Contacts of the strand formed by residues 63 - 70 (chain B) in PDB entry 5D4P
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 63 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A THR* 5.9 0.2 - - + -
15B ILE* 4.7 6.5 - - + -
16B LEU* 3.5 24.9 - - - +
17B GLU* 3.9 16.6 - - + +
41B ASN 3.8 4.7 + - - -
42B LEU* 3.2 42.3 + - + +
43B SER 4.2 4.0 - - - +
44B GLY 4.2 9.2 - - - +
51B TYR* 3.7 28.5 - - + -
56B MET* 4.1 8.9 - - + +
61B ASP 5.1 0.2 - - - +
62B ALA* 1.3 74.9 - - - +
64B ILE* 1.3 66.9 + - - +
90B SER* 6.1 0.7 - - - -
201B ADP 3.6 44.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ILE 3.7 0.2 - - - +
15B ILE* 3.4 7.1 - - - +
16B LEU* 2.9 59.0 + - + +
18B GLY* 4.2 14.6 - - - -
21B LYS* 3.7 41.3 - - + +
38B ILE* 3.9 17.0 - - + -
39B VAL 3.3 12.1 - - - +
40B GLY* 4.4 7.4 - - - -
41B ASN 5.2 0.4 - - - +
42B LEU* 3.6 4.7 - - - -
59B GLU 5.7 0.7 - - - +
62B ALA* 4.7 3.4 - - + +
63B LEU* 1.3 80.0 - - - +
65B MET* 1.3 61.2 + - - +
66B ILE* 4.0 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A VAL* 4.9 5.2 - - + -
65A MET* 5.6 4.3 - - + -
67A ILE* 4.1 25.1 - - + -
13B GLU* 4.0 39.3 - - + +
14B ILE 3.3 4.7 - - - +
15B ILE* 3.8 21.3 - - + -
37B THR 3.6 1.2 - - - +
38B ILE* 3.4 1.3 - - - -
39B VAL* 2.7 65.9 + - + +
42B LEU* 3.4 14.6 - - + +
64B ILE* 1.3 74.5 - - - +
66B ILE* 1.3 65.4 + - - +
67B ILE* 3.8 14.5 + - + -
65C MET* 5.7 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LEU 3.3 4.5 - - - +
13B GLU* 3.5 0.7 - - - -
14B ILE* 2.8 53.4 + - + +
16B LEU* 4.6 7.2 - - + -
21B LYS 4.8 0.7 - - - +
24B ALA* 3.6 31.4 - - + -
25B THR* 4.5 11.9 - - + -
28B LEU* 3.7 27.4 - - + -
36B TYR* 4.1 15.7 - - + -
37B THR 3.4 5.2 - - - +
38B ILE* 4.0 16.8 - - + -
64B ILE* 4.0 22.9 - - + -
65B MET* 1.3 73.7 - - - +
67B ILE* 1.3 64.4 + - - +
68B ALA 3.9 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LYS* 3.6 34.5 - - + +
12B LEU 3.3 3.1 - - - -
13B GLU* 4.6 8.7 - - + +
36B TYR* 3.3 2.9 - - - +
37B THR* 2.6 51.0 + - + +
39B VAL* 3.7 26.9 - - + -
65B MET* 4.1 22.0 - - + +
66B ILE* 1.3 74.1 - - - +
68B ALA* 1.3 61.9 + - - +
13C GLU* 4.7 2.9 - - - +
15C ILE* 5.2 1.3 - - + -
65C MET* 4.2 23.6 - - + -
94C PHE* 4.1 15.9 - - + -
201C ADP 3.3 6.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LYS* 3.4 2.9 - - - -
12B LEU* 2.8 44.5 + - + +
14B ILE* 5.0 1.6 - - + -
28B LEU* 4.2 24.5 - - + -
33B VAL* 4.3 1.3 - - + -
35B GLY 4.3 9.9 - - - +
36B TYR* 4.4 4.9 - - + -
66B ILE* 3.9 2.0 + - + -
67B ILE* 1.3 75.8 - - - +
69B ALA* 1.3 61.5 + - - +
70B VAL* 3.6 17.3 + - + +
201C ADP 3.8 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B LEU* 3.9 18.8 - - + -
10B LYS 3.4 6.3 - - - +
11B LYS* 4.1 3.5 - - + +
33B VAL* 4.4 3.6 - - - +
34B LYS 5.3 1.2 + - - -
68B ALA* 1.3 70.6 - - - +
70B VAL* 1.3 61.8 + - - +
71B PRO* 4.7 1.0 - - - +
98B ILE* 4.1 6.1 - - + -
106B PHE* 4.1 7.5 - - + +
94C PHE* 3.4 37.2 - - + -
201C ADP 3.0 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B LEU* 3.3 6.0 - - - +
10B LYS* 2.7 39.9 + - + +
12B LEU* 4.3 11.4 - - + -
33B VAL* 3.8 31.6 - - + -
68B ALA* 3.7 13.7 - - + +
69B ALA* 1.3 81.5 - - - +
71B PRO* 1.3 81.5 - - + +
74B LEU* 4.5 6.7 - - + -
75B VAL* 3.7 21.5 - - + +
78B LEU* 4.1 13.5 - - + -
----------------------------------------------------------
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