Contacts of the strand formed by residues 83 - 91 (chain B) in PDB entry 3W58
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 SER 83 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B GLU* 3.4 11.6 + - - +
23B VAL* 2.7 40.4 + - - +
80B GLN* 2.6 49.4 + - - +
82B GLY* 1.3 78.1 - - - +
84B VAL* 1.3 65.4 + - - +
85B ALA* 5.4 0.7 - - - +
103C GLY 3.8 6.1 - - - -
104C TYR* 4.5 11.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ARG* 3.6 33.2 - - + -
21B GLY 3.3 8.5 - - - +
22B GLU* 3.1 22.4 - - - +
83B SER* 1.3 79.5 + - - +
85B ALA* 1.3 66.9 + - - +
86B GLU* 6.0 0.2 - - + -
129B LYS* 5.7 4.3 - - + +
99C LYS* 5.5 1.6 - - - +
102C ASP 3.9 10.3 + - - +
103C GLY* 3.7 22.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ARG* 3.4 1.1 - - - -
21B GLY 2.9 31.1 + - - +
23B VAL* 4.2 14.4 - - + -
78B PRO 5.6 0.2 - - - +
79B PHE* 3.8 34.5 - - + -
83B SER* 5.4 1.6 - - - +
84B VAL* 1.3 79.9 - - - +
86B GLU* 1.3 60.8 + - - +
87B VAL* 5.5 0.7 - - + -
101B PRO* 4.3 8.3 - - + -
126B PHE* 3.8 10.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ARG* 3.7 25.3 + - - +
19B VAL 3.2 15.3 - - - +
20B ARG* 3.1 42.6 + - + +
84B VAL* 6.0 0.2 - - + -
85B ALA* 1.3 76.0 - - - +
87B VAL* 1.3 70.6 + - - +
88B CYS* 3.7 14.8 - - - -
101B PRO* 3.5 15.7 - - - +
202B BME 2.7 42.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B LEU 3.8 0.9 - - - +
18B ARG* 3.6 0.3 - - - -
19B VAL* 2.9 40.5 + - + +
30B PHE* 5.6 1.8 - - + -
32B LEU* 3.5 29.6 - - + -
45B PHE* 4.1 14.8 - - + -
79B PHE* 4.0 28.7 - - + -
85B ALA 5.5 0.7 - - - -
86B GLU* 1.3 79.3 - - - +
88B CYS* 1.3 64.8 + - - +
89B ILE* 4.0 13.2 - - + +
98B VAL* 5.0 3.6 - - + -
99B LYS 3.4 7.0 - - - +
100B LEU* 4.2 9.9 - - + -
126B PHE* 5.7 3.6 - - + -
202B BME 4.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B CYS* 4.0 12.8 - - - -
17B LEU 3.2 5.4 - - - +
18B ARG* 3.8 19.7 - - - -
86B GLU* 3.7 15.9 - - - -
87B VAL* 1.3 78.3 - - - +
89B ILE* 1.3 67.4 + - - +
97B THR 3.6 1.0 - - - +
98B VAL* 3.5 0.5 - - - -
99B LYS* 2.8 45.0 + - + +
202B BME 2.5 44.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU* 4.3 2.3 - - - +
15B GLU 3.8 0.9 - - - +
16B CYS* 3.6 2.8 - - - -
17B LEU* 2.8 58.1 + - + +
19B VAL* 4.9 4.3 - - + -
32B LEU* 5.2 5.4 - - + -
34B LEU* 3.9 35.2 - - + -
43B LEU* 4.8 4.5 - - + -
87B VAL* 4.0 24.0 - - + +
88B CYS* 1.3 81.1 - - - +
90B THR* 1.3 72.9 + - - +
96B LEU* 4.2 16.4 - - + -
97B THR 3.4 7.4 - - - +
98B VAL* 4.3 22.0 - - + -
117B ILE* 4.9 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU* 5.3 0.4 - - - -
14B GLY* 3.8 17.5 + - - -
15B GLU 3.1 19.7 + - - -
16B CYS* 4.7 6.3 - - - -
89B ILE* 1.3 80.1 - - - +
91B PHE* 1.3 73.9 + - - +
96B LEU* 3.4 2.3 - - - -
97B THR* 2.8 50.9 + - + +
99B LYS* 6.2 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU* 3.6 21.5 - - + -
12B LYS 3.8 12.3 - - - -
13B PRO* 3.5 32.7 - - + +
14B GLY* 3.3 23.8 + - - +
90B THR* 1.3 85.7 + - - +
92B ASP* 1.3 74.3 + - - +
95B ASN 3.4 11.7 - - - +
96B LEU* 3.8 19.1 - - + -
97B THR* 5.9 0.2 - - - -
110B ASN* 4.1 4.0 - - - -
114B LEU* 3.5 25.8 - - + -
115B GLU 3.7 2.2 - - - -
116B ALA* 3.7 23.6 - - - -
117B ILE* 3.8 27.4 - - + -
----------------------------------------------------------
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