Contacts of the strand formed by residues 41 - 48 (chain B) in PDB entry 5DPR
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 LYS 41 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ILE* 5.4 0.3 - - - +
35B ARG* 4.3 9.5 + - - +
38B HIS* 3.1 25.7 + - + +
39B PRO 3.3 1.4 - - - +
40B SER* 1.3 98.8 + - - +
42B ILE* 1.3 68.1 + - - +
43B PRO* 3.9 5.7 - - - +
64B LEU* 3.7 47.2 - - + +
65B VAL 3.1 11.4 - - - +
66B PRO* 3.8 24.4 - - + +
67B ASP* 4.1 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ARG* 4.0 12.1 - - - +
41B LYS* 1.3 74.1 - - - +
43B PRO* 1.4 68.0 - - + +
44B VAL* 3.4 18.6 + - + +
63B PHE 3.4 3.3 - - - +
64B LEU* 3.6 2.8 - - - -
65B VAL* 2.5 36.9 + - + +
67B ASP* 3.3 23.8 - - - +
106B ILE* 3.8 28.7 - - + +
107B ALA* 4.0 11.2 - - + +
110B TYR* 3.4 53.6 - - + -
120B LEU* 4.2 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 43 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B VAL* 4.3 16.4 - - + -
34B ILE* 4.2 19.7 - - + -
35B ARG* 4.4 11.9 - - + -
41B LYS 3.9 6.1 - - - +
42B ILE* 1.4 84.7 - - + +
44B VAL* 1.3 62.3 + - - +
63B PHE 3.8 3.4 - - - +
64B LEU* 4.2 6.0 - - + -
110B TYR* 4.0 12.1 - - + +
118B GLY 4.0 15.9 - - - +
119B PHE* 3.8 23.0 - - + -
120B LEU* 3.0 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ILE* 3.7 17.5 - - + +
43B PRO* 1.3 77.7 - - - +
45B ILE* 1.3 65.6 - - - +
46B ILE* 3.6 26.5 - - + -
61B THR 3.6 0.5 - - - +
62B LYS* 3.5 3.8 - - - +
63B PHE* 2.7 45.9 + - + +
65B VAL* 3.8 9.6 - - + -
74B LEU* 5.2 0.2 - - + -
106B ILE* 3.7 28.3 - - + -
119B PHE* 5.1 0.4 - - - -
120B LEU* 3.3 15.3 - - + +
122B MET* 3.8 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 45 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B PHE* 3.7 34.1 - - + -
44B VAL* 1.3 73.8 - - - +
46B ILE* 1.3 60.1 + - - +
47B GLU* 3.8 17.0 - - + -
61B THR* 3.4 19.3 - - + +
62B LYS* 3.9 27.1 - - + -
119B PHE* 3.7 31.9 - - + -
120B LEU 2.8 9.2 + - - +
121B TYR* 3.7 27.4 - - + -
122B MET* 2.8 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B VAL* 3.6 22.4 - - + -
45B ILE* 1.3 77.2 - - - +
47B GLU* 1.3 68.4 + - - +
58B LEU* 3.8 19.3 - - + +
60B LYS 3.9 5.4 - - - +
61B THR* 2.8 26.9 + - - +
63B PHE* 3.8 24.2 - - + -
74B LEU* 4.7 6.7 - - + -
78B ILE* 3.4 34.8 - - + -
92B LEU* 4.1 16.4 - - + -
122B MET* 3.5 15.5 - - + +
124B TYR* 3.9 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ASP* 5.2 4.8 - - + +
16B ARG 4.1 0.3 - - - +
17B PRO* 3.6 11.9 - - - +
18B PHE* 2.9 31.1 + - - +
19B LYS 5.4 0.2 + - - -
21B ARG* 3.5 13.2 + - - +
45B ILE* 3.8 23.4 - - + +
46B ILE* 1.3 79.3 - - - +
48B ARG* 1.3 67.2 + - - +
58B LEU* 6.0 1.1 - - - -
61B THR* 4.1 5.4 - - + +
121B TYR* 4.6 8.3 - - - -
122B MET 3.2 9.5 + - - +
123B VAL* 3.3 12.7 - - + +
124B TYR* 3.1 31.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B GLU* 1.3 80.6 - - - +
49B TYR* 1.3 75.5 + - - +
50B LYS* 3.6 1.7 + - - -
52B GLU* 3.2 35.7 + - + -
53B LYS* 3.9 17.9 + - - +
55B LEU 2.5 39.2 + - - -
56B PRO* 3.8 10.5 - - - +
57B VAL* 3.3 34.3 - - + +
58B LEU* 5.8 0.6 - - - +
123B VAL* 4.1 1.4 - - - +
124B TYR* 3.5 31.2 + - + +
----------------------------------------------------------
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