Contacts of the strand formed by residues 112 - 117 (chain B) in PDB entry 5DPT
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 112 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B VAL* 4.3 4.0 - - + -
37B PRO 3.1 17.6 + - - +
38B VAL* 3.2 12.8 - - + +
39B ILE 2.7 32.0 + - - -
87B VAL* 3.8 26.2 - - + -
98B MET* 3.9 29.4 - - + +
101B LEU* 3.9 23.1 - - + +
102B TYR* 3.7 32.2 - - + +
105B ASN 3.9 15.7 - - - +
106B HIS* 4.6 1.1 - - - +
111B PHE* 1.3 71.2 - - - +
113B TYR* 1.3 59.3 + - - +
114B VAL* 4.4 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B TYR* 3.7 12.8 - + - -
13B LYS* 3.6 31.6 - - + +
21B ARG* 3.6 14.4 + - - -
39B ILE* 3.5 33.9 - - + +
41B GLU* 4.2 8.1 - - + -
86B PHE 4.0 4.5 - - - +
87B VAL* 3.9 18.7 - - - +
88B ASN 4.7 1.9 + - - -
105B ASN 5.1 1.8 + - - -
107B GLU* 3.4 41.3 - - + +
109B ASP* 2.7 24.7 + - - -
111B PHE* 3.7 26.6 + - + -
112B LEU* 1.3 76.2 - - - +
114B VAL* 1.3 63.4 + - - +
115B ALA 4.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B VAL* 3.7 22.4 - - + -
39B ILE 2.8 11.7 + - - +
40B VAL* 3.3 13.9 - - + +
41B GLU* 3.2 24.9 + - - +
67B PHE* 5.1 2.7 - - + -
85B PHE* 3.7 47.3 - - + -
86B PHE 3.8 2.9 - - - +
87B VAL* 3.7 19.7 - - + -
98B MET* 4.9 6.5 - - + -
101B LEU* 5.1 1.1 - - + -
112B LEU* 4.4 10.1 - - + -
113B TYR* 1.3 77.4 - - - +
115B ALA* 1.3 62.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B GLU* 3.2 12.6 - - + +
42B LYS 4.8 0.2 - - - -
43B ALA* 4.1 19.5 - - + -
84B PHE 3.6 0.2 - - - +
85B PHE* 3.3 3.8 - - - -
86B PHE* 2.6 54.1 + - + +
113B TYR 4.2 0.4 - - - -
114B VAL* 1.3 75.5 - - - +
116B TYR* 1.3 59.9 + - - +
123B GLY* 4.2 11.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B VAL* 3.6 27.6 - - + -
41B GLU* 3.3 26.7 + - - -
42B LYS* 3.6 16.0 + - + +
43B ALA* 3.0 21.2 + - - -
46B ALA* 4.1 2.6 - - - +
48B VAL* 3.6 23.8 - - + -
49B PRO 3.4 8.5 + - - -
50B ASP* 3.2 11.8 + - - -
51B LEU* 3.2 32.6 + - + +
71B ILE* 5.2 0.4 - - + -
75B ILE* 3.7 15.7 - - + -
83B LEU* 3.8 22.9 - - + -
84B PHE 3.2 9.4 - - - +
85B PHE* 3.9 17.0 - + + -
86B PHE* 4.7 0.4 - - - -
115B ALA* 1.3 75.3 - - - +
117B SER* 1.3 61.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B ALA* 4.0 16.8 - - - -
44B PRO 5.2 0.9 + - - -
45B LYS 4.8 2.4 + - - -
46B ALA* 3.9 19.6 - - - +
48B VAL* 4.4 2.0 - - - -
83B LEU* 3.3 10.6 - - - +
84B PHE* 2.8 30.5 + - - +
86B PHE* 4.0 13.7 - - - -
116B TYR* 1.3 78.2 - - - +
118B ASP* 1.3 70.2 + - - +
119B GLU* 3.3 19.8 + - - +
121B VAL 4.5 5.7 + - - -
----------------------------------------------------------
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