Contacts of the strand formed by residues 141 - 148 (chain A) in PDB entry 1V72
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 GLN 141 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A PRO* 6.3 0.2 - - + -
83A TRP* 2.9 29.6 + - + +
84A GLY* 3.2 5.5 - - - -
85A ASN* 2.6 35.7 + - - -
133A LYS 3.0 21.9 + - - -
134A VAL* 3.4 10.8 - - - +
135A GLY* 2.7 27.2 + - - +
136A ASP 3.1 13.1 + - - +
139A THR 3.0 21.9 + - - +
140A THR* 1.3 74.1 + - - +
142A PRO* 1.3 70.5 - - + +
143A ALA* 3.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ASN* 3.7 1.7 - - - +
87A TYR* 3.1 36.1 - - + +
129A ARG 4.5 0.2 - - - +
130A THR* 3.1 29.8 - - - +
132A GLU 4.2 15.5 - - - +
134A VAL* 4.3 12.6 - - + -
140A THR 4.4 0.2 - - - +
141A GLN* 1.3 98.4 - - + +
143A ALA* 1.3 58.4 + - - +
172A SER* 5.7 0.4 - - - -
174A LEU* 3.4 20.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A MET 3.6 5.7 - - - +
80A THR* 3.2 37.5 - - - +
81A PRO* 3.9 11.0 - - + -
85A ASN 3.1 17.9 + - - +
87A TYR* 4.2 0.6 - - - -
141A GLN 3.9 1.8 - - - +
142A PRO* 1.3 75.2 - - - +
144A CYS* 1.3 62.9 + - - +
173A SER 4.2 2.5 - - - +
174A LEU* 3.3 12.9 - - - +
175A GLY 3.1 16.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A LEU* 3.9 20.9 - - - -
79A MET* 3.7 26.2 - - + +
80A THR* 4.3 6.1 - - - -
85A ASN 3.1 3.5 + - - +
86A ILE* 3.5 30.1 - - - -
87A TYR* 3.0 29.9 + - - -
143A ALA* 1.3 79.7 - - - +
145A VAL* 1.3 66.2 + - - +
174A LEU* 4.1 3.0 - - - +
175A GLY 3.1 21.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ILE* 5.4 0.2 - - - -
87A TYR* 3.5 16.6 - - + +
121A LEU* 3.8 27.1 - - + -
126A LEU* 4.2 15.3 - - + -
130A THR* 4.5 0.4 - - + -
144A CYS* 1.3 82.6 - - - +
146A SER* 1.3 65.9 - - - +
147A ILE* 4.4 1.6 - - + -
165A ILE* 4.1 17.9 - - + -
168A VAL* 6.1 0.4 - - + -
169A CYS* 3.5 27.4 - - - -
174A LEU* 4.1 16.6 - - + -
175A GLY 2.7 8.1 + - - -
176A LEU* 3.5 3.0 - - + +
177A HIS* 2.8 28.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A LEU* 4.2 9.2 - - - -
86A ILE* 4.6 1.3 - - - -
87A TYR 2.8 18.9 + - - +
88A CYS* 3.8 12.3 - - - +
89A HIS 4.7 0.3 + - - -
92A SER* 5.9 0.9 - - - -
94A ILE* 3.9 29.4 - - - +
121A LEU* 3.9 6.4 - - - +
145A VAL* 1.3 76.1 - - - +
147A ILE* 1.3 68.9 + - - +
148A THR* 5.3 0.9 + - - -
177A HIS* 3.0 32.2 + - - -
179A ASP* 4.7 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LEU* 4.0 15.3 - - + -
145A VAL* 4.4 2.2 - - + -
146A SER* 1.3 81.3 + - - +
148A THR* 1.3 62.5 + - - +
149A GLN 3.6 0.5 + - - -
157A TYR* 4.0 22.4 - - + +
162A ILE* 4.1 33.0 - - + -
165A ILE* 3.7 36.8 - - + -
176A LEU* 4.3 14.4 - - + -
177A HIS 3.0 11.0 + - - +
178A MET* 3.3 21.3 - - + -
179A ASP 2.9 22.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A SER* 4.5 7.4 - - - -
119A ALA 5.8 1.1 - - - -
121A LEU* 5.6 0.4 - - - +
146A SER* 5.3 1.2 + - - -
147A ILE* 1.3 72.6 - - - +
149A GLN* 1.3 64.7 - - - +
150A ALA 3.1 20.6 - - - +
151A THR* 3.4 14.9 - - - +
152A GLU* 2.7 43.4 + - - +
157A TYR* 3.3 23.5 + - - -
179A ASP* 3.4 25.0 + - + +
181A SER 5.6 0.2 - - - +
513A PLP 3.6 15.3 - - + -
----------------------------------------------------------
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