Contacts of the strand formed by residues 108 - 116 (chain A) in PDB entry 2KE0
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 LEU 108 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A TRP 3.8 7.4 - - - +
41A LEU* 5.4 0.2 - - - +
47A PHE* 4.5 11.2 - - + -
85A LEU 4.2 0.3 - - - +
86A THR* 3.7 1.0 - - - -
87A ILE* 3.0 58.2 + - + +
88A PRO 3.9 14.6 - - - +
89A PRO* 4.7 1.3 - - + -
92A GLY* 4.0 10.5 - - - -
93A TYR* 4.0 32.5 - - + +
102A ILE* 4.8 10.3 - - + -
106A ALA 4.6 6.1 - - - +
107A THR* 1.3 76.3 - - - +
109A VAL* 1.3 62.6 + - - +
110A PHE* 3.2 42.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A THR 3.4 0.8 - - - +
39A GLY* 3.4 2.9 - - - -
40A TRP* 2.7 55.0 + - + +
41A LEU 5.2 5.2 - - - +
42A THR* 6.1 1.8 - - - -
47A PHE* 4.4 0.7 - - - -
84A ARG* 3.3 49.1 - - + +
85A LEU 3.6 2.5 - - - +
86A THR* 3.4 27.1 - - + +
107A THR* 4.9 4.5 - - + +
108A LEU* 1.3 78.1 - - - +
110A PHE* 1.3 67.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A TYR* 3.6 33.9 - + + -
38A THR 3.2 3.6 - - - +
39A GLY* 3.2 30.1 - - - -
47A PHE* 3.8 18.6 - + - -
48A ASP* 4.6 4.7 - - + -
67A ILE* 5.9 2.7 - - + -
70A TRP* 4.4 28.7 - + + +
84A ARG* 3.6 0.9 - - - +
85A LEU* 2.7 48.0 + - + +
87A ILE* 5.0 6.7 - - + -
93A TYR* 4.8 10.8 - + - -
108A LEU* 3.2 35.9 - - + -
109A VAL* 1.3 76.9 - - - +
111A GLU* 1.3 59.7 + - - +
112A VAL* 3.7 2.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 4.8 7.6 - - + +
36A HIS 2.8 14.6 - - - +
37A TYR* 4.1 0.2 - - - -
38A THR* 2.9 44.1 + - - +
40A TRP* 3.5 33.4 - - + -
82A VAL* 3.5 32.6 - - + +
83A ARG 3.9 4.5 - - - +
84A ARG* 4.4 11.0 - - + +
110A PHE* 1.3 70.2 - - - +
112A VAL* 1.3 62.2 + - - +
113A GLU* 3.9 16.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A VAL* 4.0 26.9 - - + -
36A HIS 3.2 4.0 - - - +
37A TYR* 4.9 3.8 - - + -
70A TRP* 4.4 24.5 - - + +
73A GLY* 6.2 2.7 - - - -
74A VAL* 5.6 7.4 - - + -
77A MET* 3.4 8.3 - - + +
82A VAL* 3.6 2.1 - - - +
83A ARG* 2.8 44.3 + - + +
85A LEU* 3.2 32.3 - - + -
110A PHE 4.6 2.5 - - - +
111A GLU* 1.3 72.6 - - - +
113A GLU* 1.3 62.5 + - - +
114A LEU* 4.3 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A VAL* 3.4 1.6 - - - -
36A HIS* 2.9 60.7 + - + +
38A THR* 5.0 4.4 + - - +
51A LYS* 4.4 14.2 + - - +
80A GLY 6.1 0.2 - - - -
81A GLY 3.3 8.1 - - - +
82A VAL* 4.7 9.4 - - + -
111A GLU* 3.9 16.6 - - - +
112A VAL* 1.3 75.2 - - - +
114A LEU* 1.3 67.4 + - - +
115A LEU* 2.9 24.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ALA* 5.1 7.0 - - + -
33A VAL* 4.3 15.5 - - + -
34A SER 4.4 1.6 - - - +
35A VAL* 3.3 28.7 - - + -
73A GLY 5.3 0.9 - - - +
74A VAL* 5.6 5.8 - - + -
77A MET* 3.5 36.1 - - + -
78A LYS 2.9 33.2 - - - +
79A VAL* 3.8 1.1 - - - -
80A GLY* 2.8 28.7 + - - +
81A GLY 2.9 9.2 + - - +
112A VAL* 4.3 6.3 - - + -
113A GLU* 1.3 71.5 - - - +
115A LEU* 1.3 63.0 + - - +
116A ASP 4.5 0.9 - - - +
117A VAL* 4.3 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A SER* 2.9 20.0 + - - +
35A VAL 3.9 2.9 - - - -
36A HIS* 3.2 33.2 - - + -
56A PRO* 3.3 23.8 - - + -
79A VAL* 3.7 14.4 - - - +
113A GLU* 2.9 41.7 - - - +
114A LEU* 1.3 76.0 - - - +
116A ASP* 1.3 70.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A VAL* 3.3 5.4 - - - +
34A SER* 3.0 52.8 + - - +
79A VAL* 4.2 10.3 - - + +
114A LEU* 3.8 2.1 - - - +
115A LEU* 1.3 86.1 - - - +
117A VAL* 1.3 79.4 + - - +
----------------------------------------------------------
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