Contacts of the strand formed by residues 152 - 159 (chain A) in PDB entry 5MGS
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 152 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A PHE* 3.8 22.7 - + + -
109A SER 3.9 10.1 - - - -
145A ILE* 3.9 42.4 - - + -
150A ILE* 3.5 29.4 - - + -
151A LEU* 1.3 77.4 - - - +
153A TRP* 1.3 64.6 + - - +
154A ILE* 3.6 2.8 + - - +
191A SER* 3.1 4.1 - - - -
192A ILE* 2.8 37.8 + - + +
207A ARG* 3.3 34.8 - - + -
208A TRP* 3.9 6.5 - - - -
209A ILE* 3.6 33.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ASN 2.9 21.6 + - - -
115A TRP* 3.3 32.1 - + + +
118A SER* 3.3 24.9 - - - +
129A LEU* 4.1 3.5 - - + +
152A PHE* 1.3 73.5 - - - +
154A ILE* 1.3 62.9 + - - +
189A CYS* 3.3 35.0 - - + -
190A ILE 3.4 20.9 - - - -
191A SER* 4.2 2.7 - - - -
200A GLU* 3.9 16.2 - - + -
201A TYR 3.3 24.2 - - - -
202A CYS 3.8 8.7 - - - -
204A THR* 3.2 19.1 - - - -
206A ILE* 3.3 28.1 - - + +
207A ARG 2.7 16.8 + - - +
208A TRP* 3.7 8.2 - - + +
209A ILE* 3.2 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A TRP* 2.9 20.3 + - - -
129A LEU* 4.1 5.8 - - - -
130A LEU* 3.6 35.0 - - + +
132A ILE* 3.9 20.9 - - + -
152A PHE 3.9 9.2 - - - +
153A TRP* 1.3 79.4 - - - +
155A GLY* 1.3 59.3 + - - +
156A LEU* 2.9 15.4 + - + -
167A TRP* 3.9 22.9 - - + -
178A LEU* 4.8 4.0 - - + -
190A ILE* 3.0 41.1 + - + +
192A ILE* 3.9 20.6 - - + -
209A ILE* 4.9 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A TRP* 4.3 0.2 - - - -
129A LEU* 3.5 26.4 - - - +
130A LEU 2.7 20.8 + - - -
131A LEU* 4.7 0.2 - - - -
154A ILE* 1.3 68.8 - - - +
156A LEU* 1.3 58.0 - - - -
167A TRP* 3.2 11.5 - - - -
168A ILE* 2.9 40.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A TRP* 3.8 7.3 + - - -
154A ILE* 2.9 8.7 + - + +
155A GLY* 1.3 75.2 - - - -
157A ASN* 1.3 64.0 + - - +
165A TRP* 4.0 10.5 - - + -
166A LYS 3.5 34.5 - - - +
167A TRP* 3.6 35.0 - - + +
173A LEU* 4.3 13.5 - - + -
178A LEU* 3.8 29.6 - - + -
180A ILE* 4.5 0.9 - - + -
189A CYS* 3.8 0.7 - - - -
190A ILE* 2.9 53.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A TRP* 3.5 11.0 - - + -
156A LEU* 1.3 76.8 - - - +
158A PHE* 1.3 64.7 + - - +
159A SER* 4.5 1.0 + - - -
165A TRP* 3.3 10.1 - - - -
166A LYS* 2.8 41.0 + - - +
168A ILE* 6.0 0.6 - - - +
188A SER 3.7 2.7 - - - +
189A CYS* 3.5 24.0 - - - +
502A NAG 1.5 69.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A ASN* 1.3 77.7 + - - +
159A SER* 1.3 75.1 + - - +
160A LEU* 3.5 6.4 + - + +
163A LYS* 3.5 48.5 - - + -
164A ASN* 3.7 13.5 - - - -
165A TRP* 3.6 14.1 - + + -
184A ALA* 3.6 35.7 - - + -
185A LYS* 3.2 37.9 - - - +
186A GLU* 3.7 9.0 - - - -
187A ASN 5.2 3.5 + - - -
188A SER 2.9 21.6 + - - +
502A NAG 4.8 10.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A ASN* 3.6 5.2 + - - -
158A PHE* 1.3 75.4 - - - +
160A LEU* 1.3 53.9 + - - +
161A SER* 3.5 8.0 + - - -
162A GLU* 3.3 31.7 + - - +
163A LYS* 2.7 35.5 + - - -
164A ASN 2.9 14.9 + - - -
166A LYS* 4.5 27.7 + - - -
172A PHE* 5.8 0.2 - - - -
502A NAG 5.9 2.0 - - - -
----------------------------------------------------------
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