Contacts of the strand formed by residues 162 - 172 (chain A) in PDB entry 1QQG
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 GLU 162 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ASN* 3.7 7.9 - - - +
75A ARG* 2.7 33.1 + - - -
160A PHE* 3.7 0.9 - - - +
161A LYS* 1.3 96.5 - - + +
163A VAL* 1.3 69.6 + - - +
164A TRP* 3.2 32.7 - - + -
187A LEU* 2.8 37.6 + - + +
248A ASN* 5.7 0.2 + - - -
252A THR* 3.8 19.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A PHE* 3.8 13.5 - - + -
71A ASN* 3.2 36.1 - - + +
73A ASN* 2.9 5.7 - - - +
75A ARG* 2.7 23.7 + - - +
87A TYR* 3.1 34.8 + - + -
160A PHE* 3.8 15.7 - - + -
162A GLU* 1.3 79.3 - - - +
164A TRP* 1.3 59.0 + - - +
184A ARG* 3.5 30.5 - - + -
185A LEU 3.3 5.8 - - - +
186A CYS* 4.3 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ARG* 3.5 32.1 - - - +
87A TYR* 4.2 2.9 - - - -
162A GLU* 3.2 35.7 - - + -
163A VAL* 1.3 75.1 - - - +
165A GLN* 1.3 60.3 + - - +
166A VAL* 4.3 3.6 - - + -
184A ARG* 3.4 3.8 - - - -
185A LEU* 2.6 57.3 + - + +
187A LEU* 3.9 19.5 - - + -
240A VAL* 5.9 0.2 - - + -
245A VAL* 4.2 14.4 - - + +
248A ASN* 4.1 9.6 - - - +
249A MET* 3.6 54.2 - - + +
252A THR* 3.6 36.6 - - + -
253A ILE* 4.2 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A TYR* 4.0 15.2 + - + +
91A GLU* 4.6 0.5 - - - +
92A HIS* 3.4 27.1 + - + +
164A TRP* 1.3 73.9 - - - +
166A VAL* 1.3 66.5 + - - +
182A ILE* 3.7 24.2 - - + +
183A TYR 3.4 11.9 - - - +
184A ARG* 2.7 42.5 + - - +
197A LEU* 3.8 8.4 - - - +
240A VAL* 4.8 5.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A TRP* 4.2 9.4 - - + +
165A GLN* 1.3 81.3 - - - +
167A ILE* 1.3 64.7 + - - +
168A LEU* 4.6 2.7 - - + +
182A ILE* 3.4 9.5 - - - +
183A TYR* 2.9 47.0 + - + +
185A LEU* 4.5 6.3 - - + +
194A PHE* 4.5 7.6 - - + -
238A MET* 3.8 31.2 - - + -
239A GLN 3.8 6.3 - - - +
240A VAL* 3.7 23.8 - - + -
249A MET* 3.9 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A VAL* 1.3 75.5 - - - +
168A LEU* 1.3 65.0 + - - +
169A LYS* 3.0 29.1 + - + +
181A GLY* 3.9 8.7 - - - -
182A ILE* 3.8 21.3 - - + -
238A MET* 4.1 1.3 - - - -
239A GLN* 2.9 61.6 + - + +
240A VAL* 5.7 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A VAL* 3.7 2.5 - - + -
167A ILE* 1.3 72.9 - - - +
169A LYS* 1.3 64.9 + - - +
174A GLY* 5.8 0.4 - - - -
179A LEU* 3.6 28.5 - - + +
180A ILE* 3.3 5.5 - - - +
181A GLY* 2.9 40.8 + - - +
183A TYR* 3.4 41.3 - - + -
194A PHE* 3.8 29.8 - - + -
236A PHE* 4.3 22.7 - - + -
237A TRP 3.7 14.8 - - - +
238A MET* 4.0 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ILE* 3.0 27.9 + - + +
168A LEU* 1.3 77.0 - - - +
170A PRO* 1.4 73.1 - - + +
171A LYS* 3.1 38.0 + - + +
174A GLY* 3.6 17.0 - - - -
179A LEU 3.9 1.4 - - - +
180A ILE* 4.5 0.7 - - - -
220A PHE* 4.5 8.1 - - + -
237A TRP* 2.8 25.5 + - + +
238A MET* 4.9 0.2 - - - -
239A GLN* 3.9 34.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A LYS* 1.4 99.1 - - + +
171A LYS* 1.3 61.4 + - + +
172A GLY 4.0 0.2 + - - -
175A GLN* 3.3 30.9 - - - +
180A ILE* 3.6 39.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A LYS* 3.1 28.8 - - + +
170A PRO* 1.3 82.1 - - + +
172A GLY* 1.3 66.1 + - - +
173A LEU 3.3 0.5 + - - -
174A GLY* 2.9 13.9 + - - -
220A PHE* 3.8 31.0 - - - -
235A GLU 3.8 5.6 - - - +
237A TRP* 3.7 48.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A PRO 4.0 0.6 + - - -
171A LYS* 1.3 71.3 - - - +
173A LEU* 1.3 60.3 + - - -
174A GLY 3.0 4.7 + - - -
175A GLN* 3.4 11.8 + - - +
176A THR* 3.5 15.6 + - - -
235A GLU* 3.7 14.8 - - - -
237A TRP* 4.9 1.1 - - - -
----------------------------------------------------------
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