Contacts of the strand formed by residues 149 - 153 (chain A) in PDB entry 4MCA
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 MET 149 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LYS* 3.2 29.8 - - + +
12A ILE* 3.9 16.8 - - + -
21A VAL* 6.4 0.2 - - - -
24A TYR* 3.5 48.0 - - + +
25A ALA 4.4 0.4 - - - -
27A SER* 4.4 4.3 - - - +
28A LEU* 3.8 19.5 - - + -
111A VAL 3.3 2.6 + - - +
112A VAL* 3.4 27.9 - - + -
113A LEU* 2.9 25.3 + - - +
147A PRO* 3.3 2.3 - - - +
148A ASP* 1.3 80.8 - - - +
150A VAL* 1.3 68.4 + - - +
151A VAL* 4.0 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A PRO* 4.5 6.5 - - + -
10A LYS 3.1 6.6 + - - +
11A TYR* 3.5 24.4 - - + -
12A ILE* 2.9 27.0 + - - +
113A LEU* 3.4 12.1 - - + +
115A PRO* 4.2 8.1 - - + -
123A PRO* 3.9 28.3 - - + +
124A THR* 4.1 17.7 - - + -
147A PRO* 4.4 9.6 - - + -
149A MET* 1.3 80.1 - - - +
151A VAL* 1.3 64.8 + - - +
152A MET* 4.0 20.0 - - - -
238A THR* 4.6 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ILE* 3.4 18.6 - - + +
17A ALA* 3.9 24.2 - - + +
18A LEU* 5.0 0.7 - - - +
21A VAL* 3.7 31.9 - - + -
24A TYR* 5.7 1.8 - - + -
112A VAL* 4.0 23.6 - - + -
113A LEU 2.8 12.0 + - - +
114A ILE* 3.5 18.5 - - + +
115A PRO* 3.3 18.5 - - - +
149A MET* 4.0 14.4 - - + -
150A VAL* 1.3 78.8 - - - +
152A MET* 1.3 62.1 + - - +
153A ASP 5.0 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A TYR* 3.4 31.4 - - + +
12A ILE 2.8 12.0 + - - +
13A GLN* 3.3 14.2 - - + +
14A GLY 2.9 25.8 + - - +
17A ALA* 4.0 3.0 - - - +
115A PRO* 3.4 41.3 - - + -
117A ILE 4.2 7.4 - - - +
118A ALA* 4.3 4.3 - - + -
123A PRO* 5.8 0.2 - - + -
150A VAL* 4.0 3.4 - - + -
151A VAL* 1.3 70.0 - - - +
153A ASP* 1.3 62.2 + - - +
154A VAL 3.4 1.0 + - - -
157A ILE* 3.3 31.2 - - + -
234A ILE* 4.1 10.5 - - + -
238A THR* 3.7 29.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLY 3.3 3.8 - - - -
16A ASN* 2.9 32.9 + - - +
17A ALA* 3.5 4.5 - - + +
18A LEU* 3.0 39.5 + - + +
114A ILE* 5.6 4.9 - - + +
115A PRO 4.8 3.6 + - - +
151A VAL* 4.0 4.0 + - + -
152A MET* 1.3 69.4 - - - +
154A VAL* 1.3 62.7 + - - +
155A ALA* 3.0 9.4 + - - +
156A ILE* 3.4 30.8 + - + +
157A ILE* 3.1 27.3 + - - +
----------------------------------------------------------
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