Contacts of the strand formed by residues 55 - 68 (chain D) in PDB entry 5JTO
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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D GLN* 3.4 25.8 - - - +
50D GLN* 3.5 3.6 - - - +
51D LEU* 3.0 37.2 + - + -
52D ALA* 3.0 26.5 + - + +
53D ASP 3.0 15.1 - - - +
54D ASP* 1.3 79.4 - - - +
56D TYR* 1.3 62.7 + - - +
83D ILE* 3.6 30.7 - - + -
84D PHE 3.4 6.1 - - - +
85D SER* 4.6 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 56 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D SER 4.3 2.5 - - - -
50D GLN* 3.5 36.9 + - + -
51D LEU* 4.8 1.8 - - - -
54D ASP* 3.8 14.3 - - - -
55D VAL* 1.3 76.2 - - - +
57D GLU* 1.3 60.6 + - - +
58D VAL 4.0 0.2 + - - -
84D PHE* 3.0 35.2 + - - +
86D ILE* 3.3 54.4 - - + +
274G GLN* 3.0 35.1 + - + +
277G LEU* 3.4 33.6 - - + +
278G LEU* 3.7 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 57 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C PRO* 3.4 11.5 - - - +
17D TYR* 2.9 26.9 + - - -
19D LYS* 2.8 31.0 + - - +
48D SER* 3.6 6.4 - - - -
49D SER* 3.2 40.8 + - - +
51D LEU* 3.7 20.0 - - + +
56D TYR* 1.3 72.1 - - - +
58D VAL* 1.3 61.3 + - - +
59D VAL* 3.6 19.7 - - + +
82D GLY 3.4 22.7 - - - +
83D ILE* 4.4 0.7 - - - +
278G LEU* 3.5 16.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 58 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D THR* 4.5 8.1 - - - +
47D ALA 4.0 3.1 - - - +
56D TYR 4.0 0.2 + - - -
57D GLU* 1.3 73.7 - - - +
59D VAL* 1.3 67.9 + - - +
60D LEU* 5.3 0.9 - - + -
82D GLY 3.0 27.6 + - - +
84D PHE* 3.8 24.0 - - + -
86D ILE* 4.5 10.8 - - + -
98D LEU* 5.1 13.9 - - + +
102D CYS* 4.3 20.9 - - + -
103D PRO* 4.9 11.0 - - + -
106D LEU* 3.2 20.1 - - + +
278G LEU* 3.8 20.6 - - + -
281G PHE* 5.3 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 59 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D LYS* 3.7 20.4 - - + +
46D THR* 2.9 23.6 + - - -
47D ALA* 2.9 41.3 + - + +
57D GLU* 3.6 27.1 - - + +
58D VAL* 1.3 74.1 - - - +
60D LEU* 1.3 63.3 + - - +
61D ARG* 4.1 1.3 - - + +
79D GLN* 3.8 35.9 - - + +
80D GLN 3.7 3.1 - - - -
81D GLY* 3.8 11.7 - - - +
106D LEU* 4.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 60 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D LEU* 5.0 11.2 - - + -
45D ASP 3.8 11.9 - - - +
46D THR* 4.3 2.7 - - - -
58D VAL* 5.3 1.3 - - + -
59D VAL* 1.3 74.9 - - - +
61D ARG* 1.3 68.2 + - - +
62D VAL* 3.7 25.6 + - + -
78D VAL 3.4 2.6 - - - +
79D GLN* 4.4 0.7 - - - -
80D GLN* 3.0 38.3 + - + +
103D PRO* 3.8 31.2 - - + +
106D LEU* 3.8 24.7 - - + +
107D PHE* 4.9 9.6 - - + -
110D ALA* 4.6 3.3 - - + +
133D PHE* 6.1 2.5 - - + -
281G PHE* 4.1 22.4 - - + -
286G MET* 4.9 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 61 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D ASP 4.2 0.2 - - - +
44D LEU* 3.6 5.2 - - - -
45D ASP* 2.8 71.5 + - - +
46D THR* 4.6 1.5 + - - +
47D ALA* 5.8 4.6 - - - +
59D VAL* 4.1 2.3 - - + +
