Contacts of the strand formed by residues 76 - 81 (chain F) in PDB entry 3SKU
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 GLN 76 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B ASP 4.1 2.0 - - - +
216B SER* 3.8 14.6 - - - +
218B GLY* 4.8 0.7 - - - -
68F GLN* 3.7 2.1 - - - +
69F LYS* 2.7 74.1 + - + +
71F THR* 4.9 15.3 - - + +
75F LYS* 1.3 75.4 - - - +
77F ASN* 1.3 71.1 + - - +
91F ALA 4.6 2.6 + - - -
92F PRO* 4.0 24.5 - - - +
93F TYR* 4.4 4.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 77 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B ARG* 4.6 1.0 - - - +
215B ASP* 3.0 41.1 + - - +
218B GLY* 4.4 2.8 - - - -
219B MET 3.1 21.9 + - - +
220B LEU* 3.5 12.2 - - - +
67F TRP 4.3 2.2 - - - -
68F GLN* 3.0 33.6 + - - +
76F GLN* 1.3 83.3 + - - +
78F VAL* 1.3 62.6 + - - +
80F ILE* 4.0 8.4 - - + +
90F LEU* 3.7 24.6 - - + +
91F ALA 4.4 2.8 - - - +
93F TYR* 4.1 11.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 78 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67F TRP* 3.0 28.5 + - + +
68F GLN* 4.0 13.2 - - - +
69F LYS* 4.2 3.6 - - + +
77F ASN* 1.3 76.5 - - - +
79F ALA* 1.3 62.4 + - + +
89F VAL* 3.2 4.9 - - - +
90F LEU* 2.7 35.9 + - - +
93F TYR* 3.3 49.1 - - + -
97F VAL* 4.3 9.6 - - + -
109F ILE* 5.2 5.6 - - + -
111F LEU* 5.7 0.9 - - + -
122F TYR* 4.2 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 79 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65F VAL 4.2 1.8 - - - -
66F THR* 3.3 5.0 - - - +
67F TRP* 2.7 45.2 + - + +
78F VAL* 1.3 80.6 - - + +
80F ILE* 1.3 67.0 + - - +
81F TYR 4.4 0.2 - - - -
88F SER 4.1 0.9 - - - -
89F VAL* 3.1 26.9 - - + -
97F VAL* 5.0 7.0 - - + -
99F PHE* 3.8 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 80 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B TYR* 6.5 1.1 - - + -
132B GLN* 6.0 1.1 - - - +
134B ARG* 5.5 0.7 - - - +
215B ASP* 4.4 7.4 - - - +
220B LEU* 4.4 4.0 - - + -
221B PRO* 4.0 24.2 - - + -
64F GLN* 2.9 28.7 - - + +
65F VAL 3.4 3.4 - - - -
66F THR* 4.1 10.5 - - + +
77F ASN* 4.0 25.6 - - - +
79F ALA* 1.3 83.6 - - - +
81F TYR* 1.3 60.5 + - - +
82F ASN* 3.8 7.0 + - + +
86F GLY 4.4 0.4 - - - +
87F VAL* 3.5 17.3 - - - +
88F SER* 3.4 26.4 + - - +
89F VAL* 4.5 0.6 - - - +
90F LEU* 4.6 5.6 - - + -
99F PHE* 4.4 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 81 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64F GLN* 3.3 4.7 - - - -
65F VAL* 2.8 51.9 + - + +
80F ILE* 1.3 70.7 - - - +
82F ASN* 1.4 59.8 + - - +
83F PRO* 3.7 36.9 - - + +
86F GLY 4.9 2.5 - - - -
87F VAL* 3.1 23.1 - - + -
99F PHE* 3.8 21.3 - + + -
102F PRO* 2.8 60.6 + - + +
103F SER 5.3 0.2 - - - -
104F PHE* 4.6 11.0 - + - -
106F ASP 5.4 0.2 - - - -
107F GLY* 6.0 0.2 - - - -
----------------------------------------------------------
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