Contacts of the strand formed by residues 82 - 89 (chain A) in PDB entry 5F70
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 GLY 82 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ASP 3.4 2.3 + - - -
81A SER* 1.3 75.5 - - - +
83A VAL* 1.3 66.2 + - - -
84A TYR* 3.6 8.5 - - - -
100A THR* 3.8 2.6 - - - -
101A VAL 2.8 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ARG* 3.7 1.4 - - - +
31A GLY* 2.7 32.4 + - - -
32A SER* 3.8 32.5 - - - +
82A GLY* 1.3 74.8 - - - -
84A TYR* 1.3 65.9 + - - +
98A LYS* 3.7 45.8 - - + +
99A ILE 3.6 4.9 - - - +
100A THR* 4.2 11.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 3.6 25.1 - - + -
28A TRP* 4.3 6.1 - + + -
29A ASN 3.2 16.2 - - - +
30A ARG* 3.6 35.7 + - + -
31A GLY 3.5 3.1 - - - -
42A ILE* 3.9 20.0 - - + -
58A TYR* 4.8 2.3 + - - -
71A LEU* 4.6 2.7 - - + -
73A ILE* 4.0 20.6 - - + +
80A ASP* 2.6 38.1 + - - +
82A GLY* 3.6 12.1 - - - -
83A VAL* 1.3 81.1 - - - +
85A CYS* 1.3 63.9 + - - +
98A LYS* 3.6 3.1 - - - -
99A ILE* 2.8 32.5 + - - +
101A VAL* 3.6 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A CYS 3.6 0.2 - - - +
28A TRP* 3.4 9.6 - - - -
29A ASN* 2.8 47.8 + - + +
31A GLY 3.6 0.9 + - - +
33A CYS* 2.0 60.6 - - - +
34A SER 4.9 1.3 - - - -
38A CYS* 4.7 0.6 - - - -
84A TYR* 1.3 75.7 - - - +
86A CYS* 1.3 65.6 + - - +
87A ARG* 3.6 8.5 + - - -
96A ASP* 3.6 18.6 - - - -
97A MET 3.5 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A CYS* 2.0 49.3 - - + -
26A MET* 3.4 22.9 - - - -
27A CYS 3.9 2.5 - - - -
28A TRP* 3.6 24.0 - - + -
69A VAL* 3.8 4.5 - - - -
85A CYS* 1.3 72.5 - - - +
87A ARG* 1.3 57.7 + - - +
88A VAL* 4.2 5.1 - - - +
95A ASN 3.6 1.6 - - - +
96A ASP* 3.2 5.0 - - - -
97A MET* 3.0 37.1 + - + +
99A ILE* 5.1 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A MET* 3.2 3.9 - - - +
27A CYS* 2.9 49.3 + - - +
34A SER 3.2 25.3 + - - -
35A LEU 3.3 12.5 + - - -
36A PHE* 3.1 24.4 + - - +
37A THR* 3.4 30.9 + - - +
38A CYS* 3.9 7.9 - - - -
85A CYS* 3.6 6.5 + - - -
86A CYS* 1.3 74.0 - - - +
88A VAL* 1.3 61.6 + - - +
89A GLU* 2.8 33.3 + - + +
94A PHE* 3.6 39.2 - - + +
95A ASN 3.6 6.1 - - - +
96A ASP* 4.3 7.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A CYS* 4.5 0.9 - - - -
19A TYR* 3.7 43.3 - - + -
24A THR* 3.5 24.2 - - + -
25A SER 4.2 1.8 - - - +
26A MET* 3.9 13.9 - - + -
69A VAL* 4.5 0.2 - - + -
86A CYS* 4.2 17.5 - - - +
87A ARG* 1.3 74.5 - - - +
89A GLU* 1.3 62.9 + - - +
90A HIS* 3.5 17.3 + - - +
94A PHE* 3.2 5.9 - - - +
95A ASN* 2.8 40.3 + - + +
97A MET* 5.6 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A THR* 2.7 28.5 + - - +
25A SER* 3.0 22.5 + - - +
26A MET* 5.4 3.0 - - - -
27A CYS* 5.0 5.9 - - - -
36A PHE 4.1 7.1 - - - +
37A THR* 4.2 6.4 + - - -
44A TRP* 4.4 15.7 - - - -
87A ARG* 2.8 46.8 + - + +
88A VAL* 1.3 72.8 - - - +
90A HIS* 1.3 59.4 + - - +
93A TRP 4.1 3.6 - - - +
94A PHE* 4.3 4.7 - - + -
----------------------------------------------------------
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