
161B GLN 3.6 2.0 + - - -
162B LEU* 1.3 78.4 - - - +
164B GLU* 1.3 78.2 + - - +
165B GLY 3.3 0.7 + - - -
166B GLY* 2.9 17.0 + - - -
184B ARG* 3.6 7.8 - - - -
195C GLU* 5.0 4.5 - - + +
196C ALA* 4.6 15.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 164 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B ASP* 1.3 85.4 - - - +
165B GLY* 1.3 68.6 + - - +
184B ARG* 3.5 7.3 - - - +
185B ARG* 3.5 6.4 - - - -
186B GLY* 2.5 47.7 + - - +
16C GLN* 6.3 0.9 - - - +
60C GLN* 5.4 3.6 - - - +
63C MET* 6.2 2.0 - - + -
195C GLU* 5.2 9.0 + - - +
196C ALA* 4.1 29.2 + - - +
197C VAL* 6.0 2.5 - - - -
198C ARG* 6.4 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 165 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B ASP 4.7 1.0 - - - +
163B ASP* 3.3 0.4 + - - -
164B GLU* 1.3 79.6 - - - +
166B GLY* 1.3 63.9 + - - +
167B ILE* 3.8 10.9 + - - +
183B ARG* 5.7 1.7 + - - +
184B ARG 3.1 21.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 166 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B PHE 4.4 0.2 - - - -
143B ASP* 3.3 15.7 - - - -
162B LEU* 3.8 12.4 - - - +
163B ASP* 2.9 23.3 + - - -
164B GLU 3.1 1.4 + - - -
165B GLY* 1.3 82.4 - - - +
167B ILE* 1.3 59.8 + - - +
182B VAL 3.9 0.3 - - - +
183B ARG* 3.5 3.1 - - - -
184B ARG* 2.9 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 167 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B LEU 3.7 15.3 - - - +
71B LEU* 3.7 23.0 - - - +
72B GLU* 3.6 36.8 - - + +
143B ASP 3.2 8.0 + - - +
144B ALA* 3.2 5.2 - - - +
145B ILE 2.9 25.6 + - - +
162B LEU* 3.8 4.4 - - - +
165B GLY 4.0 9.4 - - - +
166B GLY* 1.3 78.8 - - - +
168B LEU* 1.3 65.0 + - - +
169B VAL* 3.9 8.5 - - + -
181B ARG* 3.9 23.1 - - + -
182B VAL 3.3 4.0 - - - +
183B ARG* 3.7 23.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 168 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B ILE* 3.3 32.3 - - + +
147B VAL* 3.9 17.7 - - + -
154B ILE* 3.8 28.3 - - + -
158B LEU* 3.8 25.4 - - + +
159B MET* 4.2 3.6 - - + -
162B LEU* 3.8 16.3 - - + +
167B ILE* 1.3 73.3 - - - +
169B VAL* 1.3 71.1 + - - +
170B LEU* 3.9 13.5 - - + -
180B LYS 3.8 0.5 - - - +
181B ARG* 3.3 3.1 - - - -
182B VAL* 2.6 52.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 169 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B MET* 4.1 21.3 - - + -
70B LEU* 3.7 28.5 - - + -
71B LEU* 3.4 29.2 - - + -
145B ILE 2.9 7.5 + - - +
146B ILE* 3.4 4.2 - - + +
147B VAL* 3.0 26.3 + - - +
167B ILE* 3.9 9.2 - - + -
168B LEU* 1.3 78.8 - - - +
170B LEU* 1.3 65.5 + - - +
179B LEU* 3.7 25.1 - - + -
180B LYS 3.4 7.2 - - - +
181B ARG* 4.7 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 170 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B VAL* 3.4 29.2 - - + -
151B PRO* 4.0 14.1 - - + -
154B ILE* 4.3 12.8 - - + -
155B PRO* 3.8 29.8 - - + -
158B LEU* 4.7 0.2 - - + -
168B LEU* 3.9 20.9 - - + -
169B VAL* 1.3 80.2 - - - +
171B PRO* 1.3 66.4 - - + +
172B VAL* 3.7 18.8 - - + -
179B LEU* 3.7 6.3 - - - -
180B LYS* 2.8 43.6 + - + +
182B VAL* 4.6 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 171 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B MET* 4.2 6.1 - - + -
147B VAL 3.1 19.3 - - - +
149B ALA 3.6 24.7 - - - +
150B ALA* 3.4 8.5 - - + -
151B PRO* 3.2 22.2 - - - +
170B LEU* 1.3 86.4 - - + +
172B VAL* 1.3 62.2 + - - +
177B GLN* 4.2 0.9 - - - +
178B TYR 3.5 6.7 - - - +
179B LEU* 3.9 4.5 - - + -
197B VAL* 3.8 11.9 - - + -
199B PHE* 3.5 37.7 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
156A THR* 4.1 11.4 - - + +
150B ALA* 4.5 0.2 - - - +
151B PRO 3.4 7.2 - - - +
152B PRO 3.7 20.0 - - - +
153B GLU* 4.0 10.1 - - - -
154B ILE* 3.9 16.8 - - + +
170B LEU* 3.7 20.4 - - + -
171B PRO* 1.3 80.3 - - - +
173B GLY* 1.3 63.5 + - - +
176B HIS 3.9 1.7 - - - +
177B GLN* 3.1 5.0 - - - +
178B TYR* 2.9 33.1 + - - +
180B LYS* 3.6 36.2 + - + -
----------------------------------------------------------
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