Contacts of the strand formed by residues 67 - 77 (chain A) in PDB entry 5JPM
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 PRO 67 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A PHE* 3.6 33.2 - - + -
58A LEU 3.7 4.9 - - - +
59A ARG* 3.7 5.8 - - + -
65A ASN 3.4 8.7 - - - +
66A VAL* 1.3 100.4 - - + +
68A CYS* 1.3 65.2 + - - +
69A SER* 3.5 5.6 + - - +
71A LYS* 4.5 17.0 - - - +
97A CYS* 3.6 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A PHE* 4.5 1.9 - - - +
58A LEU* 2.6 44.6 + - + +
59A ARG* 4.0 7.2 - - - -
67A PRO* 1.3 70.4 - - - +
69A SER* 1.3 64.8 + - - +
70A PRO* 3.1 18.6 - - + +
89A VAL* 6.1 3.4 - - + -
93A ASP 4.6 6.5 - - - +
94A ALA* 5.5 2.0 - - - -
97A CYS* 2.0 49.1 - - + -
99A LEU* 4.0 18.8 - - - -
108A VAL* 4.7 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A PRO* 3.5 7.8 + - - +
68A CYS* 1.3 68.7 - - - +
70A PRO* 1.3 72.0 - - - +
71A LYS* 3.3 17.0 + - - +
93A ASP* 3.1 39.1 + - - +
96A SER* 5.7 1.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A PHE* 3.4 13.0 - - - +
68A CYS* 3.1 14.3 - - + +
69A SER* 1.3 91.9 - - - +
71A LYS* 1.3 59.7 + - - +
87A LEU* 3.3 26.7 - - + +
88A GLN* 4.7 10.3 - - + +
89A VAL* 4.1 11.9 - - + +
90A PRO* 3.5 33.0 - - + -
93A ASP* 4.6 2.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A SER* 4.5 14.1 - - - +
56A VAL 3.9 4.7 - - - +
57A PHE* 3.6 44.7 - - + -
67A PRO* 4.5 17.1 - - - +
69A SER 3.3 14.5 + - - +
70A PRO* 1.3 73.9 - - - +
72A VAL* 1.3 59.9 + - - +
73A ASP* 4.0 8.3 + - - +
87A LEU* 4.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A VAL* 6.0 0.7 - - + -
55A SER* 3.7 0.2 - - - -
56A VAL* 3.2 50.2 + - + +
70A PRO 4.2 0.6 - - - -
71A LYS* 1.3 73.0 - - - +
73A ASP* 1.3 72.8 + - - +
85A LEU* 4.0 29.6 - - + -
86A SER 4.5 13.7 - - - +
87A LEU* 4.1 22.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A GLY 3.3 8.3 - - - +
55A SER* 2.5 29.4 + - - -
71A LYS* 4.0 9.7 + - - +
72A VAL* 1.3 86.1 - - - +
74A PHE* 1.3 63.6 + - - +
75A THR* 6.1 0.2 - - - +
85A LEU* 4.4 5.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 4.8 9.6 - - + -
41A VAL* 4.4 18.2 - - + -
52A VAL* 5.2 5.2 - - + -
53A LYS* 3.3 8.2 - - - +
54A GLY* 2.9 54.6 + - - +
55A SER* 3.4 31.0 - - - -
56A VAL* 3.8 10.5 - - + -
73A ASP* 1.3 77.3 - - - +
75A THR* 1.3 64.1 + - - +
76A LEU* 4.0 30.5 - - + -
83A ALA* 4.7 2.2 - - + -
85A LEU* 4.0 28.0 - - + -
112A ALA* 4.4 11.9 - - + -
113A HIS 4.3 4.3 - - - -
114A SER* 4.4 11.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A VAL* 4.1 18.8 - - + -
52A VAL 3.4 10.1 - - - +
53A LYS* 4.2 9.8 - - + +
73A ASP* 6.1 0.2 - - - +
74A PHE* 1.3 75.6 + - - +
76A LEU* 1.3 67.8 + - - +
77A SER* 4.2 5.8 + - - +
80A ARG* 4.8 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 4.0 11.4 - - + -
41A VAL* 3.8 28.9 - - + +
43A LEU* 3.7 28.0 - - + +
50A GLN 4.3 0.2 - - - +
51A VAL* 3.4 4.0 - - - +
52A VAL* 2.8 52.7 + - + +
74A PHE* 4.0 16.2 - - + -
75A THR* 1.3 79.5 - - - +
77A SER* 1.3 61.3 + - - +
80A ARG 3.9 5.2 - - - +
81A ASP 4.5 2.7 - - - +
82A PHE 4.0 15.7 - - - +
83A ALA* 3.7 30.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LEU* 4.5 4.4 - - - +
46A VAL* 5.5 0.9 - - - -
50A GLN 3.6 8.5 - - - -
51A VAL* 3.8 18.3 - - - +
75A THR* 4.2 6.7 + - - +
76A LEU* 1.3 75.5 + - - +
78A SER* 1.3 63.6 + - - +
79A GLU* 3.1 25.1 + - - -
80A ARG* 3.1 34.9 + - - +
81A ASP* 3.1 8.5 + - - +
----------------------------------------------------------
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