Contacts of the helix formed by residues 50 - 67 (chain B) in PDB entry 1ULT
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 TYR 50 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU* 4.2 10.2 - - + +
27B ALA* 3.8 31.0 - - + +
28B ALA* 4.6 1.3 - - - -
31B PHE* 3.6 25.4 - - + +
32B GLY 3.6 0.4 + - - -
34B LYS* 3.3 23.7 + - + -
35B GLU 5.0 0.2 - - - -
36B VAL* 4.0 17.2 - - + +
49B THR* 1.3 73.8 - - - +
51B ALA* 1.3 52.7 + - - +
53B VAL* 3.2 6.6 + - + +
54B TYR* 2.7 37.0 + - - +
86B LEU* 4.8 3.8 - - + -
240B ALA 3.4 7.1 + - - -
241B THR* 3.6 29.8 - - + -
244B GLY* 4.0 11.0 - - - -
245B ALA 2.6 29.7 + - - -
247B GLN* 2.8 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ALA* 4.3 15.9 - - + +
32B GLY* 3.1 28.4 + - - +
49B THR* 4.0 3.6 - - - +
50B TYR* 1.3 76.6 - - - +
52B GLU* 1.3 61.9 - - - +
54B TYR* 3.4 5.0 - - - +
55B GLN* 3.1 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 52 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B HIS* 5.7 2.6 + - - -
47B ARG 4.8 1.9 - - - +
48B THR* 3.2 33.3 + - - +
49B THR* 3.1 13.2 + - - +
51B ALA* 1.3 76.9 - - - +
53B VAL* 1.3 60.5 - - - +
55B GLN* 3.2 19.6 + - - +
56B ARG* 2.8 46.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU* 4.0 20.2 - - + -
36B VAL* 4.5 12.1 - - + -
48B THR* 3.9 22.7 - - + +
49B THR 2.8 22.7 + - - +
50B TYR* 3.6 7.9 - - + +
52B GLU* 1.3 75.7 - - - +
54B TYR* 1.3 56.5 + - - +
57B ALA* 2.8 32.4 + - - +
83B PHE* 5.1 2.7 - - + -
86B LEU* 4.4 22.9 - - + +
87B GLU* 3.7 34.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B TRP* 3.4 31.8 + + - -
24B LEU* 3.7 22.2 - - + -
25B GLU* 3.8 40.3 + - + +
28B ALA* 3.5 20.9 - - + -
50B TYR 2.7 17.6 + - - +
51B ALA 3.4 6.5 - - - +
53B VAL* 1.3 78.5 - - - +
55B GLN* 1.3 59.4 + - + +
57B ALA* 3.3 2.9 + - - +
58B ARG* 3.0 59.4 + - - +
170B PRO* 5.9 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B ALA 3.1 12.9 + - - +
52B GLU* 3.5 27.5 + - - +
54B TYR* 1.3 85.0 - - + +
56B ARG* 1.3 74.3 + - - +
58B ARG* 3.4 10.7 + - - +
59B ARG* 3.2 45.9 + - - +
167B GLU* 3.2 25.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B THR* 5.3 2.0 - - - -
52B GLU* 2.8 42.5 + - - +
53B VAL 4.1 0.2 - - - +
55B GLN* 1.3 87.1 - - - +
57B ALA* 1.3 59.5 + - - +
59B ARG* 3.1 14.0 + - - +
60B LEU* 2.8 27.5 + - - +
83B PHE* 3.7 20.2 - - - -
87B GLU* 2.7 45.0 + - - +
160B TYR* 3.5 9.7 - - - -
161B GLU* 2.7 44.4 + - - -
164B LEU* 3.7 17.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B TRP* 3.9 11.9 - - + -
24B LEU* 3.9 18.8 - - + -
53B VAL 2.8 20.4 + - - +
54B TYR 3.5 4.9 - - - +
55B GLN 3.3 0.2 - - - -
56B ARG* 1.3 74.4 - - - +
58B ARG* 1.3 65.6 + - - +
60B LEU* 3.1 10.2 + - - +
61B MET* 3.0 26.3 + - - +
87B GLU* 4.1 22.4 - - + +
91B ALA* 3.6 2.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B TRP* 3.7 16.4 - - + -
54B TYR* 3.0 55.1 + - - +
55B GLN* 3.6 7.9 - - - +
56B ARG 3.2 0.2 - - - -
57B ALA* 1.3 76.7 - - - +
59B ARG* 1.3 61.1 + - - +
61B MET* 3.4 10.8 + - - +
62B GLY 3.2 11.3 + - - -
167B GLU* 2.7 43.4 + - + +
168B ALA 3.0 41.2 + - - +
169B ASP* 3.1 31.7 + - - +
