Contacts of the strand formed by residues 15 - 20 (chain B) in PDB entry 6EKK
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 15 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B PHE* 3.7 6.3 - - - -
14B GLU* 1.3 81.2 - - - +
16B TYR* 1.3 71.4 + - - +
17B VAL* 4.3 7.6 - - + -
36B GLN* 4.6 1.8 - - + -
37B PHE 3.3 16.2 - - - +
41B TYR* 3.5 48.9 - - + +
46B VAL* 4.7 0.4 - - + -
47B LEU* 4.5 2.0 - - + -
50B LEU* 3.7 28.4 - - + +
98B CYS 4.0 0.9 - - - +
99B ILE* 3.7 0.9 - - - -
100B LEU* 2.9 36.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 16 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B PHE* 3.9 4.7 - - + -
15B VAL* 1.3 74.5 - - - +
17B VAL* 1.3 70.3 + - - +
18B GLU* 2.6 33.8 + - + -
36B GLN* 3.2 6.7 - - - +
37B PHE* 2.8 38.9 + - + +
97B PHE* 3.0 16.7 - - + -
98B CYS 3.3 8.3 - - - -
99B ILE* 3.4 23.3 - - + +
113B LEU* 3.9 16.8 - - + -
116B LEU* 3.8 25.7 - - + +
128B TRP* 3.5 32.9 + + - -
132B LEU* 3.7 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 17 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B VAL* 4.3 2.9 - - + -
16B TYR* 1.3 82.2 - - - +
18B GLU* 1.3 65.3 + - - +
19B VAL* 3.7 23.6 - - + -
33B VAL* 4.2 16.2 - - + -
35B ARG 3.4 4.5 - - - +
36B GLN* 4.2 3.1 - - + -
47B LEU* 3.8 28.9 - - + -
50B LEU* 3.8 26.7 - - + -
96B CYS 3.8 0.5 - - - +
97B PHE* 3.5 2.1 - - - -
98B CYS* 2.8 57.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 18 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B TYR* 2.6 37.2 + - + +
17B VAL* 1.3 73.7 - - - +
19B VAL* 1.3 54.2 + - - +
33B VAL* 3.5 3.3 - - - -
34B GLN* 2.7 39.5 + - + +
35B ARG* 2.8 48.4 + - + +
95B SER* 6.1 0.9 - - - +
96B CYS 3.7 4.3 - - - -
97B PHE* 3.2 21.5 - - + -
120B THR* 2.7 27.8 + - - +
128B TRP* 3.1 6.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 19 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B VAL* 3.7 28.9 - - + -
18B GLU* 1.3 77.4 - - - +
20B ALA* 1.3 63.5 + - - +
31B PRO* 4.1 2.5 - - + -
32B GLU 3.4 28.5 - - - +
33B VAL* 4.1 8.1 - - + +
34B GLN* 4.5 0.2 - - - -
50B LEU 5.1 0.9 - - - +
51B THR* 4.1 21.1 - - + -
54B CYS* 4.2 12.8 - - + -
55B PHE* 3.6 23.6 - - + -
95B SER* 3.4 2.8 + - - -
96B CYS 2.8 42.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 20 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B VAL* 1.3 78.1 - - - +
21B TYR* 1.3 69.7 + - - +
22B PRO* 3.4 4.2 - - - +
31B PRO* 4.1 4.5 - - - -
32B GLU 3.0 28.5 + - - -
34B GLN* 3.5 23.8 + - + +
55B PHE* 4.3 1.6 - - - -
94B LYS 3.2 13.2 - - - +
95B SER* 4.2 11.2 - - - +
----------------------------------------------------------
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