Contacts of the helix formed by residues 49 - 65 (chain D) in PDB entry 2UZ1
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 HIS 49 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C HIS* 4.1 21.8 + + - -
51C ALA* 5.5 4.6 - - + +
452C GLY 5.9 0.4 - - - +
453C TYR* 3.5 43.6 + + - +
25D LEU* 3.5 6.0 - - - +
47D THR* 2.7 20.7 + - - -
48D ARG* 1.3 78.1 - - - +
50D GLU* 1.3 68.3 + - - +
51D ALA* 3.0 37.5 + - + +
52D ALA* 3.2 15.0 + - + +
53D ALA 3.2 0.2 + - - -
80D ASN* 3.8 30.0 + - + -
453D TYR 5.0 6.3 - - - -
454D SER* 6.0 4.0 - - - +
457D GLU* 3.4 7.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 50 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453C TYR* 2.8 19.9 + - - -
1557C TPP 2.6 32.5 + - - -
25D LEU* 3.6 21.0 - - + +
47D THR* 4.6 0.2 - - - -
49D HIS* 1.3 74.4 + - - +
51D ALA* 1.3 56.4 + - - +
53D ALA* 3.2 7.9 + - - +
54D GLY* 2.9 26.9 + - - -
72D VAL* 3.6 27.7 - - + +
73D THR* 4.6 1.6 - - - +
77D GLY* 3.6 30.3 - - - +
80D ASN* 3.0 24.2 + - + +
81D ALA* 4.5 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 51 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C HIS* 5.6 4.9 - - + +
80C ASN* 5.9 2.0 - - - +
49D HIS* 3.0 23.6 + - + +
50D GLU* 1.3 76.5 - - - +
52D ALA* 1.3 58.3 + - - +
54D GLY 3.1 1.4 + - - -
55D HIS* 2.9 42.3 + - + +
80D ASN 3.3 20.0 + - - +
83D THR* 5.7 2.5 - - - -
84D PRO* 3.3 14.4 - - + +
454D SER* 5.8 2.5 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
47D THR* 4.1 4.4 - - + +
49D HIS* 3.2 10.6 + - + +
51D ALA* 1.3 78.0 - - - +
53D ALA* 1.3 57.4 + - - +
55D HIS* 4.5 3.1 - - - -
56D ALA* 2.8 30.1 + - - +
426D GLY* 3.5 18.0 - - - +
429D LEU* 6.1 0.4 - - + -
454D SER* 4.6 10.6 + - - +
457D GLU* 3.3 44.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 53 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D PHE* 3.3 16.5 - - - +
24D GLY* 3.6 33.2 - - - +
47D THR* 3.4 25.9 + - + +
49D HIS 3.2 6.0 + - - +
50D GLU* 3.2 12.4 + - + +
52D ALA* 1.3 76.0 - - - +
54D GLY* 1.3 57.6 + - - +
56D ALA* 3.3 1.0 + - - +
57D ALA* 3.0 25.1 + - - +
70D ALA* 4.8 1.8 - - + -
72D VAL* 5.3 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 54 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D GLU 2.9 13.4 + - - -
51D ALA 3.1 3.1 + - - -
53D ALA* 1.3 78.2 - - - +
55D HIS* 1.3 55.6 + - - +
57D ALA* 3.2 5.7 + - - +
58D GLU* 3.0 27.9 + - - +
70D ALA* 4.1 8.2 - - - +
81D ALA* 5.6 1.3 - - - -
84D PRO* 3.6 20.3 - - - +
97D PHE* 4.1 16.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 55 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D ALA* 2.9 31.3 + - + +
52D ALA* 4.6 1.6 - - - -
54D GLY* 1.3 72.9 - - - +
56D ALA* 1.3 61.2 + - - +
58D GLU* 2.6 28.2 + - - +
59D GLY 2.8 23.7 + - - -
83D THR* 3.8 9.0 - - - +
84D PRO* 3.3 34.7 - - + +
87D ASN* 4.4 3.1 - - + -
422D GLY 5.0 2.4 - - - -
423D VAL* 3.4 48.4 - - + +
426D GLY* 3.7 8.3 - - - -
427D THR* 3.2 26.0 + - - +
454D SER* 5.6 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 56 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D PHE* 3.4 28.3 - - + -
47D THR* 5.1 0.9 - - + -
52D ALA 2.8 19.3 + - - +
53D ALA* 3.5 5.2 - - - +
54D GLY 3.2 0.2 - - - -
55D HIS* 1.3 73.9 - - - +
57D ALA* 1.3 59.0 + - - +
59D GLY 3.1 0.5 + - - -
60D TYR* 2.8 28.6 + - - +
426D GLY 3.0 17.4 + - - +
429D LEU* 4.2 8.3 - - + -
430D GLY* 3.2 17.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 57 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D PHE* 3.8 11.6 - - + -
53D ALA 3.0 13.3 + - - +
