Contacts of the strand formed by residues 160 - 170 (chain A) in PDB entry 1QYO
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 GLY 160 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A PHE* 3.8 12.1 - - - -
154A ALA* 4.0 0.2 - - - -
155A ASP* 2.9 30.6 + - - +
158A LYS* 3.2 4.8 - - - -
159A ASN* 1.3 80.5 - - - +
161A ILE* 1.3 66.8 + - - +
185A ASN 3.3 14.8 - - - -
187A PRO* 4.3 0.7 - - - -
195A LEU* 3.5 10.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A PHE* 3.8 18.4 - - + -
84A PHE* 3.6 38.4 - - + -
152A ILE* 3.9 18.6 - - + -
153A THR 3.5 11.2 - - - +
154A ALA* 4.6 0.2 - - - -
155A ASP* 4.1 6.2 - - - +
160A GLY* 1.3 79.2 - - - +
162A LYS* 1.3 68.6 + - - +
163A ALA* 5.4 0.7 - - + -
183A GLN* 4.8 2.2 - - - +
184A GLN* 3.6 3.3 - - - +
185A ASN* 3.0 50.7 + - + +
196A PRO* 3.6 35.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A ILE* 3.4 5.9 - - - +
153A THR* 2.9 46.1 + - - +
154A ALA 5.2 3.1 - - - +
155A ASP* 3.6 33.8 + - + +
157A GLN* 5.7 2.2 + - - -
161A ILE* 1.3 80.3 - - - +
163A ALA* 1.3 60.4 + - - +
164A ASN* 5.1 2.2 - - - +
182A TYR* 3.4 30.6 + - + +
183A GLN* 3.3 12.6 - - - +
184A GLN* 4.0 14.4 - - + +
185A ASN* 5.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A VAL* 3.9 17.5 - - + -
151A TYR 3.2 10.8 - - - +
152A ILE* 4.3 7.0 - - + -
153A THR* 5.2 0.2 - - - -
161A ILE* 5.4 2.0 - - + -
162A LYS* 1.3 76.8 - - - +
164A ASN* 1.3 69.6 + - - +
165A PHE* 4.6 2.2 - - + -
181A HIS 4.0 0.4 - - - +
182A TYR* 3.6 1.7 - - - -
183A GLN* 2.8 66.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A TYR* 3.0 37.0 + - + +
153A THR* 5.1 4.9 + - - +
162A LYS* 5.1 2.1 - - - +
163A ALA* 1.3 79.9 + - - +
165A PHE* 1.3 64.5 + - - +
181A HIS 3.5 7.4 + - - -
182A TYR* 3.3 32.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A THR* 3.9 17.7 - - + -
69A GLN* 5.0 0.4 - - - -
96A ARG* 3.7 27.1 - - - -
148A HIS* 3.7 26.0 - + + -
149A ASN 3.2 22.7 - - - +
150A VAL* 3.7 25.8 - - + -
151A TYR* 4.9 3.4 - - - -
164A ASN* 1.3 82.8 - - - +
166A LYS* 1.3 63.8 + - - +
167A ILE* 4.0 7.4 - - + -
180A ASP* 3.8 1.9 - - - +
181A HIS* 2.8 70.6 + + + +
183A GLN* 3.4 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A HIS* 3.9 18.9 - - - +
149A ASN 5.0 0.4 + - - -
165A PHE* 1.3 77.2 - - - +
167A ILE* 1.3 62.5 + - - +
168A ARG* 4.1 9.0 + - + +
178A LEU* 3.9 25.0 - - + +
179A ALA 3.9 3.4 - - - -
180A ASP* 2.8 36.5 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
62A THR* 3.9 3.8 - - + -
145A TYR* 3.5 23.1 - - + +
146A ASN 5.4 1.3 - - - +
148A HIS* 3.4 50.3 - - + +
165A PHE* 4.0 4.5 - - + -
166A LYS* 1.3 74.0 - - - +
168A ARG* 1.3 64.3 - - - +
169A HIS* 3.5 35.4 - - + +
177A GLN 3.7 1.0 - - - +
178A LEU* 3.6 6.3 - - - +
179A ALA* 2.8 40.9 + - + +
181A HIS* 3.4 28.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A TYR* 5.6 1.6 - - - -
146A ASN* 2.9 46.2 + - + +
166A LYS* 4.1 7.8 + - + +
167A ILE* 1.3 80.9 - - - +
169A HIS* 1.3 61.3 + - - +
170A ASN* 5.0 0.2 - - - -
176A VAL* 3.8 38.4 - - + +
177A GLN 3.9 3.4 - - - -
178A LEU* 4.7 17.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A PRO* 3.2 42.9 - - + +
59A THR* 3.9 11.4 + - - -
100A PHE* 3.9 25.1 - + - -
141A LEU* 4.0 28.7 - - + -
144A ASN 5.4 1.2 + - - -
145A TYR* 3.9 10.8 - + - -
167A ILE* 3.5 23.7 - - + +
168A ARG* 1.3 71.4 + - - +
170A ASN* 1.3 63.7 + - - +
171A ILE 3.4 0.5 + - - -
176A VAL* 3.5 2.8 - - - -
177A GLN* 2.8 45.9 + - + +
179A ALA* 3.9 14.9 - - + +
181A HIS* 5.6 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A LEU* 3.6 5.0 - - - +
142A GLU* 2.9 40.0 + - - +
144A ASN* 3.3 35.5 + - - +
145A TYR 5.5 0.6 - - - +
146A ASN* 3.0 34.0 + - - +
168A ARG 3.8 0.6 + - - -
169A HIS* 1.3 71.6 - - - +
171A ILE* 1.3 61.7 + - - +
175A SER 3.8 5.6 - - - +
176A VAL* 4.4 11.8 - - - +
----------------------------------------------------------
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