Contacts of the strand formed by residues 142 - 149 (chain D) in PDB entry 1MA1
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 ARG 142 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107D LYS* 4.4 2.0 - - - +
108D ASP* 3.6 15.8 + - - +
136D TYR* 3.4 5.8 - - - -
137D CYS* 2.8 30.6 + - - +
140D THR* 3.1 39.5 - - - +
141D ASP* 1.3 79.0 - - - +
143D LEU* 1.3 64.8 + - - +
144D PHE* 3.6 12.6 + - + -
5F LYS* 4.0 15.5 - - + +
6F LYS 2.7 39.9 + - - +
7F PHE* 4.0 10.3 - - - -
48F LEU* 3.8 34.4 + - - +
52F ASP* 2.7 38.8 + - - -
55F ARG* 5.3 4.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 143 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101D LEU* 4.4 7.2 - - + -
104D TYR* 3.6 29.2 - - + +
105D ILE* 3.7 30.3 - - + +
108D ASP* 2.9 19.8 + - - +
109D PHE* 4.0 23.6 - - + -
134D LEU* 4.2 11.9 - - + -
135D THR 3.3 14.8 - - - +
136D TYR* 4.3 3.1 - - + -
142D ARG* 1.3 73.3 - - - +
144D PHE* 1.3 67.2 + - - +
162D LEU* 3.7 22.7 - - + -
200D PHE* 3.9 17.7 - - + -
55F ARG* 5.6 4.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 144 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134D LEU* 3.3 4.8 - - - +
135D THR* 2.8 46.9 + - + +
137D CYS* 3.6 15.9 - - + -
140D THR* 4.0 5.8 - - - -
142D ARG* 3.6 20.1 + - + -
143D LEU* 1.3 79.4 - - - +
145D ILE* 1.3 68.5 + - - +
156D ILE* 4.2 13.5 - - + -
159D PHE* 3.7 21.1 - + - -
8F TYR* 3.1 31.4 - + - -
48F LEU* 3.7 30.7 - - + -
70F LEU* 4.2 13.9 - - + -
74F VAL* 4.1 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 145 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D PHE* 3.8 33.8 - - + -
115D PHE* 4.2 2.9 - - + -
118D GLU* 4.2 8.7 - - + +
119D PHE* 3.8 45.1 - - + +
122D ALA* 4.0 13.7 - - + -
133D VAL 3.4 9.6 - - - +
134D LEU* 4.1 9.4 - - + -
144D PHE* 1.3 79.2 - - - +
146D MET* 1.3 68.1 + - - +
156D ILE* 6.1 0.3 - - - +
55F ARG* 5.8 0.2 - - - +
67F LEU* 3.2 45.4 - - + +
70F LEU* 4.4 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 146 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132D ALA* 3.7 2.8 - - - -
133D VAL* 2.9 51.0 + - + +
135D THR* 3.8 25.6 - - + -
144D PHE* 5.5 0.2 - - + -
145D ILE* 1.3 79.4 - - - +
147D GLN* 1.3 61.3 + - - +
148D VAL* 3.8 6.1 + - + -
154D ASN 4.2 10.8 - - - +
155D VAL* 4.1 13.2 - - - -
156D ILE* 3.2 64.4 - - + +
159D PHE* 4.3 7.6 - - + +
67F LEU* 4.3 4.5 - - - +
71F SER* 5.2 6.3 - - - -
157F PRO* 5.9 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 147 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122D ALA* 2.9 32.8 + - + +
125D SER* 3.0 22.6 + - - -
126D ALA* 3.3 26.5 - - + +
131D TRP 3.5 8.1 - - - +
132D ALA* 4.9 1.1 - - - +
146D MET* 1.3 73.2 - - - +
148D VAL* 1.3 62.2 + - - +
149D GLU* 3.6 5.4 + - + +
154D ASN* 3.5 25.7 + - - +
64F LYS* 3.4 28.7 - - - +
67F LEU* 4.1 24.9 + - + +
68F LYS* 3.9 17.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 148 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D LEU* 4.6 5.2 - - + -
126D ALA* 5.3 0.5 - - - +
130D GLY* 2.9 5.0 - - - -
131D TRP* 2.7 46.7 + - + +
133D VAL* 4.0 25.1 - - + -
146D MET* 4.7 7.9 - - + +
147D GLN* 1.3 73.1 - - - +
149D GLU* 1.3 74.1 - - - +
150D LYS 4.0 3.6 - - - +
151D HIS* 3.6 8.7 - - - +
152D ASN 3.5 18.2 - - - +
153D VAL 3.3 9.9 - - - +
154D ASN 4.6 2.0 - - - +
155D VAL* 4.1 21.3 - - + -
157F PRO* 5.5 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 149 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150C LYS* 3.0 44.0 + - + +
126D ALA* 5.8 2.2 - - + -
127D GLU* 3.8 18.0 + - - +
129D SER 3.5 8.7 - - - +
130D GLY* 4.1 0.2 - - - -
147D GLN* 3.6 7.7 + - + +
148D VAL* 1.3 71.8 - - - +
150D LYS* 1.3 74.7 + - + +
152D ASN 3.3 0.9 + - - -
153D VAL* 3.0 48.6 + - + +
154D ASN* 3.7 22.4 + - - +
68F LYS* 3.2 18.6 + - - -
----------------------------------------------------------
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