Contacts of the strand formed by residues 62 - 68 (chain A) in PDB entry 1J7D
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 ILE 62 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A MET* 3.5 34.5 - - + -
50A ILE 3.7 2.7 - - - -
51A ILE* 3.7 22.4 - - + -
60A ASN 5.7 1.3 - - - +
61A ARG* 1.3 75.8 - - - +
63A TYR* 1.3 64.9 + - - +
64A SER* 4.0 6.1 + - - +
84A THR* 3.7 14.7 + - - +
139A GLU* 4.9 2.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A MET* 3.2 7.4 - - - +
50A ILE* 2.8 50.2 + - + +
52A GLY* 4.0 4.7 - - - -
57A ASN 4.6 0.3 + - - -
58A TYR* 3.4 42.5 - + + -
61A ARG* 3.3 45.5 + - + -
62A ILE* 1.3 73.7 - - - +
64A SER* 1.3 60.2 + - - +
65A LEU* 3.6 1.9 - - + +
82A PHE* 4.0 24.2 - + + -
84A THR* 3.4 22.4 - - + -
85A LYS 3.7 18.4 - - - -
86A ILE* 3.8 20.0 - - + -
126A MET* 4.2 9.9 - - + -
136A GLN* 4.3 4.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A THR* 5.2 8.3 - - - +
48A GLY 3.3 7.8 + - - -
49A MET* 5.5 2.3 - - - +
62A ILE* 4.0 7.6 + - - +
63A TYR* 1.3 74.8 - - - +
65A LEU* 1.3 64.5 + - - +
82A PHE* 3.8 1.7 - - - +
83A VAL* 2.9 34.5 + - - -
84A THR* 2.9 18.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A THR* 3.5 8.8 - - - +
48A GLY* 2.8 42.0 + - - +
50A ILE* 4.0 20.4 - - + -
63A TYR 3.6 17.3 - - - +
64A SER* 1.3 81.1 - - - +
66A LYS* 1.3 69.9 + - - +
67A VAL* 4.8 2.7 - - + -
80A VAL* 3.7 15.7 - - + -
81A ARG 3.2 9.6 - - - +
82A PHE* 3.7 30.1 - - + -
83A VAL* 4.1 3.5 - - - +
119A LEU* 4.2 7.9 - - + -
122A LEU* 3.7 30.1 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
36A GLU* 3.5 31.9 + - - +
46A TRP 3.4 4.0 - - - +
47A THR* 5.8 0.2 - - - -
65A LEU* 1.3 75.2 - - - +
67A VAL* 1.3 63.4 + - - +
68A GLU 4.2 0.2 - - - -
79A SER 3.8 0.5 - - - +
80A VAL* 3.4 3.5 - - - +
81A ARG* 2.7 81.4 + - + +
83A VAL* 3.7 23.5 - - + +
145A ASN 3.5 13.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A THR 3.5 1.9 - - - +
45A ARG* 3.7 1.3 - - - -
46A TRP* 2.7 47.8 + - + +
48A GLY* 4.8 9.0 - - - +
65A LEU* 4.8 0.9 - - + -
66A LYS* 1.3 80.5 - - - +
68A GLU* 1.3 62.1 + - - +
69A CYS* 4.3 3.8 - - - -
78A PRO* 3.8 28.9 - - + -
79A SER 3.3 4.9 - - - +
80A VAL* 4.3 18.2 - - + -
115A ILE* 4.1 33.4 - - + -
118A VAL* 5.9 2.2 - - + -
119A LEU* 4.6 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A THR* 3.4 27.1 - - + +
45A ARG* 4.0 20.8 + - - +
66A LYS 4.2 1.0 - - - -
67A VAL* 1.3 72.7 - - - +
69A CYS* 1.3 66.6 + - - +
70A GLY* 3.6 5.3 + - - +
78A PRO* 3.2 5.5 - - - +
79A SER* 2.8 52.2 + - - +
----------------------------------------------------------
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