Contacts of the strand formed by residues 119 - 126 (chain A) in PDB entry 2QBX
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 PHE 119 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A TRP* 4.9 6.5 - + + -
98A MET* 4.1 11.4 - - - -
100A PHE* 3.8 37.5 - + + -
102A VAL* 5.4 1.6 - - + -
118A THR* 1.3 75.8 - - - +
120A ASN* 1.3 69.2 + - - +
121A LEU* 5.2 0.2 - - + -
148A THR 3.5 0.2 - - - -
149A ILE* 2.6 73.8 + - + +
186A PHE* 4.1 26.5 - + + -
187A GLN 3.4 18.2 - - - +
188A ASP* 4.8 0.4 - - - -
189A TYR* 3.7 8.1 - - - -
193A MET* 3.6 29.4 - - + -
195A LEU* 4.4 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A PHE* 1.3 78.3 - - - +
121A LEU* 1.3 59.8 - - - +
122A TYR* 3.2 23.5 + - + -
145A LYS* 3.0 26.4 + - - +
147A ASP 3.6 3.6 - - - +
148A THR* 2.6 31.0 + - - -
185A ALA 3.8 0.3 - - - +
186A PHE* 3.4 6.8 - - - -
187A GLN* 2.9 52.8 + - + +
189A TYR* 3.5 19.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A VAL* 4.5 13.0 - - + -
98A MET* 3.9 26.7 - - + -
119A PHE* 4.1 0.4 + - + -
120A ASN* 1.3 73.6 - - - +
122A TYR* 1.3 70.0 + - - +
145A LYS* 3.5 6.6 - - - +
146A VAL* 2.8 57.8 + - + -
147A ASP 3.1 15.4 + - - +
149A ILE* 4.3 10.8 - - + -
172A ARG* 4.4 5.4 - - + -
184A LEU* 4.4 12.1 - - + -
185A ALA 3.3 6.1 - - - +
186A PHE* 3.5 33.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A TRP* 3.6 24.6 - + - -
120A ASN* 3.2 27.5 + - + -
121A LEU* 1.3 75.8 - - - +
123A TYR* 1.3 63.1 + - - +
140A GLU* 3.8 26.9 + - + +
143A TRP* 3.8 32.3 - - + -
144A VAL 3.1 9.4 - - - +
145A LYS* 3.3 40.3 + - + +
146A VAL* 4.2 4.3 - - - +
184A LEU* 3.3 8.3 - - - +
185A ALA* 2.9 34.1 + - + +
187A GLN* 2.5 37.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A TYR* 1.3 73.5 - - - +
124A TYR* 1.3 66.1 + - - +
125A GLU* 4.0 32.2 + - + -
143A TRP* 3.4 5.1 - - - -
144A VAL* 2.8 78.5 + - + +
145A LYS 5.3 0.2 - - - -
146A VAL* 3.6 14.4 - - + -
174A PHE* 3.3 60.6 - + + +
175A GLY* 4.9 9.1 + - - -
176A PRO 5.4 3.1 + - - -
177A VAL* 5.4 0.9 - - + -
182A PHE* 5.0 2.5 - - + -
183A TYR 3.2 13.0 - - - +
184A LEU* 3.9 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A TYR* 1.3 79.1 - - - +
125A GLU* 1.3 77.7 + - - +
126A ALA* 4.0 11.2 - - + -
130A SER* 4.4 7.5 + - - -
135A PHE* 3.4 21.7 - + - -
136A PRO* 3.7 27.6 - - + -
142A PRO* 3.7 37.7 - - + -
143A TRP* 3.5 22.7 - - + -
144A VAL* 5.0 1.3 - - - -
182A PHE* 3.3 2.4 - - - -
183A TYR* 2.8 43.3 + + - -
404A SO4 5.5 0.6 + - - -
127B ASP* 4.3 6.9 + - - -
178B SER* 6.4 1.3 - - - -
179B ARG* 3.5 22.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A TYR* 4.0 22.8 + - + -
124A TYR* 1.3 84.3 - - - +
126A ALA* 1.3 66.1 + - - +
176A PRO 4.3 4.5 - - - +
177A VAL* 2.9 27.1 - - + +
178A SER* 2.9 31.8 + - - -
179A ARG* 3.2 17.8 + - + -
181A GLY 3.4 10.5 - - - +
182A PHE* 3.9 2.5 - - + -
405A SO4 4.1 17.5 + - - +
179B ARG* 3.0 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A PHE* 4.0 8.5 - - + -
124A TYR* 4.0 9.2 - - + -
125A GLU* 1.3 77.8 - - - +
127A ASP* 1.3 65.1 + - - +
128A PHE 3.3 19.7 - - - +
130A SER* 3.6 12.8 - - - +
179A ARG* 3.5 1.7 - - - +
180A SER* 3.1 15.2 + - - -
181A GLY 3.0 19.7 + - - +
183A TYR* 4.3 6.5 - - + -
127B ASP* 3.3 13.0 - - - +
179B ARG* 4.0 1.8 - - - +
----------------------------------------------------------
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