Contacts of the strand formed by residues 64 - 69 (chain A) in PDB entry 2MKJ
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 SER 64 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A TYR* 1.3 70.6 - - - +
65A ARG* 1.3 60.4 + - - +
66A LYS* 3.1 27.1 + - - +
67A VAL* 4.6 0.3 - - - +
121A VAL* 4.2 3.2 - - - +
153A PRO* 4.0 6.9 - - - +
154A TRP* 2.7 56.7 + - - +
156A LEU* 3.4 19.6 - - - +
211A LEU* 3.9 14.7 + - - +
213A TYR* 4.5 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A TYR 3.3 3.6 + - - -
64A SER* 1.3 69.7 + - - +
66A LYS* 1.3 63.8 + - + +
67A VAL* 3.5 11.2 + - - +
114A LEU* 3.6 45.7 - - + +
115A PHE* 2.8 49.6 + - + +
116A GLN* 4.2 10.3 + - - +
117A ASP 4.6 0.7 - - - +
118A GLU* 4.0 29.6 + - + +
121A VAL* 3.7 27.1 - - + -
211A LEU* 6.1 6.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A SER* 3.1 17.4 + - - +
65A ARG* 1.3 79.3 - - - +
67A VAL* 1.3 63.1 + - - +
68A PHE 5.4 0.2 - - - +
112A PHE* 5.5 16.4 - - + -
113A LEU 3.6 16.4 - - - +
114A LEU* 4.0 12.6 - - + -
152A ARG 3.9 1.3 - - - +
153A PRO* 3.4 15.6 - - - +
154A TRP* 3.9 1.4 + - - +
211A LEU* 3.9 29.4 - - + +
213A TYR* 3.2 56.7 - - + -
215A LYS* 5.4 5.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A SER 4.6 0.7 - - - +
65A ARG 3.6 13.9 - - - +
66A LYS* 1.3 82.9 - - - +
68A PHE* 1.3 65.6 + - - +
69A VAL* 3.9 3.4 + - + +
85A PHE* 5.9 0.9 - - + -
88A PHE* 5.0 8.5 - - + -
112A PHE* 5.1 0.7 - - - -
113A LEU* 3.0 45.5 + - + +
115A PHE* 4.2 16.6 - - + -
121A VAL* 5.6 1.1 - - + -
125A ILE* 5.5 5.8 - - + -
151A ILE* 3.6 37.0 - - + -
152A ARG 3.4 8.1 - - - +
153A PRO* 4.1 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A VAL* 1.3 71.0 - - - +
69A VAL* 1.3 85.8 + - - +
70A GLY* 4.4 5.6 - - - -
110A TYR* 4.7 14.6 - + + -
111A ALA 3.4 19.1 - - - -
112A PHE* 3.5 40.2 - + + -
150A GLN* 4.0 22.2 - - + -
151A ILE* 3.5 6.4 - - - -
152A ARG* 2.9 59.2 + - + +
213A TYR* 6.1 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A VAL* 3.9 12.3 - - + +
68A PHE* 1.3 92.9 - - - +
70A GLY* 1.3 63.1 + - - +
71A GLY 4.1 2.9 - - - +
72A LEU* 3.2 30.5 - - + -
85A PHE* 3.9 24.2 - - + -
109A GLY 3.9 1.3 - - - -
110A TYR* 3.4 1.7 - - - -
111A ALA* 2.8 35.8 + - + +
113A LEU* 3.9 14.8 - - + -
149A VAL* 4.6 6.1 - - + -
150A GLN 3.4 13.0 - - - +
151A ILE* 4.1 12.1 - - + -
----------------------------------------------------------
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