Contacts of the strand formed by residues 77 - 82 (chain B) in PDB entry 1SKW
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 THR 77 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B VAL 3.3 3.3 - - - +
26B ASP* 3.5 1.7 - - - -
27B PHE* 2.8 40.2 + - + -
72B ILE* 3.7 28.8 - - + +
73B ARG 5.1 0.2 + - - -
74B GLY 2.3 31.2 + - - -
75B ILE* 3.7 0.8 - - - +
76B PRO* 1.3 71.2 + - - +
78B LEU* 1.3 64.1 + - - +
79B LEU* 3.3 26.7 - - + -
89B THR* 4.7 2.5 - - - +
90B LYS 3.9 6.7 - - - +
91B VAL* 4.0 15.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU* 4.1 16.6 - - + -
25B VAL 3.3 3.1 - - - +
26B ASP* 3.6 38.1 - - + +
38B ILE* 3.7 31.0 - - + -
42B LEU* 4.7 6.7 - - + -
76B PRO* 5.0 4.5 - - + +
77B THR* 1.3 73.7 - - - +
79B LEU* 1.3 67.7 + - - +
80B LEU 4.2 0.4 + - - -
88B ALA 4.1 0.2 - - - +
89B THR* 3.4 2.9 - - - -
90B LYS* 2.8 42.3 + - + +
92B GLY 4.9 2.9 - - - +
94B LEU* 4.1 16.8 - - + -
99B LEU* 4.0 24.5 - - + -
102B PHE* 5.1 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ILE 3.3 2.6 - - - +
24B LEU* 3.4 2.9 - - - -
25B VAL* 2.7 39.2 + - - +
27B PHE* 3.5 25.1 - - + -
70B TYR* 3.9 27.4 - - + -
72B ILE* 4.7 2.2 - - + -
77B THR* 3.3 26.7 - - + -
78B LEU* 1.3 80.0 - - - +
80B LEU* 1.3 59.5 + - - +
81B PHE* 3.5 32.1 - - + -
86B VAL* 4.0 18.2 - - + -
88B ALA 3.8 1.8 - - - -
89B THR* 3.9 13.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ALA* 3.9 21.8 - - + -
23B ILE 3.4 10.1 - - - +
24B LEU* 4.0 15.8 - - + +
53B LEU* 4.3 7.0 - - + -
78B LEU 4.2 0.4 + - - -
79B LEU* 1.3 71.8 - - - +
81B PHE* 1.3 73.3 + - - +
82B LYS* 5.6 1.3 - - + -
86B VAL* 3.7 2.0 - - - -
87B ALA* 2.8 34.2 + - + +
88B ALA* 3.0 23.0 + - + +
102B PHE* 4.5 11.2 - - + +
103B LEU* 4.8 5.2 - - + -
106B ASN* 3.5 35.0 - - + +
107B LEU* 4.0 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B PHE* 3.9 9.6 - + - -
16B VAL* 3.6 25.1 - - + +
17B LEU* 3.8 20.0 - - + -
21B GLY 3.8 1.8 - - - +
22B ALA* 3.5 6.8 - - - -
23B ILE* 2.7 40.0 + - + +
25B VAL* 3.8 19.7 - - + -
27B PHE* 5.0 0.2 - + - -
70B TYR* 3.7 31.0 - + - -
79B LEU* 3.5 34.1 - - + -
80B LEU* 1.3 77.5 - - - +
82B LYS* 1.3 60.6 + - - +
83B ASN 4.3 0.2 - - - -
84B GLY 5.2 1.3 - - - +
85B GLU* 3.3 22.4 - - - +
86B VAL* 3.4 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B GLY 4.5 5.6 - - - -
22B ALA* 5.4 4.5 - - + -
80B LEU* 4.1 2.4 + - + -
81B PHE* 1.3 74.7 - - - +
83B ASN* 1.3 75.6 + - + +
84B GLY 3.3 0.7 - - - -
85B GLU* 2.9 21.4 + - - +
87B ALA* 4.3 17.5 - - + +
----------------------------------------------------------
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