Contacts of the strand formed by residues 60 - 68 (chain B) in PDB entry 3U7X
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 60 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B TRP* 4.1 31.0 - - + -
47B PHE 3.6 17.0 - - - +
48B PHE* 3.9 20.4 - - + -
56B TRP 3.8 14.2 + - - +
57B GLN* 3.6 14.9 + - - +
58B ALA 3.6 3.3 - - - +
59B ASN* 1.3 78.7 - - - +
61B ARG* 1.3 61.0 + - - +
92B SER* 5.6 2.2 - - - +
100B PRO* 4.2 22.4 - - + +
101B MET* 4.4 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B TRP* 3.2 7.4 - - - -
47B PHE* 2.8 58.4 + - + +
58B ALA 5.9 0.4 - - - +
59B ASN 4.5 4.5 - - - +
60B LEU* 1.3 78.6 - - - +
62B LEU* 1.3 80.0 + - - +
63B ILE* 3.4 11.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ALA* 3.7 27.4 - - + -
45B LEU 3.7 15.5 - - - +
46B TRP* 3.7 31.2 - - + -
61B ARG* 1.3 87.6 + - - +
63B ILE* 1.3 63.9 + - - +
64B SER* 3.9 14.1 - - - +
65B LYS* 4.1 25.8 - - + -
218B SO4 4.9 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B LEU* 2.7 40.1 + - + +
46B TRP 4.3 0.7 - - - -
47B PHE* 3.8 32.3 - - + +
61B ARG* 4.1 14.1 + - - +
62B LEU* 1.3 79.0 - - - +
64B SER* 1.3 62.2 + - - +
75B LEU* 4.0 24.5 - - + -
78B HIS* 6.0 1.6 - - + -
79B ILE* 4.8 11.4 - - + -
91B TYR* 3.9 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B TRP 4.2 0.2 - - - +
44B ALA* 3.6 1.2 - - - -
45B LEU* 2.9 27.8 + - - +
62B LEU* 3.7 7.3 - - - +
63B ILE* 1.3 85.9 - - - +
65B LYS* 1.3 74.3 + - - +
66B PHE* 4.7 0.5 - - - +
75B LEU* 3.9 30.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ARG* 3.7 35.9 + - - +
43B TRP 3.2 9.0 - - - +
44B ALA* 3.9 20.2 - - + -
46B TRP* 5.9 2.7 - - - -
62B LEU* 4.1 21.7 - - + +
64B SER* 1.3 87.0 + - - +
66B PHE* 1.3 63.8 + - - +
71B ASP* 5.7 0.2 - - - +
96B ASP* 2.5 35.1 + - - +
97B GLY 4.9 0.8 - - - +
218B SO4 2.7 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LEU* 3.5 28.3 - - + -
41B ASN 4.2 0.5 - - - +
42B ARG* 3.5 4.4 - - - +
43B TRP* 2.9 47.4 + - + -
45B LEU 5.0 1.6 - - - -
64B SER* 4.7 0.9 - - - +
65B LYS* 1.3 77.1 - - - +
67B ASP* 1.3 63.1 + - - +
68B THR 3.8 7.9 - - - -
71B ASP* 3.7 25.6 - - + +
72B PHE* 3.6 34.5 - + + -
75B LEU* 3.7 30.1 - - + -
93B LEU* 3.5 33.2 - - + -
138B ILE* 3.9 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B PRO* 3.6 3.3 - - - +
39B LEU* 2.8 33.1 + - - +
41B ASN 4.1 9.4 - - - +
42B ARG* 4.0 27.8 - - + -
66B PHE* 1.3 77.6 - - - +
68B THR* 1.3 68.6 + - - +
71B ASP* 4.4 5.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LYS* 3.7 37.7 - - + +
37B HIS 3.3 12.6 - - - +
38B PRO* 4.2 7.2 - - + -
39B LEU* 3.7 10.6 - - - +
66B PHE* 3.8 1.6 - - - -
67B ASP* 1.3 95.9 - - - +
69B VAL* 1.3 63.8 + - - +
70B GLU* 3.7 1.2 + - - -
71B ASP* 2.7 34.6 + - - +
72B PHE* 3.0 22.2 + - - +
----------------------------------------------------------
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