Contacts of the strand formed by residues 85 - 91 (chain C) in PDB entry 1XIW
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 ALA 85 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C GLN* 3.6 29.8 - - + +
39C GLN 3.2 18.2 - - - +
40C LYS* 4.3 5.6 - - + +
41C PRO* 4.9 1.8 - - - -
83C ASP 3.0 8.3 + - - +
84C ILE* 1.3 76.1 - - - +
86C THR* 1.3 62.1 + - - +
87C TYR* 3.7 4.8 - - + +
104C LYS* 3.6 12.6 - - - +
105C LEU* 2.8 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 86 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C TYR 3.8 0.5 - - - +
38C GLN* 3.6 1.9 - - - -
39C GLN* 2.8 40.8 + - - +
85C ALA* 1.3 73.9 - - - +
87C TYR* 1.3 63.4 + - - +
88C PHE* 3.6 31.7 - - + -
101C GLY 5.1 1.1 - - - +
102C GLY* 4.1 2.9 - - - -
103C THR 3.4 24.2 - - - +
104C LYS* 2.8 27.7 - - + +
43D LYS* 6.4 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 87 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C GLN* 2.9 9.8 + - - -
22C ILE* 3.8 32.8 - - + -
36C TRP* 4.8 4.0 - - + -
37C TYR 3.4 4.9 - - - +
38C GLN* 3.1 38.7 + - + -
48C LEU* 3.6 29.8 - - + -
63C PHE* 3.9 10.9 - + - -
74C LEU* 3.8 13.0 - - + -
76C ILE* 3.7 7.2 - - + -
83C ASP* 2.6 36.9 + - - +
85C ALA 3.7 15.3 - - - -
86C THR* 1.3 73.2 - - - +
88C PHE* 1.3 60.6 - - - +
102C GLY* 3.1 1.2 - - - -
103C THR 2.8 39.6 + - - +
105C LEU* 3.8 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 88 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C GLN* 3.4 2.9 - - - -
35C ASN 3.7 0.2 - - - +
36C TRP* 3.3 8.8 - - - -
37C TYR* 2.9 45.1 + - + +
39C GLN* 3.5 36.8 - - + -
45C VAL* 6.2 1.1 - - + -
86C THR* 3.6 27.8 - - + -
87C TYR* 1.3 76.2 - - - +
89C CYS* 1.3 65.7 + - - +
99C PHE* 4.8 4.7 - - + -
100C ALA 3.6 10.5 - - - -
101C GLY 3.6 18.6 - - - -
102C GLY* 3.4 16.4 - - - -
39D GLN* 3.8 3.4 - - - -
42D GLY 5.6 0.4 - - - -
43D LYS* 3.3 29.8 - - + -
45D LEU* 3.6 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 89 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C MET* 4.1 4.3 - - - -
7C GLN* 3.2 12.1 + - - -
24C CYS* 2.1 49.1 - - + -
34C LEU* 3.9 5.4 - - + -
35C ASN 3.1 9.2 - - - +
36C TRP* 3.7 18.3 - - + -
88C PHE* 1.3 75.4 - - - +
90C GLN* 1.3 62.9 + - - +
99C PHE* 3.4 5.6 - - - +
100C ALA* 3.1 45.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 90 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C MET* 4.9 0.9 - - - -
33C TYR 3.9 0.2 - - - +
34C LEU* 3.4 6.8 - - - +
35C ASN* 2.8 45.2 + - - +
37C TYR* 2.6 35.8 + - + -
89C CYS* 1.3 76.9 - - - +
91C GLN* 1.3 84.0 + - - +
92C GLY* 3.7 1.4 - - - -
97C TRP* 4.0 7.4 - - + +
98C THR 3.2 16.6 - - - +
99C PHE* 3.5 32.3 - - + +
107D TRP 3.0 22.3 + - - +
109D PHE* 3.5 15.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 91 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C ILE* 3.7 21.2 - - + +
5C MET* 3.7 24.7 - - - +
30C ILE* 3.8 20.6 - - + -
33C TYR 3.3 5.2 - - - +
34C LEU* 4.3 0.6 - - - +
90C GLN* 1.3 84.9 + - - +
92C GLY* 1.3 58.3 + - - +
93C ASN* 2.8 32.2 + - - +
94C THR 2.9 29.9 + - - -
96C PRO 3.1 15.8 + - - -
97C TRP* 3.8 2.8 - - - -
98C THR* 2.9 42.5 + - - +
----------------------------------------------------------
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