60D LEU* 1.3 74.3 - - - +
62D VAL* 1.3 59.8 + - - +
63D THR* 3.7 9.1 + - - +
77D GLU* 2.9 57.6 + - + -
78D VAL 3.2 6.3 - - - +
79D GLN* 2.9 48.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 62 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D LEU* 3.8 23.3 - - + -
43D ASP 4.0 2.5 - - - -
44D LEU* 5.0 3.1 - - + +
60D LEU* 3.7 22.9 + - + -
61D ARG* 1.3 72.1 - - - +
63D THR* 1.3 62.3 + - - +
64D VAL* 4.2 6.7 - - + -
77D GLU* 3.4 2.3 - - - -
78D VAL 3.1 31.3 + - - +
107D PHE* 3.9 23.8 - - + -
110D ALA* 3.8 22.7 - - + -
111D ARG* 5.3 0.7 - - - +
114D ILE* 3.5 27.8 - - + +
128D LEU* 4.9 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 63 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D LYS 3.8 0.2 - - - +
42D LEU* 3.4 9.7 - - - +
43D ASP* 2.9 52.9 + - + +
44D LEU 5.8 0.2 - - - -
45D ASP 5.7 0.2 + - - -
61D ARG* 3.7 10.4 - - - +
62D VAL* 1.3 73.4 - - - +
64D VAL* 1.3 64.3 + - - +
65D THR* 4.1 15.5 - - - +
76D CYS 3.5 12.1 - - - +
77D GLU* 3.2 34.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 64 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D VAL* 5.0 3.4 - - + -
41D LYS 3.6 6.7 - - - +
42D LEU* 5.1 3.6 - - + -
62D VAL* 4.2 7.0 - - + -
63D THR* 1.3 76.7 - - - +
65D THR* 1.3 63.5 + - - +
66D ALA 4.0 0.3 + - - -
74D PHE* 4.2 17.9 - - + +
75D LEU* 3.7 3.1 - - - -
76D CYS* 2.9 46.6 + - + +
114D ILE* 3.7 34.1 - - + -
126D LEU* 3.5 29.2 - - + -
128D LEU* 4.7 14.6 - - + -
290G TRP* 5.1 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 65 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D GLU 4.1 0.3 - - - +
40D VAL* 3.7 1.3 - - - -
41D LYS* 2.9 52.1 + - + +
43D ASP* 4.4 6.6 + - - -
63D THR* 4.1 14.6 - - - +
64D VAL* 1.3 73.3 + - - +
66D ALA* 1.3 62.9 + - - +
67D SER* 4.1 5.4 + - - +
72D THR* 5.7 1.3 - - + +
75D LEU* 3.6 25.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 66 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D PRO* 4.4 4.7 - - + -
39D GLU 3.8 4.3 - - - -
40D VAL* 4.3 13.0 - - + +
64D VAL 4.0 1.8 + - - -
65D THR* 1.3 75.0 - - - +
67D SER* 1.3 60.7 + - - +
72D THR* 3.4 8.5 - - - +
73D ALA* 3.0 35.4 + - + -
74D PHE* 3.0 46.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 67 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D GLU* 3.0 42.6 + - - +
65D THR* 4.1 6.7 + - - +
66D ALA* 1.3 75.0 - - - +
68D LEU* 1.3 60.3 + - - +
71D GLU 3.5 17.0 - - - -
72D THR* 4.4 2.5 - - - -
73D ALA* 3.9 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 68 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D VAL* 3.7 16.6 - - + -
34D LYS* 3.5 26.8 + - + +
35D ASP* 3.1 22.2 - - - +
36D TRP* 3.2 27.8 - - + +
37D GLN 3.8 8.7 - - - +
38D PRO* 3.7 23.8 - - + -
39D GLU 4.6 0.9 - - - +
67D SER* 1.3 74.1 - - - +
69D GLY* 1.3 64.7 + - - +
70D GLU 3.4 2.3 + - - -
71D GLU* 3.0 22.9 + - - +
73D ALA* 3.6 23.9 - - + +
----------------------------------------------------------
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