Contacts of the strand formed by residues 141 - 150 (chain A) in PDB entry 5MW5
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 SER 141 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A TYR* 3.4 29.2 - - - +
90A TYR* 4.1 4.3 + - - -
139A PRO* 2.8 33.2 + - - +
140A ARG* 1.3 74.2 - - - +
142A PHE* 1.3 64.1 + - - +
170A GLY 3.3 9.4 - - - -
171A MET* 3.9 14.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A PHE* 4.4 6.7 - + - -
75A LEU* 3.7 16.6 - - + -
76A LYS 3.7 10.3 - - - +
78A TYR* 3.6 13.1 - - - +
90A TYR* 4.3 9.4 - - + -
138A TRP* 4.0 15.0 - + + -
140A ARG 3.5 13.2 - - - -
141A SER* 1.3 75.7 - - - +
143A THR* 1.3 71.3 + - - +
144A LEU* 3.5 26.0 - - + -
168A HIS* 4.4 12.6 - + - -
169A ALA* 3.4 3.1 - - - -
170A GLY 3.1 43.9 + - - -
171A MET 4.3 0.4 - - - -
172A ILE* 3.4 28.9 - - + -
194A ILE* 3.8 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A CYS 3.7 1.2 - - - +
75A LEU* 3.7 4.0 - - - -
76A LYS* 2.8 58.3 + - - +
77A GLU 2.8 22.9 + - - -
78A TYR* 3.5 0.5 - - - -
79A GLN* 3.1 22.7 + - - +
82A VAL* 3.7 26.5 - - + -
142A PHE* 1.3 75.8 + - - +
144A LEU* 1.3 63.5 + - - +
145A ILE* 4.1 7.4 - - + -
168A HIS 3.8 4.9 - - - +
169A ALA* 4.0 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A PHE* 4.3 4.5 - - + -
32A LEU* 4.0 10.8 - - + -
73A VAL* 3.6 30.1 - - + -
74A CYS 3.7 3.8 - - - +
75A LEU* 4.1 12.1 - - + -
142A PHE* 3.5 17.0 - - + -
143A THR* 1.3 71.6 - - - +
145A ILE* 1.3 63.2 + - - +
146A VAL* 3.8 15.4 - - + +
167A SER* 3.2 7.8 - - - -
168A HIS* 2.9 41.6 + - + +
181A LEU* 4.2 17.7 - - + -
183A PHE* 5.2 2.9 - - + -
192A LEU* 4.6 2.0 - - + -
194A ILE* 4.0 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ARG 3.9 0.5 - - - +
73A VAL* 3.5 1.6 - - - +
74A CYS* 2.6 59.7 + - + +
76A LYS* 3.6 20.6 - - + +
82A VAL* 4.6 2.9 - - + -
83A THR 3.5 24.9 - - - +
84A PRO* 4.0 15.3 - - + +
143A THR* 4.1 11.9 - - + -
144A LEU* 1.3 77.2 - - - +
146A VAL* 1.3 62.8 + - - +
147A GLU* 4.0 28.2 - - + +
165A ARG* 4.2 8.5 - - + -
166A VAL 3.5 7.0 - - - +
167A SER* 4.3 9.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 4.0 16.6 - - + -
34A LEU* 6.3 0.2 - - + -
71A VAL* 3.6 26.0 - - + -
72A ARG 3.4 3.6 - - - +
73A VAL* 4.6 4.9 - - + -
144A LEU* 3.8 28.0 - - + -
145A ILE* 1.3 77.9 - - - +
147A GLU* 1.3 65.6 + - - +
164A GLU 4.0 0.3 - - - +
165A ARG* 3.5 1.9 - - - -
166A VAL* 2.9 48.3 + - + +
183A PHE* 5.7 1.8 - - + -
190A LEU* 3.9 22.8 - - + +
192A LEU* 4.5 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A VAL* 3.2 9.0 - - - +
72A ARG* 2.8 48.1 + - + +
74A CYS* 5.9 2.9 - - - +
84A PRO 5.0 3.3 - - - +
145A ILE* 4.0 15.3 - - + +
146A VAL* 1.3 80.8 - - - +
148A ALA* 1.3 60.8 + - - +
149A TRP* 3.4 29.3 + - - +
162A LEU* 4.3 4.7 - - + -
164A GLU 3.2 6.5 - - - +
165A ARG* 2.9 48.6 + - + +
190A LEU* 6.3 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LEU* 4.3 24.2 - - + -
69A THR* 4.4 5.4 - - + -
70A TYR 3.5 6.7 - - - +
71A VAL* 4.6 2.2 - - + +
147A GLU* 1.3 72.3 - - - +
149A TRP* 1.3 70.7 + - - +
162A LEU* 3.8 2.8 - - - +
163A ILE* 2.8 43.7 + - + -
164A GLU* 2.8 18.6 + - + +
190A LEU* 5.5 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ASP 3.3 1.0 - - - +
69A THR* 3.2 6.9 - - - -
70A TYR* 2.8 66.2 + - + +
72A ARG* 3.3 44.1 - - + +
147A GLU* 3.4 25.1 + - - +
148A ALA* 1.3 91.6 - - - +
150A ASP* 1.3 59.5 + - - +
158A ASN 3.9 5.6 - - - -
159A GLU* 3.2 53.8 - - + -
161A LEU* 3.4 24.0 - - + -
162A LEU* 3.6 22.0 - - + -
163A ILE* 3.8 7.2 - - - -
165A ARG* 5.2 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LEU* 4.0 11.0 - - + -
50A CYS* 4.0 24.0 - - - -
51A ASP* 3.6 2.1 - - - +
67A CYS* 3.3 5.7 - - - -
68A ASP* 2.7 29.0 + - - +
70A TYR* 4.2 5.2 + - - -
149A TRP* 1.3 73.2 - - - +
151A TRP* 1.3 57.9 + - - +
152A ASP* 2.4 30.1 - - - +
161A LEU* 3.2 29.6 + - + +
163A ILE* 3.8 4.4 - - + +
403A CA 2.4 17.9 - - - -
404A CA 2.4 12.4 - - - -
----------------------------------------------------------
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