Contacts of the strand formed by residues 88 - 96 (chain A) in PDB entry 3ZXR
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 88 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A VAL* 4.3 3.8 - - - -
20A TYR* 3.3 20.5 - - + +
22A ASP 3.9 8.7 - - - +
80A ILE* 3.5 7.9 - - - +
81A ASP* 2.8 35.6 + - - +
84A ARG* 3.3 46.3 + - - +
86A ALA 2.6 21.6 + - - -
87A LYS* 1.3 76.4 + - - +
89A LEU* 1.3 71.7 + - - +
90A ASN* 3.9 8.1 - - - +
200B ASP* 4.3 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL* 3.8 30.5 - - + +
12A LEU* 3.9 16.6 - - + -
13A ALA* 4.2 21.1 - - + +
18A VAL* 3.8 19.2 - - + +
20A TYR 3.0 7.4 + - - +
21A VAL* 3.3 10.3 - - + +
22A ASP 2.8 25.7 + - - -
42A PHE* 4.4 4.0 - - + -
78A ALA* 4.1 2.0 - - + -
79A ARG 3.4 32.8 - - - +
80A ILE* 3.7 13.5 - - + -
88A THR* 1.3 74.0 - - - +
90A ASN* 1.3 64.2 + - - +
91A ILE* 3.9 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ASP* 3.3 22.4 - - - +
24A ARG* 3.6 33.0 + - - +
77A THR 3.6 2.6 - - - +
78A ALA* 3.2 5.7 - - - +
79A ARG* 2.7 43.1 + - + +
80A ILE 4.9 0.4 - - - -
81A ASP* 3.0 43.9 + - - +
82A PRO* 5.1 0.6 - - - +
84A ARG* 4.9 0.3 + - - -
88A THR* 3.9 2.3 - - - +
89A LEU* 1.3 73.5 - - - +
91A ILE* 1.3 61.7 + - - +
92A ASN* 5.8 0.4 - - - +
244A LEU* 4.9 9.1 - - + +
247A TYR* 4.1 5.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL* 3.8 12.3 - - + -
21A VAL* 3.8 15.0 - - + -
22A ASP 3.0 9.1 + - - +
24A ARG* 2.8 26.1 + - - +
42A PHE* 3.4 37.9 - - + -
47A PHE* 5.6 1.1 - - + -
73A PRO* 4.2 5.6 - - + -
74A ASP 3.8 15.7 - - - +
75A PRO* 4.9 1.8 - - + -
77A THR* 3.8 10.1 - - - +
78A ALA* 4.0 14.6 - - + +
89A LEU* 3.9 8.3 - - + -
90A ASN* 1.3 81.2 - - - +
92A ASN* 1.3 76.0 + - - +
93A PHE* 3.3 19.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ARG* 3.3 24.9 - - - +
32A MET* 3.9 15.0 - - - +
74A ASP* 2.9 27.0 + - - +
77A THR* 2.7 30.2 + - + +
90A ASN* 5.6 0.9 - - - +
91A ILE* 1.3 75.4 - - - +
93A PHE* 1.3 63.6 + - - +
109A ARG* 4.0 14.3 - - - +
240A ASP* 3.0 34.2 + - - +
243A GLN* 5.6 1.2 - - - +
244A LEU* 6.3 0.4 - - - +
377A TYR* 3.9 6.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A VAL* 5.6 0.2 - - + -
23A VAL* 3.7 38.8 - - + -
24A ARG 2.6 13.8 + - - +
25A PHE* 3.9 11.8 - - - +
42A PHE* 5.4 2.0 - + - -
46A VAL* 4.0 18.6 - - + -
51A LEU* 4.2 6.5 - - + -
71A LEU* 3.6 34.3 - - + -
72A LEU 3.3 9.0 - - - +
73A PRO* 3.2 40.8 - - + -
74A ASP 4.4 0.4 - - - +
91A ILE* 3.3 37.5 - - + -
92A ASN* 1.3 79.6 - - - +
94A PHE* 1.3 61.2 + - - +
95A VAL 4.2 0.2 + - - -
107A ASP* 4.4 1.9 - - - +
109A ARG* 3.3 24.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A LEU* 3.3 5.8 - - - -
72A LEU* 2.8 40.0 + - + +
73A PRO 4.7 3.1 - - - -
74A ASP* 3.3 34.5 - - + -
93A PHE* 1.3 73.2 - - - +
95A VAL* 1.3 61.0 + - - +
96A HIS* 3.3 23.3 - - + +
107A ASP* 3.3 13.9 - - - +
109A ARG* 3.4 46.4 - - + -
113A ARG* 3.2 52.0 - - + +
236A LEU* 4.4 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A PHE* 4.1 12.3 - - + -
26A CYS 5.2 0.4 - - - +
53A PHE* 3.9 15.0 - - + -
61A PHE* 4.0 20.6 - - + -
69A MET* 3.7 15.0 - - + -
70A LEU 3.4 9.4 - - - +
71A LEU* 3.8 17.0 - - + -
94A PHE* 1.3 73.5 - - - +
96A HIS* 1.3 64.3 + - - +
103A PRO* 3.8 1.4 - - - +
104A TYR* 2.9 44.8 + - + +
107A ASP* 2.7 36.7 + - + +
113A ARG* 5.3 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A MET* 3.6 10.0 - - - +
70A LEU* 2.8 50.7 + - + +
72A LEU* 3.6 30.1 - - + +
94A PHE* 3.3 40.8 - - + +
95A VAL* 1.3 76.8 - - - +
97A ASP* 1.3 65.8 + - - +
98A PRO 3.4 0.3 - - - -
101A LEU 2.8 25.6 + - - +
102A GLU 3.3 9.8 - - - +
103A PRO* 3.9 22.2 - - + -
104A TYR 4.2 0.7 - - - +
113A ARG* 3.9 9.3 + - - -
----------------------------------------------------------
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