54D GLY 3.2 8.9 + - - +
56D ALA* 1.3 75.3 - - - +
58D GLU* 1.3 57.4 + - - +
60D TYR* 3.5 1.1 + - - +
61D ALA* 3.0 23.6 + - - +
68D GLY* 3.4 12.9 - - - -
69D VAL 3.8 36.6 - - - +
70D ALA* 3.9 3.8 - - + +
95D VAL* 3.9 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 58 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D GLY 3.0 12.2 + - - +
55D HIS* 2.6 40.5 + - - +
57D ALA* 1.3 78.5 - - - +
59D GLY* 1.3 57.1 + - - +
61D ALA* 3.3 2.1 + - - +
62D ARG* 2.8 43.4 + - - +
84D PRO* 3.3 23.0 - - + +
87D ASN* 2.9 27.2 - - - +
88D ALA* 3.5 16.1 + - + -
91D ASP* 4.5 3.5 - - - +
93D THR* 4.1 7.0 + - + -
95D VAL* 3.8 22.0 - - + +
97D PHE* 5.1 0.4 - - + -
427D THR* 5.0 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 59 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D HIS 2.8 15.0 + - - -
56D ALA 3.1 1.5 + - - -
58D GLU* 1.3 70.6 - - - +
60D TYR* 1.3 59.6 + - - +
62D ARG* 4.5 0.2 - - - -
63D ALA* 2.8 35.3 + - - +
413D LEU* 3.9 5.0 - - - +
427D THR* 3.3 35.4 - - - +
431D ALA* 3.6 7.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 60 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D VAL* 6.5 0.4 - - + -
20D GLU* 4.4 6.5 + - - +
21D HIS* 2.7 57.3 + + + +
23D PHE* 3.6 26.5 - + + -
56D ALA 2.8 15.8 + - - +
57D ALA 3.6 3.8 - - - +
59D GLY* 1.3 76.3 - - - +
61D ALA* 1.3 56.6 + - - +
64D GLY* 2.9 28.9 + - - -
66D LYS* 3.7 32.9 + - + +
67D LEU 3.6 25.4 - - - -
68D GLY* 4.1 5.8 - - - -
69D VAL 5.3 0.4 - - - -
430D GLY 3.6 10.0 - - - +
433D VAL* 4.0 6.3 - - + -
434D ALA* 3.8 29.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 61 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D ALA 3.0 18.9 + - - +
58D GLU 3.6 4.5 - - - +
60D TYR* 1.3 77.6 - - - +
62D ARG* 1.3 56.6 + - - +
65D ALA* 2.9 26.5 + - - -
66D LYS* 3.1 31.9 + - - +
68D GLY 3.6 3.8 - - - +
93D THR* 4.0 13.2 - - + -
94D PRO* 3.6 23.1 - - + +
217D ARG* 5.3 3.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 62 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58D GLU* 2.8 34.5 + - - +
61D ALA* 1.3 74.5 - - - +
63D ALA* 1.3 63.5 + - - +
65D ALA* 3.8 6.2 + - - +
87D ASN* 4.8 5.9 + - - -
91D ASP* 4.1 17.5 + - - -
93D THR* 3.7 24.9 + - + +
216D SER* 4.8 7.3 + - - -
217D ARG* 4.0 13.8 + - - +
240D GLU* 2.8 42.6 + - - +
413D LEU* 3.5 31.0 - - + +
414D CYS 2.9 38.4 + - - +
423D VAL* 6.0 2.0 - - - +
427D THR* 3.6 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 63 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D GLY 2.8 23.1 + - - +
62D ARG* 1.3 74.0 - - - +
64D GLY* 1.3 58.4 + - - +
65D ALA* 3.7 1.0 + - - +
388D THR* 4.8 7.6 - - + +
411D GLY* 6.1 3.1 - - - -
413D LEU* 4.2 9.1 - - + +
431D ALA* 3.8 27.4 - - + +
434D ALA* 4.0 8.3 - - + -
435D ASP* 4.2 9.4 - - - +
440D ARG* 3.5 18.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 64 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60D TYR 2.9 16.0 + - - -
63D ALA* 1.3 76.7 - - - +
65D ALA* 1.3 70.4 + - - +
66D LYS* 3.3 22.0 + - - +
434D ALA* 4.0 8.9 - - - +
440D ARG* 5.0 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 65 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D ALA 2.9 12.4 + - - -
62D ARG 3.8 5.4 + - - +
63D ALA 3.5 3.8 + - - +
64D GLY* 1.3 78.4 - - - +
66D LYS* 1.3 55.9 + - - +
94D PRO* 6.0 0.7 - - - -
216D SER 4.0 12.6 - - - +
217D ARG* 3.7 29.5 - - - +
219D ALA* 4.5 12.3 - - + -
----------------------------------------------------------
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