Contacts of the strand formed by residues 65 - 71 (chain A) in PDB entry 1D5R
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 TYR 65 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A VAL* 4.6 2.4 - - - +
57A LEU* 3.7 40.0 - - + +
58A ASP* 3.3 28.0 + - - -
61A HIS* 3.1 35.7 - - + -
62A LYS 3.8 5.8 - - - -
63A ASN* 3.8 1.0 - - - -
64A HIS* 1.3 81.0 - - - +
66A LYS* 1.3 56.8 + - - +
67A ILE* 4.0 11.4 - - + -
81A PHE* 4.0 9.8 - + - +
82A ASN* 3.3 25.4 + - - -
83A CYS* 2.8 62.4 - - + +
111A TRP* 3.5 9.7 - - - -
119A VAL* 3.3 13.9 - - + +
120A ALA* 5.8 0.4 - - - -
121A ALA* 6.0 1.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A TYR* 1.3 75.4 - - - +
67A ILE* 1.3 68.5 + - - +
68A TYR* 3.6 28.2 + - + +
83A CYS* 4.2 0.4 - - - -
84A ARG* 3.4 35.4 - - + +
86A ALA* 4.0 17.2 - - - +
107A ASP* 2.9 28.6 + - - -
111A TRP* 3.5 42.5 - - + +
119A VAL 3.1 6.7 + - - -
120A ALA* 3.5 5.0 - - - -
121A ALA 3.2 20.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A MET* 5.2 2.5 - - - -
38A PRO* 5.6 0.2 - - + -
57A LEU* 3.7 23.6 - - + -
65A TYR* 4.0 6.7 - - + -
66A LYS* 1.3 77.9 - - - +
68A TYR* 1.3 68.8 + - - +
69A ASN 4.8 0.2 - - - +
76A TYR* 4.0 11.4 - - - +
81A PHE* 3.5 28.5 - - + -
83A CYS* 3.7 9.2 - - - -
84A ARG 3.1 10.0 + - - +
85A VAL* 3.4 9.9 - - + -
86A ALA 2.8 26.2 + - - -
121A ALA* 3.4 35.0 - - + +
123A HIS* 3.7 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LYS* 3.6 38.3 - - + +
67A ILE* 1.3 76.9 - - - +
69A ASN* 1.3 60.0 + - - +
70A LEU* 3.7 3.8 + - + -
86A ALA* 3.3 19.1 - - + +
88A TYR* 4.0 8.3 - + + -
104A PHE* 3.4 29.8 - + + -
107A ASP* 2.7 40.2 + - + -
108A LEU* 3.4 21.4 - - + -
111A TRP* 4.2 4.7 - + - +
120A ALA* 4.0 15.0 - - + -
121A ALA 3.1 7.4 + - - -
122A ILE* 3.9 29.2 - - + +
123A HIS* 3.1 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PHE* 5.1 0.4 - - - -
67A ILE* 4.2 1.2 - - - +
68A TYR* 1.3 69.5 - - - +
70A LEU* 1.3 59.5 + - - +
71A CYS* 2.9 39.3 + - - +
74A ARG 4.2 1.4 + - - -
75A HIS* 3.3 35.9 + - - +
76A TYR* 4.0 13.2 - - + +
85A VAL* 4.7 4.9 - - + +
86A ALA 2.8 12.8 + - - +
87A GLN* 3.6 11.8 - - + +
88A TYR 3.0 24.0 + - - +
89A PRO* 3.8 2.8 - - - +
123A HIS* 2.8 37.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A TYR* 4.4 3.4 - - + +
69A ASN* 1.3 73.2 - - - +
71A CYS* 1.3 59.2 - - - +
72A ALA 3.3 0.9 + - - -
88A TYR* 3.2 33.4 - - + +
89A PRO* 3.7 3.1 - - - -
90A PHE* 3.1 43.2 + - + +
104A PHE* 4.7 8.3 - - + -
122A ILE* 3.6 20.6 - - + -
123A HIS 3.1 13.4 + - - +
124A CYS* 4.4 6.3 - - + -
130A ARG* 3.6 17.8 + - + +
131A THR* 3.6 37.5 - - - +
134A MET* 3.9 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PHE* 3.8 15.0 - - + -
46A TYR* 5.9 1.8 - - - -
69A ASN* 2.9 25.7 + - - +
70A LEU* 1.3 74.3 - - - +
72A ALA* 1.3 65.6 + - - +
73A GLU* 3.4 6.2 + - + +
74A ARG* 3.5 24.8 - - - +
75A HIS* 5.1 1.9 - - - -
89A PRO* 3.8 6.9 - - - +
124A CYS* 3.2 39.3 - - - -
125A LYS* 3.7 6.3 - - - -
130A ARG* 4.1 11.4 - - - +
----------------------------------------------------------
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