170B PRO* 4.2 7.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B GLN* 3.2 33.1 + - - +
56B ARG* 3.1 14.9 + - - +
58B ARG* 1.3 76.3 - - - +
60B LEU* 1.3 60.0 + - - +
62B GLY* 3.2 0.9 + - - -
63B GLY 2.9 24.3 + - - -
161B GLU 4.8 4.2 + - - -
164B LEU* 3.2 51.9 + - + +
165B GLY* 2.7 37.0 + - - +
166B GLU 3.9 4.7 - - - -
167B GLU* 3.6 17.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B ARG 2.8 12.7 + - - +
57B ALA* 3.1 10.1 + - - +
59B ARG* 1.3 77.8 - - - +
61B MET* 1.3 56.6 + - - +
63B GLY 3.3 0.4 + - - +
64B LEU* 2.9 54.3 + - + +
87B GLU* 4.0 2.2 - - + -
88B ALA* 3.8 22.0 - - + +
91B ALA* 3.8 20.0 - - + -
124B LEU* 4.8 7.0 - - + -
160B TYR* 3.0 40.4 - - + +
163B ALA* 5.6 6.3 - - + -
164B LEU* 3.6 23.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B TRP* 3.4 36.3 - - + -
57B ALA 3.0 12.2 + - - +
58B ARG* 3.6 9.9 - - - +
59B ARG 3.2 0.2 - - - -
60B LEU* 1.3 78.3 - - - +
62B GLY* 1.3 61.6 + - - +
64B LEU 3.5 0.2 + - - -
65B ARG* 3.0 27.1 + - - +
91B ALA* 3.3 31.2 - - - +
94B GLY* 3.5 26.0 - - - +
95B MET* 3.6 23.9 - - + +
168B ALA* 3.5 30.1 - - + +
169B ASP 4.2 1.3 - - - +
170B PRO* 3.9 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ARG 3.2 5.1 + - - -
59B ARG 3.2 3.2 + - - -
60B LEU 3.2 0.6 - - - -
61B MET* 1.3 79.8 - - - +
63B GLY* 1.3 56.4 + - - +
65B ARG* 3.1 7.7 + - - +
66B ALA* 2.9 28.3 + - - +
165B GLY* 4.6 3.6 - - - -
166B GLU 3.4 21.8 - - - -
168B ALA* 3.9 10.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B ARG 2.9 11.3 + - - -
60B LEU* 3.8 3.1 - - - -
62B GLY* 1.3 75.3 - - - +
64B LEU* 1.3 61.2 + - - +
66B ALA* 3.1 10.3 + - - +
67B LEU* 3.0 28.9 + - - +
163B ALA* 3.1 28.4 - - - +
164B LEU* 4.6 0.2 - - - -
165B GLY* 3.7 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LEU* 2.9 42.3 + - + +
63B GLY* 1.3 75.3 - - - +
65B ARG* 1.3 63.5 + - - +
67B LEU* 3.0 22.2 + - + +
68B GLY 3.3 0.3 + - - -
69B VAL* 3.0 31.7 + - + +
75B VAL* 4.5 12.1 - - + -
91B ALA* 4.8 0.7 - - + -
92B VAL* 4.1 26.5 - - + +
95B MET* 3.7 30.3 - - + -
122B VAL* 4.2 24.7 - - + -
124B LEU* 5.0 7.9 - - + -
163B ALA* 6.5 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B MET* 3.0 16.0 + - - +
62B GLY* 3.3 11.0 - - - +
64B LEU* 1.3 76.7 - - - +
66B ALA* 1.3 58.3 + - - +
68B GLY* 2.8 21.1 + - - -
69B VAL 3.8 15.6 + - - +
95B MET* 3.7 32.2 + - + +
168B ALA* 4.2 19.6 - - - +
169B ASP 4.5 7.1 + - - +
171B VAL* 3.6 30.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B GLY 2.9 12.6 + - - +
63B GLY* 3.4 13.5 - - - +
65B ARG* 1.3 76.9 - - - +
67B LEU* 1.3 61.6 + - + +
68B GLY 3.2 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B GLY 3.0 17.6 + - - +
64B LEU* 3.0 23.6 + - + +
65B ARG 3.0 1.2 - - - -
66B ALA* 1.3 80.5 - - + +
68B GLY* 1.3 60.5 + - - +
69B VAL* 3.5 2.5 + - - +
121B LYS* 4.7 3.8 - - - +
122B VAL* 4.7 7.0 - - + -
144B GLN* 4.7 5.4 + - - -
145B HIS* 3.4 59.4 + - + +
147B VAL* 4.5 11.2 - - + -
158B LEU* 4.1 27.6 - - + -
163B ALA* 4.7 8.3 - - + +
----------------------------------------------------------
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