Contacts of the strand formed by residues 136 - 144 (chain B) in PDB entry 1QA7
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 LYS 136 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B LEU* 4.4 2.2 - - - -
134B PRO 3.9 1.7 + - - +
135B LEU* 1.3 75.9 - - - +
137B MET* 1.3 58.7 + - - +
138B GLU* 3.5 28.9 + - - +
161B TRP* 3.0 11.7 - - - +
162B ARG* 2.7 59.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B LYS* 5.1 9.4 - - - +
109B VAL* 4.1 13.2 - - + -
113B LEU* 3.5 22.2 - - + +
136B LYS* 1.3 71.8 - - - +
138B GLU* 1.3 74.7 + - - +
139B GLU 4.3 0.5 + - - -
159B GLN* 4.1 21.8 - - + +
160B ALA 3.5 24.2 - - - +
161B TRP* 3.9 28.0 - - + -
203B LEU* 4.2 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B LYS* 3.5 35.4 + - + +
137B MET* 1.3 88.0 - - - +
139B GLU* 1.3 62.3 + - - +
140B LYS 3.0 21.1 - - - +
141B ALA* 3.8 8.1 + - - +
142B THR* 4.4 4.0 + - - -
159B GLN* 3.0 7.0 + - - -
160B ALA 2.9 33.6 + - - +
162B ARG* 3.5 30.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B MET 4.3 0.4 + - - -
138B GLU* 1.3 73.8 - - - +
140B LYS* 1.3 81.6 + - + +
158B ASP* 3.1 13.0 - - - +
159B GLN* 3.0 39.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B GLU* 3.8 10.8 - - - +
139B GLU* 1.3 104.1 - - + +
141B ALA* 1.3 63.6 + - - +
142B THR* 3.3 10.2 + - - -
156B THR* 4.3 23.6 + - + +
157B VAL 3.5 6.5 - - - -
158B ASP* 2.6 36.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B GLU* 3.8 13.5 - - + +
139B GLU 4.2 0.2 - - - -
140B LYS* 1.3 69.8 - - - +
142B THR* 1.3 58.0 + - - +
143B TYR* 3.9 4.4 + - - -
156B THR* 2.8 10.2 - - - -
157B VAL* 2.7 40.5 + - - +
160B ALA* 3.9 29.8 - - + +
162B ARG* 4.2 14.6 - - + +
200B VAL* 4.3 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B GLU* 4.4 4.4 + - - -
140B LYS 3.3 8.0 + - - -
141B ALA* 1.3 72.7 - - - +
143B TYR* 1.3 65.2 + - - +
154B ASP* 4.5 19.7 - - + +
155B LEU 3.1 15.5 - - - +
156B THR* 3.8 14.5 - - + +
162B ARG* 2.8 44.6 + - - +
198B ILE* 4.1 0.9 - - - +
200B VAL* 4.7 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B ALA 4.0 6.7 - - - -
142B THR* 1.3 79.7 - - - +
144B VAL* 1.3 71.4 + - - +
145B HIS* 3.7 25.6 + + - -
154B ASP* 3.8 2.8 - - - -
155B LEU* 2.6 78.3 + - + +
156B THR 3.9 2.1 + - - -
157B VAL* 3.8 15.9 - - + +
162B ARG* 4.8 2.5 - - - +
193B ALA* 3.7 28.0 - - + +
194B GLY* 3.7 22.4 - - - -
198B ILE* 4.4 11.9 - - + -
200B VAL* 4.1 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B TYR* 1.3 85.7 - - - +
145B HIS* 1.3 76.2 + - - +
146B LYS* 4.9 2.4 - - - +
152B THR* 4.1 17.9 - - + +
153B VAL 3.7 7.0 - - - +
154B ASP* 4.8 11.7 - - - +
194B GLY 3.8 2.4 - - - +
195B GLY* 3.7 16.5 + - - +
196B ASN* 2.8 50.9 - - + +
198B ILE* 5.9 2.2 - - + -
----------------------------------------------------------
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