Contacts of the strand formed by residues 170 - 178 (chain B) in PDB entry 2QCT
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 ILE 170 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B GLU* 3.7 33.7 - - + +
164B LYS 3.3 9.6 - - - +
165B ARG* 2.9 52.3 - - + +
166B LYS 5.8 0.4 - - - +
169B TYR* 1.3 77.7 - - - +
171B ILE* 1.3 62.9 + - - +
172B ARG* 3.7 14.4 + - + +
187B GLN 3.6 2.3 - - - +
188B PHE* 3.7 1.0 - - - -
189B HIS* 3.0 37.5 + - + +
191B LYS* 4.2 26.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 171 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B GLU* 2.9 6.6 - - - -
164B LYS* 2.7 52.7 + - + +
166B LYS* 3.5 28.3 - - + +
169B TYR* 3.9 10.1 - - + -
170B ILE* 1.3 71.0 - - - +
172B ARG* 1.3 69.4 + - - +
173B THR* 4.5 4.1 - - + +
186B TYR* 4.8 3.6 - - + -
187B GLN 3.6 4.5 - - - +
188B PHE* 3.5 39.5 - - + +
211B ASP* 3.7 11.4 - - + +
215B TYR* 3.7 29.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 172 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B TRP* 3.4 31.4 - - - +
144B ALA 3.8 14.6 + - - -
145B GLU* 3.8 14.1 + - - +
160B CYS* 4.2 4.7 - - - -
162B ALA 4.5 0.7 - - - +
163B GLU* 3.1 35.3 + - + -
165B ARG* 5.2 2.4 - - - +
170B ILE* 4.2 19.7 - - + +
171B ILE* 1.3 74.4 - - - +
173B THR* 1.3 62.6 + - - +
174B LEU* 4.1 11.9 - - + -
186B TYR* 3.1 9.7 - - - +
187B GLN* 2.6 66.4 + - + +
189B HIS* 3.5 28.9 + - - +
191B LYS* 4.5 10.7 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
160B CYS* 3.6 4.7 - - - -
161B GLU* 3.3 33.8 + - - +
162B ALA* 3.1 31.3 + - + +
163B GLU* 4.9 0.7 - - - -
164B LYS* 5.8 2.2 - - + +
171B ILE* 4.5 8.1 - - + +
172B ARG* 1.3 80.3 - - - +
174B LEU* 1.3 62.2 + - - +
175B LYS* 4.8 3.2 + - - +
184B THR* 4.6 5.1 - - - +
185B ILE 3.4 5.2 - - - -
186B TYR* 3.4 32.8 - - + -
215B TYR* 6.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 174 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B TRP* 3.5 32.5 - - + -
125B ILE* 5.1 1.8 - - + -
142B TYR* 5.7 1.6 - - + -
143B TRP* 4.7 8.1 - - + -
144B ALA 4.5 13.5 - - - +
158B VAL* 4.5 4.9 - - + -
159B SER 3.3 4.9 - - - +
160B CYS* 4.3 15.0 - - + -
172B ARG* 4.1 20.0 - - + -
173B THR* 1.3 81.1 - - - +
175B LYS* 1.3 69.6 + - - +
176B VAL* 3.8 11.7 - - + -
184B THR* 3.1 27.9 - - - +
185B ILE* 2.7 32.4 + - + +
187B GLN* 4.6 13.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 175 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B GLN* 5.6 1.2 + - - +
157B SER 3.4 5.2 - - - +
159B SER* 2.7 51.5 + - - +
161B GLU* 3.8 43.2 + - + +
173B THR* 4.8 2.0 + - - +
174B LEU* 1.3 81.5 - - - +
176B VAL* 1.3 60.4 + - - +
177B LYS* 3.9 4.6 + - + +
182B THR* 4.6 18.4 - - + -
183B ARG 3.5 2.2 - - - -
184B THR* 2.6 35.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 176 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B TRP* 3.5 45.5 - - + -
117B ILE* 5.9 0.4 - - + -
118B TRP* 3.3 31.5 - - + -
156B PHE* 4.4 11.7 - - + -
157B SER 3.2 6.7 - - - +
158B VAL* 4.2 8.7 - - + -
174B LEU* 4.0 11.9 - - + -
175B LYS* 1.3 76.5 - - - +
177B LYS* 1.3 60.9 + - - +
182B THR* 3.8 0.8 - - - +
183B ARG 2.9 31.9 + - - +
185B ILE* 3.8 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 177 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B GLN* 5.0 14.0 - - - +
155B PRO 3.7 3.6 - - - +
156B PHE* 4.7 0.4 - - - -
157B SER* 2.7 52.4 + - - +
175B LYS* 3.9 5.1 + - + +
176B VAL* 1.3 71.0 - - - +
178B PHE* 1.3 60.5 + - - +
179B ASN 5.3 0.9 - - - +
180B SER* 4.5 14.8 - - - +
181B GLU 3.0 16.2 - - - +
182B THR* 2.4 35.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 178 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B LEU* 3.9 26.9 - - + -
76B ILE 5.5 0.9 - - - -
77B THR* 3.6 19.3 - - + -
118B TRP* 3.6 48.4 - + + -
155B PRO* 3.5 38.4 - - + -
156B PHE* 3.9 18.4 - + + -
177B LYS* 1.3 73.5 - - - +
179B ASN* 1.3 99.5 + - - +
180B SER 2.6 17.5 + - - -
181B GLU* 2.8 18.7 + - - +
----------------------------------------------------------
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