Contacts of the strand formed by residues 140 - 148 (chain A) in PDB entry 3AA6
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 140 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A PRO* 3.6 31.6 - - + -
72A ASP* 3.7 30.1 - - - +
73A GLN* 3.5 41.7 - - + +
74A VAL* 6.0 0.2 - - - -
75A LEU* 3.9 19.6 - - + +
132A VAL* 3.8 4.2 - - - +
133A LYS* 3.8 6.1 - - - +
138A ASN* 3.6 26.5 - - + -
139A GLY* 1.3 77.5 - - - -
141A CYS* 1.3 62.5 + - - +
158A ILE* 3.4 3.6 - - - +
159A GLU* 2.8 37.7 + - - +
161A HIS* 5.4 5.6 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ASP* 5.1 2.2 + - - -
73A GLN 4.7 5.4 - - - +
75A LEU* 4.2 2.2 - - - -
91A ARG* 3.1 42.0 + - - +
125A ASP* 4.6 2.2 - - - -
128A LEU* 3.8 20.2 - - + -
129A ARG* 3.8 29.8 - - - -
132A VAL* 3.8 18.2 - - + -
133A LYS* 6.5 0.4 - - - -
140A PHE* 1.3 78.4 - - - +
142A THR* 1.3 67.4 + - - +
157A CYS 3.1 13.9 - - - +
158A ILE* 4.3 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A VAL* 3.7 10.8 - - + +
75A LEU* 3.0 38.7 + - - +
90A PRO* 3.5 25.6 - - + -
91A ARG* 4.9 3.1 - - + +
125A ASP* 4.9 0.2 - - - -
141A CYS* 1.3 78.3 + - - +
143A VAL* 1.3 64.6 + - - +
144A TYR* 3.4 33.5 - - + +
155A ILE 3.7 1.4 - - - +
156A ALA* 3.7 0.9 - - - -
157A CYS* 2.9 33.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A PRO* 3.2 10.5 - - - +
91A ARG* 6.3 0.2 - - - +
121A ARG* 2.9 53.1 + - + +
124A CYS* 4.2 6.5 - - + +
125A ASP* 3.5 30.8 + - + +
128A LEU* 3.4 33.4 - - + -
142A THR* 1.3 75.6 - - - +
144A TYR* 1.3 65.3 + - - +
154A ILE* 3.7 29.2 - - + -
155A ILE 3.3 6.1 - - - +
156A ALA* 4.3 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LEU 3.5 19.8 + - - -
77A THR* 2.7 30.6 + - - +
79A HIS* 3.6 26.5 - + + -
80A GLY* 3.6 24.7 + - - -
88A LEU* 4.2 14.6 + - + -
90A PRO* 3.8 21.1 - - + -
121A ARG* 3.9 3.8 - - - -
142A THR* 3.4 24.7 - - + +
143A VAL* 1.3 76.7 - - - +
145A GLY* 1.3 58.9 + - - +
146A LYS* 4.1 18.8 - - + -
153A THR 3.8 0.2 - - - +
154A ILE* 3.5 6.2 - - - +
155A ILE* 2.8 47.6 + - + +
157A CYS* 4.0 15.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A PRO* 5.7 0.2 - - - +
113A THR* 4.2 9.3 - - - +
114A GLU* 3.4 21.0 - - - +
117A LEU* 3.5 18.3 - - - +
121A ARG* 3.8 12.5 - - - +
144A TYR* 1.3 74.0 - - - +
146A LYS* 1.3 63.6 + - - +
153A THR 3.5 7.0 - - - -
154A ILE* 4.1 9.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A HIS* 3.0 49.4 + - - +
88A LEU* 6.2 0.8 - - - +
113A THR* 5.8 3.4 - - + -
114A GLU* 3.4 13.7 - - - +
117A LEU* 3.7 3.4 - - - -
144A TYR* 4.1 9.4 - - + -
145A GLY* 1.3 81.6 - - - +
147A SER* 1.3 60.5 + - - +
148A ILE* 4.2 15.3 - - + -
153A THR* 2.8 40.7 + - - +
155A ILE* 4.1 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A GLU* 3.1 16.8 + - - +
146A LYS* 1.3 73.5 - - - +
148A ILE* 1.3 63.0 + - - +
149A ASP 4.1 0.9 + - - -
150A GLY* 3.6 25.1 + - - -
151A GLN 3.5 6.1 - - - -
152A GLN* 3.6 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A LYS* 4.0 18.2 - - + +
147A SER* 1.3 76.9 + - - +
149A ASP* 1.3 76.8 + - - +
150A GLY 3.1 0.4 - - - -
151A GLN* 2.8 37.6 + - - +
153A THR* 3.8 26.5 - - + +
155A ILE* 4.0 26.2 - - + -
178A LYS* 6.1 2.7 - - + +
----------------------------------------------------------
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