Contacts of the strand formed by residues 39 - 52 (chain D) 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 GLU 39 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D TRP* 3.6 28.2 - - + -
37D GLN 3.7 0.4 + - - -
38D PRO* 1.3 67.6 - - - +
40D VAL* 1.3 61.3 + - - +
65D THR 4.0 1.0 - - - +
66D ALA* 3.3 2.4 - - - -
67D SER* 2.9 44.1 + - - +
69D GLY* 4.3 19.2 + - - +
470H LEU* 4.1 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 40 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D GLN* 5.1 1.8 - - - +
38D PRO 3.1 16.4 + - - +
39D GLU* 1.3 73.4 - - - +
41D LYS* 1.3 60.9 + - - +
42D LEU* 4.2 2.0 - - + +
64D VAL* 4.1 13.9 - - + -
65D THR 3.6 3.1 - - - -
66D ALA* 3.8 17.5 - - + -
74D PHE* 3.9 17.3 - - + -
126D LEU* 4.8 5.4 - - + -
465H LYS* 3.9 1.2 - - - +
466H ALA* 3.2 50.9 + - - +
467H ALA* 4.4 6.7 - - + +
468H LEU* 3.8 31.0 - - + -
470H LEU* 4.6 3.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 41 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D VAL* 1.3 76.0 - - - +
42D LEU* 1.3 88.7 + - - +
43D ASP* 3.0 32.8 + - - +
63D THR 4.0 0.2 - - - +
64D VAL* 3.5 2.7 - - - -
65D THR* 2.9 42.9 + - + +
463H THR* 3.0 30.3 + - - +
464H MET 3.5 17.7 - - - +
465H LYS* 3.8 35.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 42 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D VAL* 4.2 2.8 - - + +
41D LYS* 1.3 82.2 + - - +
43D ASP* 1.3 62.6 + - - +
44D LEU* 4.7 11.4 - - + +
62D VAL* 6.0 2.2 - - + -
63D THR 3.2 11.2 - - - +
64D VAL* 4.5 9.2 - - + +
128D LEU* 3.6 39.0 - - + -
462H TYR* 3.5 28.7 - - + +
463H THR* 2.7 36.9 - - - +
464H MET* 3.5 26.7 + - + +
467H ALA* 3.8 16.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 43 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D LYS* 3.0 40.0 + - - +
42D LEU* 1.3 71.9 - - - +
44D LEU* 1.3 72.0 + - - +
61D ARG 3.7 0.7 - - - +
62D VAL* 3.6 1.2 - - - +
63D THR* 2.9 53.6 + - + +
65D THR* 5.1 4.0 + - - -
462H TYR 6.2 0.2 - - - -
463H THR* 4.9 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 44 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D LEU* 4.7 10.0 - - + +
43D ASP* 1.3 83.9 - - - +
45D ASP* 1.3 61.9 + - - +
60D LEU* 4.3 9.2 - - + -
61D ARG 3.5 1.8 - - - +
62D VAL* 3.9 33.2 - - + -
107D PHE* 4.1 11.2 - - + -
128D LEU* 5.8 1.6 - - + -
133D PHE* 3.6 24.2 - - + -
458H THR 4.2 3.3 - - - +
460H LEU* 3.2 32.0 - - + +
461H PHE* 5.2 4.9 - - + -
462H TYR* 3.4 45.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 45 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D LEU* 1.3 75.7 - - - +
46D THR* 1.3 70.7 + - - +
47D ALA* 5.3 3.3 - - - +
60D LEU* 3.8 4.5 - - - +
61D ARG* 2.9 73.6 + - - +
458H THR* 4.0 28.9 - - - +
460H LEU* 4.0 5.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 46 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D ASP* 1.3 86.8 + - - +
47D ALA* 1.3 70.0 + - - +
58D VAL* 4.6 2.9 - - - +
59D VAL 4.1 2.5 - - - -
60D LEU* 5.2 4.6 - - - +
98D LEU 5.1 0.5 + - - -
99D GLY* 5.0 9.8 - - - +
103D PRO* 4.4 18.4 - - - +
456H ASP* 4.4 23.8 - - + +
457H GLN 4.0 20.4 + - - +
460H LEU* 3.8 24.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 47 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D ASP* 5.3 3.4 - - - +
46D THR* 1.3 78.6 + - - +
48D SER* 1.3 66.6 + - - +
58D VAL* 3.4 9.7 - - - +
59D VAL* 2.9 45.5 + - + +
61D ARG* 6.0 3.6 - - + +
79D GLN* 5.9 1.6 - - - +
456H ASP* 6.0 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 48 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D ALA* 1.3 80.8 - - - +
49D SER* 1.3 60.9 + - - +
56D TYR* 3.7 22.4 + - - -
57D GLU 3.2 18.2 - - - -
58D VAL* 4.0 6.3 - - - +
59D VAL* 4.3 3.8 - - - +
98D LEU* 4.1 15.2 - - - +
454H LEU* 4.8 4.9 - - - +
456H ASP* 5.6 5.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 49 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D LYS* 5.6 0.2 - - - -
48D SER* 1.3 74.1 - - - +
50D GLN* 1.3 65.5 + - - +
51D LEU* 3.4 12.6 + - - +
56D TYR* 3.4 6.0 - - - -
57D GLU* 2.9 55.1 + - - +
59D VAL* 5.7 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 50 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D SER* 1.3 73.8 + - - +
51D LEU* 1.3 62.1 + - - +
52D ALA 2.8 28.4 + - - +
53D ASP* 4.4 1.4 - - - +
54D ASP* 3.8 14.6 - - - +
55D VAL 3.6 10.7 + - - +
56D TYR* 3.1 39.3 - - + +
86D ILE* 5.9 0.2 - - - +
451H VAL* 5.4 2.6 - - - +
452H VAL* 3.4 15.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 51 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C PRO* 4.2 22.7 - - + -
49D SER* 3.7 27.6 - - - +
50D GLN* 1.3 74.1 - - - +
52D ALA* 1.3 63.9 + - + +
55D VAL* 3.1 18.2 + - + +
57D GLU* 3.7 24.0 - - + +
83D ILE* 3.7 47.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 52 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D GLN* 2.8 32.7 + - - +
51D LEU* 1.3 80.0 - - + +
53D ASP* 1.3 61.3 + - - +
55D VAL* 2.9 26.3 + - + +
----------------------------------------------------------
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