Contacts of the strand formed by residues 140 - 149 (chain A) in PDB entry 4O65
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 GLU 140 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ARG* 3.2 36.8 + - + +
96A LEU 3.2 4.5 - - - +
97A VAL* 3.8 24.7 - - + +
135A ILE* 5.5 0.2 - - - -
136A PRO* 4.8 6.0 - - - +
138A GLY 4.2 5.4 - - - +
139A GLY* 1.3 88.0 - - - +
141A VAL* 1.3 67.2 + - - +
142A PRO* 4.0 8.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ARG* 4.4 1.8 - - - -
96A LEU* 2.7 50.7 + - + +
128A PRO* 3.5 34.5 - - + -
133A PHE* 4.2 9.0 - - + -
134A THR 3.8 11.7 - - - +
135A ILE* 4.0 11.0 - - + -
136A PRO* 3.6 26.0 - - + -
140A GLU* 1.3 79.9 - - - +
142A PRO* 1.4 72.4 - - + +
143A TYR 3.6 0.3 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
94A GLY 3.5 10.3 - - - +
95A ARG* 4.2 10.5 - - + -
127A ASP* 4.1 9.3 - - - +
128A PRO* 3.8 6.9 - - - +
140A GLU* 4.0 8.3 - - + +
141A VAL* 1.4 100.4 - - + +
143A TYR* 1.3 60.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ILE* 3.5 14.0 - - + +
47A GLU* 3.7 12.1 - - - +
92A VAL* 4.0 9.4 - - + -
93A THR* 3.4 12.5 + - - -
94A GLY* 2.9 70.4 + - - +
95A ARG 3.5 4.7 - - - -
96A LEU* 3.7 32.1 - - + -
108A ILE* 3.6 21.8 - - + -
127A ASP* 3.1 14.8 - - - +
128A PRO* 4.2 5.8 - - + -
141A VAL 4.6 1.6 - - - +
142A PRO* 1.3 75.5 - - - +
144A LYS* 1.3 64.1 + - - +
145A LEU* 3.8 13.7 - - + -
159A THR* 2.7 41.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A CYS* 4.5 11.7 - - - -
91A ILE* 3.8 37.1 - - + +
92A VAL 3.4 5.2 - - - -
93A THR* 3.9 18.4 - - + -
125A SER* 4.0 3.9 - - - +
126A ARG* 3.3 4.9 - - - -
127A ASP* 2.8 50.5 + - + +
143A TYR* 1.3 77.5 - - - +
145A LEU* 1.3 67.7 + - - +
146A CYS* 5.3 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A LEU 3.7 0.7 - - - +
91A ILE* 3.3 6.8 - - - +
92A VAL* 2.8 45.6 + - + +
108A ILE* 3.7 38.1 - - + -
109A SER 3.8 27.1 - - - +
110A LEU* 4.8 9.0 - - + +
123A PHE* 3.7 21.8 - - + -
125A SER 3.7 2.9 - - - -
126A ARG* 4.3 4.0 - - + -
127A ASP 5.0 1.1 - - - +
143A TYR* 3.8 20.4 - - + -
144A LYS* 1.3 83.7 - - - +
146A CYS* 1.3 61.1 + - - +
147A LEU* 4.0 8.5 - - + +
159A THR* 4.5 5.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A CYS* 2.1 51.1 - - - -
89A VAL* 3.5 22.9 - - - -
90A LEU 3.4 4.0 - - - -
91A ILE* 4.2 2.0 - - + -
123A PHE* 3.7 1.4 - - - -
124A ILE* 2.8 34.3 + - - -
125A SER* 2.9 31.9 + - - +
144A LYS* 5.3 3.4 - - + -
145A LEU* 1.3 75.0 - - - +
147A LEU* 1.3 57.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ASP 3.7 0.3 - - - +
89A VAL* 3.3 6.4 - - - +
90A LEU* 2.9 42.9 + - + +
92A VAL* 4.6 9.2 - - + -
110A LEU* 3.9 34.3 - - + -
121A TRP* 4.0 28.7 - - + -
122A GLU 3.1 11.4 - - - +
123A PHE* 3.8 33.4 - - + -
124A ILE* 3.7 5.6 - - - +
145A LEU* 4.0 22.4 - - + +
146A CYS* 1.3 79.7 - - - +
148A SER* 1.3 60.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A LYS* 3.5 26.4 - - - +
86A ARG* 3.7 12.3 - - - -
88A ASP* 2.7 29.7 + - - -
121A TRP* 3.3 6.4 - - - -
122A GLU* 2.8 43.5 + - - +
124A ILE* 3.8 8.4 - - - +
147A LEU* 1.3 73.6 - - - +
149A ALA* 1.3 62.6 + - - +
150A LEU* 3.5 1.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LEU* 4.3 3.8 - - + -
55A ILE 3.9 5.5 - - - +
56A THR* 3.3 1.7 - - - -
57A LYS 2.8 26.5 + - - -
88A ASP* 2.8 16.4 + - - +
120A ARG 4.1 1.3 - - - +
121A TRP* 3.6 28.1 - - + -
148A SER* 1.3 73.0 + - - +
150A LEU* 1.3 60.3 + - - +
151A GLU 5.0 0.7 - - - +
178A VAL* 3.7 33.9 - - + -
----------------------------------------------------------
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