Contacts of the strand formed by residues 55 - 67 (chain C) in PDB entry 5JTP
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 VAL 55 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C GLN* 5.6 3.1 - - + +
50C GLN* 3.7 5.1 + - - -
51C LEU* 3.2 39.7 + - + +
52C ALA* 3.0 28.3 + - + +
53C ASP 3.8 11.4 - - - +
54C ASP* 1.3 74.8 - - - +
56C TYR* 1.3 61.2 + - - +
83C ILE* 3.8 25.4 - - + -
84C PHE 4.1 4.3 - - - +
85C SER* 4.8 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 56 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C SER* 4.1 1.3 - - - -
49C SER 4.2 1.8 - - - -
50C GLN* 5.1 0.4 - - - -
51C LEU* 5.1 0.2 - - - -
55C VAL* 1.3 72.0 - - - +
57C GLU* 1.3 60.4 + - - +
58C VAL* 3.4 34.9 + - + -
82C GLY 3.8 1.6 - - - +
83C ILE* 3.6 3.9 - - - +
84C PHE* 2.9 47.5 + + + +
86C ILE* 3.5 27.6 - - + -
94C MET* 2.8 28.5 + - + -
97C CYS* 3.6 23.6 - - + -
98C LEU* 3.2 28.7 + - + +
102C CYS* 5.0 1.3 - - - -
452G VAL* 3.5 30.7 - - + -
454G LEU* 3.6 23.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 57 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C TYR* 3.7 1.6 + - - -
19C LYS* 3.1 39.6 + - - -
48C SER* 3.1 9.2 - - - -
49C SER* 2.9 62.3 + - - +
51C LEU* 3.7 23.5 - - + +
55C VAL 3.9 0.6 + - - -
56C TYR* 1.3 72.2 - - - +
58C VAL* 1.3 64.8 + - - +
59C VAL* 4.4 7.4 - - + +
82C GLY 3.8 3.6 - - - -
83C ILE* 3.7 8.0 - - + +
29D PRO* 3.2 22.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 58 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C THR* 4.2 6.5 - - - +
47C ALA 3.9 3.8 - - - +
48C SER* 4.6 1.8 - - - -
56C TYR* 3.4 35.6 + - + -
57C GLU* 1.3 72.6 - - - +
59C VAL* 1.3 72.1 + - - +
81C GLY* 3.2 2.6 - - - -
82C GLY 2.8 33.8 + - - -
84C PHE* 4.0 5.6 - - + -
98C LEU* 4.5 7.4 - - + +
102C CYS* 3.5 31.6 - - + -
103C PRO* 4.0 13.9 - - + -
106C LEU* 3.5 21.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 59 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C LYS* 3.8 33.2 - - + +
45C ASP* 5.8 1.6 - - - +
46C THR* 3.3 10.6 + - - -
47C ALA* 2.9 42.5 + - + +
48C SER* 6.0 0.2 - - - -
57C GLU* 4.4 8.7 - - + +
58C VAL* 1.3 82.5 - - - +
60C LEU* 1.3 64.6 + - - +
61C ARG* 4.0 3.6 - - + +
79C GLN* 3.8 40.8 - - + +
80C GLN 3.5 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 60 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C LEU* 5.0 7.0 - - + -
45C ASP 3.3 18.4 - - - +
46C THR* 4.6 2.5 - - - +
59C VAL* 1.3 74.0 - - - +
61C ARG* 1.3 60.1 + - - +
62C VAL* 3.6 29.0 + - + +
78C VAL 3.4 3.8 - - - +
80C GLN* 2.8 42.2 + - + +
103C PRO* 3.4 41.3 - - + +
106C LEU* 4.3 11.0 - - + -
107C PHE* 3.7 28.7 - - + +
110C ALA* 4.2 3.8 - - + -
133C PHE* 5.3 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 61 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C ASP* 3.5 11.5 - - - +
