Contacts of the strand formed by residues 155 - 160 (chain A) in PDB entry 1M1B
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 CYS 155 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 3.7 24.7 - - + -
12A LYS* 3.6 31.6 - - - -
15A LEU* 3.6 31.0 - - + -
109A ALA 3.0 10.7 + - - -
110A GLY* 3.0 4.8 - - - -
111A ALA 2.8 28.2 + - - +
153A ASP 3.5 15.5 - - - -
154A PHE* 1.3 79.0 - - - +
156A ILE* 1.3 63.0 + - - +
157A VAL* 4.0 4.5 - - + -
185A ASP* 3.5 4.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A VAL* 3.8 20.4 - - + -
111A ALA* 3.3 12.1 - - + +
113A LEU* 4.9 6.7 - - + -
142A ILE* 4.2 36.3 - - + -
145A CYS* 3.9 18.4 - - + -
146A LYS* 3.4 26.7 - - - -
149A GLN* 3.5 9.9 - - - +
154A PHE* 3.7 18.2 - - + -
155A CYS* 1.3 80.8 - - - +
157A VAL* 1.3 61.3 + - - +
184A ALA* 3.6 2.8 - - - -
185A ASP* 2.8 37.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 4.4 16.2 - - + -
83A LEU* 4.1 29.4 - - + -
111A ALA 2.8 9.3 + - - -
112A CYS* 3.1 16.2 - - + -
113A LEU* 2.8 33.6 + - - +
155A CYS* 4.9 0.9 - - + -
156A ILE* 1.3 79.2 - - - +
158A ALA* 1.3 57.1 + - - +
186A ALA* 3.6 31.6 - - + +
188A LEU* 4.0 27.6 - - + +
213A VAL* 4.3 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A LEU 3.4 4.3 - - - -
138A PHE* 3.9 1.3 - - + -
142A ILE* 3.8 19.1 - - + -
156A ILE 4.0 2.0 + - - -
157A VAL* 1.3 71.0 - - - +
159A ARG* 1.3 55.7 + - - +
160A VAL 4.1 0.2 - - - -
179A TYR* 3.6 38.8 - - + -
184A ALA* 4.0 8.7 - - + -
186A ALA 3.2 7.1 + - - -
187A ILE* 3.3 11.1 - - + +
188A LEU* 2.6 32.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A TRP* 4.2 10.5 - - - -
85A ASP* 3.6 17.6 + - - -
112A CYS* 4.0 11.2 - - - -
113A LEU 2.7 18.0 + - - +
114A GLU* 3.4 23.3 + - + +
115A ASP* 3.0 29.5 + - - +
120A LYS* 5.4 0.2 - - - +
123A SER* 3.4 14.8 + - - -
138A PHE* 4.7 0.6 - - - -
158A ALA* 1.3 73.1 - - - +
160A VAL* 1.3 62.6 + - - +
161A GLU* 2.9 22.5 + - - +
179A TYR* 4.8 1.8 - - - -
188A LEU* 3.3 32.2 - - + +
190A HIS* 3.7 11.0 - - + -
215A VAL* 5.8 1.1 - - - -
996A SPV 2.6 55.7 + - - +
998A MG 3.7 2.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ASP* 3.5 4.3 - - - +
159A ARG* 1.3 69.8 - - - +
161A GLU* 1.3 58.3 + - - +
162A ALA* 3.3 30.2 + - + +
172A ALA* 3.7 15.0 - - - -
175A ARG* 3.6 13.2 - - + -
176A ALA* 3.6 30.5 - - - +
179A TYR* 3.8 11.7 - - + -
187A ILE* 4.2 5.2 - - + -
188A LEU 2.9 8.3 + - - -
189A MET* 3.4 28.1 - - + +
190A HIS* 3.6 23.6 + - - +
----------------------------------------------------------
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