Contacts of the strand formed by residues 90 - 96 (chain A) in PDB entry 1WG8
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 VAL 90 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A VAL* 3.6 21.5 - - + +
27A VAL* 3.9 21.3 - - + -
82A LEU* 4.0 9.2 - - + -
87A VAL* 3.5 19.5 - - + -
89A ARG* 1.3 81.0 - - - +
91A ASP* 1.3 64.8 + - - +
92A GLY 4.0 4.0 - - - +
93A ILE* 3.6 38.6 - - + -
222A VAL* 2.8 16.8 + - + +
223A LEU* 3.6 2.7 - - + -
224A ALA* 2.8 25.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU 4.9 2.6 - - - +
21A ARG* 3.1 33.8 + - - +
24A GLY* 3.3 6.5 - - - -
25A VAL* 2.8 37.9 + - - +
26A TYR* 3.8 23.7 - - + +
90A VAL* 1.3 74.8 - - - +
92A GLY* 1.3 57.8 + - - +
223A LEU* 4.5 0.2 - - - -
224A ALA* 4.3 13.3 - - - +
227A GLY* 3.1 24.9 - - - -
228A ARG 3.5 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 4.2 5.4 - - - -
26A TYR* 3.3 22.7 - - - -
27A VAL 2.9 24.3 + - - -
90A VAL* 3.4 3.8 + - - +
91A ASP* 1.3 80.8 - - - +
93A ILE* 1.3 67.1 + - - +
223A LEU* 4.0 2.9 - - - -
228A ARG* 3.3 12.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 3.7 6.0 - - - +
27A VAL* 3.4 19.7 - - + +
78A LEU* 4.4 5.4 - - + -
90A VAL* 3.6 23.6 - - + -
92A GLY* 1.3 81.1 - - - +
94A LEU* 1.3 60.7 + - - +
215A PHE* 3.7 33.9 - - + -
219A ALA* 3.6 36.8 - - + +
222A VAL* 3.8 7.2 - - + -
223A LEU* 3.8 8.1 - - + -
228A ARG 2.8 11.3 + - - +
229A LEU* 3.5 9.5 - - + -
230A VAL* 2.7 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ALA* 4.2 13.2 - - + -
15A LEU* 5.1 0.9 - - + -
18A LEU* 4.0 23.1 - - + +
27A VAL 2.8 14.0 + - - +
28A ASP* 3.7 15.8 - - - +
29A ALA* 2.8 32.9 + - - +
30A THR* 4.7 0.2 - - - -
36A HIS* 3.5 42.4 - - + +
40A ILE* 4.9 3.6 - - + -
93A ILE* 1.3 77.2 - - - +
95A ALA* 1.3 76.3 + - - +
96A ASP* 4.7 2.7 - - + +
215A PHE* 5.1 0.2 - - - -
230A VAL* 3.3 29.8 - - + +
232A ILE* 4.8 8.3 - - + -
3142A SAM 5.7 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ALA* 4.4 4.9 - - + -
30A THR* 3.4 9.2 - - + +
75A PHE* 5.1 0.4 - - + -
94A LEU* 1.3 77.5 - - - +
96A ASP* 1.3 55.5 + - - +
97A LEU* 3.7 17.7 - - + -
215A PHE* 3.8 30.5 - - + -
230A VAL 2.9 7.1 + - - +
231A VAL* 3.3 12.6 - - + +
232A ILE* 2.8 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A PRO* 5.8 0.2 - - - +
9A VAL* 5.1 1.1 + - - -
28A ASP* 5.9 0.2 - - - +
30A THR* 2.7 14.8 + - - +
36A HIS* 3.5 20.0 - - + +
94A LEU* 4.7 4.0 - - + +
95A ALA* 1.3 70.6 - - - +
97A LEU* 1.3 61.9 + - - +
232A ILE* 4.0 13.6 - - + +
234A PHE* 3.1 13.0 - - - -
271A ARG* 2.5 36.9 + - - -
3142A SAM 2.8 57.7 + - - +
----------------------------------------------------------
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