44C LEU* 3.5 1.2 - - - -
45C ASP* 2.9 67.5 + - + +
59C VAL* 4.0 4.2 - - + +
60C LEU* 1.3 72.4 - - - +
62C VAL* 1.3 60.7 + - - +
63C THR* 4.0 7.4 - - - +
77C GLU* 3.0 35.2 + - - +
78C VAL 3.4 4.7 - - - -
79C GLN* 3.3 48.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 62 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C LEU* 5.5 1.3 - - + -
43C ASP 3.9 1.8 - - - -
44C LEU* 3.6 22.0 - - + -
60C LEU* 3.7 27.4 - - + +
61C ARG* 1.3 71.2 - - - +
63C THR* 1.3 66.8 + - - +
64C VAL* 4.9 2.9 - - + -
77C GLU* 3.4 2.5 - - - -
78C VAL 2.9 31.3 + - - +
107C PHE* 5.5 2.5 - - + -
110C ALA* 3.7 26.7 - - + -
111C ARG* 5.5 0.7 - - - +
114C ILE* 3.3 29.9 - - + +
128C LEU* 3.7 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 63 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C LEU* 3.3 9.0 - - - +
43C ASP* 2.9 50.9 + - + -
61C ARG* 4.0 5.9 - - - +
62C VAL* 1.3 74.7 - - - +
64C VAL* 1.3 61.6 + - - +
65C THR* 4.2 5.8 - - - +
75C LEU* 3.9 29.8 - - + -
76C CYS 3.4 15.9 - - - +
77C GLU* 3.0 29.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 64 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C VAL* 5.7 1.8 - - + -
41C LYS 4.1 1.8 - - - +
42C LEU* 4.8 6.7 - - + +
62C VAL* 4.9 2.7 - - + -
63C THR* 1.3 76.2 - - - +
65C THR* 1.3 70.0 + - - +
66C ALA* 4.8 0.7 - - + +
74C PHE* 4.0 17.3 - - + +
75C LEU* 3.6 5.7 - - - +
76C CYS* 2.9 30.9 + - + +
114C ILE* 3.6 38.6 - - + -
126C LEU* 3.6 30.3 - - + -
128C LEU* 6.4 0.2 - - + -
468G LEU* 3.7 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 65 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C GLU 3.0 3.7 - - - +
40C VAL* 3.5 4.0 - - - -
41C LYS* 2.9 60.6 + - + +
43C ASP* 5.6 2.3 + - - +
63C THR* 4.2 6.4 - - - +
64C VAL* 1.3 76.6 - - - +
66C ALA* 1.3 63.1 + - - +
67C SER* 3.8 18.2 - - - +
72C THR* 4.6 6.7 - - + +
74C PHE 4.0 3.6 - - - +
75C LEU* 3.2 27.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 66 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C PRO* 4.1 19.3 - - + -
39C GLU 3.8 4.3 - - - -
40C VAL* 4.9 2.2 - - + +
64C VAL* 4.2 3.1 - - + -
65C THR* 1.3 72.0 - - - +
67C SER* 1.3 60.4 + - - +
68C LEU 4.1 0.2 - - - -
72C THR* 3.6 4.9 - - - +
73C ALA* 2.8 34.7 + - + +
74C PHE* 3.3 41.3 + - + -
126C LEU* 5.3 4.0 - - + -
470G LEU* 5.4 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 67 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C PRO* 4.2 0.2 - - - -
39C GLU* 2.8 46.9 + - - +
41C LYS* 6.1 0.7 - - - -
65C THR* 3.8 14.9 - - - +
66C ALA* 1.3 72.5 - - - +
68C LEU* 1.3 57.0 + - - +
69C GLY 3.0 22.7 + - - -
70C GLU 5.5 1.1 - - - -
71C GLU 3.5 8.3 - - - -
72C THR* 3.6 16.7 + - - +
----------------------------------------------------------
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