Contacts of the strand formed by residues 156 - 167 (chain A) in PDB entry 5MCO
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 VAL 156 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A ASP 3.5 0.9 - - - +
145A LEU* 3.4 4.4 - - - -
146A VAL* 2.7 36.1 + - - +
154A VAL* 4.4 2.0 - - + -
155A THR* 1.3 80.4 - - - +
157A ARG* 1.3 61.3 + - - +
158A ALA* 3.6 10.4 + - + -
197A PHE* 3.6 33.2 - - + -
200A SER* 4.8 0.9 - - - -
201A LEU* 3.5 40.4 - - + +
204A GLN* 3.4 15.0 - - + +
205A THR* 3.8 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A THR* 2.9 44.3 + - - +
122A ARG* 3.3 47.6 - - - +
143A THR* 3.1 43.7 + - + -
144A ASP* 3.4 8.1 - - - +
145A LEU* 4.1 26.2 - - + +
156A VAL* 1.3 71.1 - - - +
158A ALA* 1.3 60.3 + - - +
200A SER* 4.0 5.2 + - - -
204A GLN* 2.9 34.6 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
99A PHE* 4.7 0.9 - - + -
143A THR* 3.2 7.5 - - - -
144A ASP 3.0 27.3 + - - +
146A VAL* 4.1 15.7 - - + -
156A VAL* 4.2 5.4 - - + -
157A ARG* 1.3 75.1 - - - +
159A ASN* 1.3 70.7 + - - +
160A ILE* 3.4 2.6 + - - +
197A PHE* 3.8 31.4 - - + -
200A SER* 4.4 10.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A PHE* 3.3 27.0 + - - +
124A LEU* 3.6 11.3 - - - +
141A LEU* 5.5 0.9 - - + -
142A GLY 3.4 4.7 - - - +
143A THR* 3.3 19.7 - - - +
158A ALA* 1.3 75.7 - - - +
160A ILE* 1.3 59.3 + - - +
161A ALA 4.4 0.2 - - - -
193A SER 5.3 0.2 + - - -
194A LEU* 3.5 29.4 - - + +
195A GLU* 3.1 48.6 + - - +
197A PHE* 5.7 1.6 + - - +
200A SER* 5.0 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A VAL* 4.0 16.6 - - + -
99A PHE* 3.7 29.6 - - + -
101A VAL* 3.8 29.8 - - + +
113A TYR* 4.2 12.6 - - + +
121A TYR* 5.8 1.5 - - + -
140A GLU 3.5 2.8 - - - +
141A LEU* 3.5 5.2 - - - -
142A GLY* 2.7 38.7 + - - +
143A THR 5.2 0.2 - - - -
144A ASP* 3.9 23.3 - - + +
146A VAL* 3.8 15.9 - - + -
158A ALA 3.5 10.3 - - - +
159A ASN* 1.3 79.0 - - - +
161A ALA* 1.3 65.7 + - - +
162A ALA 3.7 0.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ASN* 5.4 2.5 - - - +
99A PHE 3.1 11.4 + - - +
100A ALA* 3.2 5.9 - - + -
101A VAL* 2.9 31.7 + - - +
128A VAL* 4.0 14.6 - - + -
137A TRP* 3.6 37.0 - - + -
140A GLU 3.5 4.7 - - - -
141A LEU* 4.1 7.3 - - + +
160A ILE* 1.3 75.8 - - - +
162A ALA* 1.3 55.8 + - - +
163A ILE 3.4 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A VAL* 3.7 9.2 - - - -
103A ALA* 3.5 20.4 - - + -
113A TYR* 4.8 6.1 - - + -
115A ARG* 3.6 34.3 - - - +
121A TYR* 6.0 0.4 - - + -
139A GLY* 3.0 20.9 - - - -
140A GLU 2.9 17.2 + - - +
160A ILE* 3.7 2.6 + - - +
161A ALA* 1.3 68.4 - - - +
163A ILE* 1.3 65.8 + - - +
164A THR* 3.2 4.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A ALA* 4.0 19.3 - - + +
101A VAL 2.8 25.1 + - - +
102A GLY* 4.0 4.1 - - - -
103A ALA* 3.0 24.8 + - - -
104A ALA* 3.7 4.0 + - - +
137A TRP* 3.7 41.5 - - + -
138A GLU 3.5 5.4 - - - -
139A GLY* 4.2 0.4 - - - -
161A ALA* 3.4 0.4 + - - +
162A ALA* 1.3 69.4 - - - +
164A THR* 1.3 60.6 + - - +
165A GLU 3.6 24.2 - - - +
169A PHE* 3.8 11.4 - - + -
170A PHE* 3.8 35.0 - - + -
178A GLY* 5.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ALA 4.9 2.5 - - - +
104A ALA* 4.0 23.8 - - + +
105A PRO 5.7 0.3 - - - +
115A ARG* 4.0 11.2 - - - +
138A GLU* 2.9 15.5 + - - +
139A GLY* 3.5 8.3 - - - -
140A GLU* 3.5 25.5 + - - +
162A ALA 3.2 11.6 + - - +
163A ILE* 1.3 74.4 - - - +
165A GLU* 1.3 70.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A TRP* 3.4 2.1 - - - +
138A GLU* 3.0 58.2 + - + +
163A ILE* 3.6 2.3 - - - +
164A THR* 1.3 84.1 + - - +
166A SER* 1.3 64.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A HIS* 3.6 20.4 + - - -
136A LYS 3.5 13.5 - - - -
137A TRP* 3.7 10.5 - - - +
163A ILE* 4.2 1.1 - - - +
165A GLU* 1.3 78.2 - - - +
167A ASP* 1.3 64.7 + - - +
169A PHE* 4.2 7.8 + - - +
170A PHE* 3.4 34.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A GLY* 3.2 1.7 - - - -
136A LYS* 3.0 53.0 + - + +
166A SER* 1.3 76.0 - - - +
168A LYS* 1.3 94.5 + - - +
169A PHE 3.0 1.9 + - - -
----------------------------------------------------------
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