Contacts of the helix formed by residues 44 - 62 (chain B) in PDB entry 3QS7
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 CYS 44 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B GLU* 3.0 6.6 + - + +
43B LEU* 1.3 90.3 - - - +
45B GLY* 1.3 54.8 + - - +
46B GLY 3.6 1.6 - - - -
47B LEU* 3.0 7.7 + - - +
48B TRP* 2.8 65.1 + - + -
126B ARG* 4.1 6.3 - - - -
127B CYS* 2.0 57.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 45 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B LEU* 4.6 0.4 - - - +
39B GLN 5.2 1.6 - - - -
41B GLU 2.7 24.9 + - - -
42B GLU* 4.7 1.3 - - - -
43B LEU 3.6 0.8 - - - -
44B CYS* 1.3 72.4 - - - +
46B GLY* 1.3 61.2 + - - +
48B TRP* 3.2 20.1 + - - +
49B ARG* 3.0 29.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B GLU 6.1 0.6 - - - -
43B LEU 5.3 1.0 + - - -
44B CYS 3.6 0.6 - - - -
45B GLY* 1.3 72.7 - - - +
47B LEU* 1.3 52.0 + - - +
49B ARG* 3.4 7.0 + - - +
50B LEU* 2.9 42.7 + - - +
111B GLN* 3.9 25.8 - - - +
115B LEU* 4.7 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B CYS* 5.1 2.7 - - - -
6B PHE* 5.4 4.3 - - + -
43B LEU 4.6 3.3 + - - +
44B CYS* 3.0 15.0 + - - +
46B GLY* 1.3 74.1 - - - +
48B TRP* 1.3 61.9 + - - +
50B LEU* 3.4 4.1 + - - +
51B VAL* 3.0 29.4 + - - +
81B PHE* 4.7 7.0 - - + -
82B VAL* 4.4 18.2 - - + -
87B PHE* 3.7 24.0 - - + -
115B LEU* 3.8 28.6 - - + +
119B ILE* 4.7 7.9 - - + -
124B PHE* 3.6 36.3 - - + -
127B CYS* 3.8 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B LEU* 3.7 27.6 - - + -
39B GLN* 3.4 46.2 - - + -
41B GLU* 3.9 15.5 - - + -
44B CYS* 2.8 31.2 + - + +
45B GLY* 3.2 17.2 + - - +
47B LEU* 1.3 73.9 - - - +
49B ARG* 1.3 58.0 + - - +
51B VAL* 3.3 7.9 + - - +
52B LEU* 3.1 32.6 + - - +
87B PHE* 4.4 5.2 - + - -
126B ARG 5.0 1.8 - - - -
127B CYS* 2.7 31.4 + - + -
129B GLU 3.5 15.9 - - - -
130B LEU* 3.4 32.2 - - + +
131B GLN* 3.6 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 49 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B VAL* 5.9 3.4 - - - +
35B ALA 4.4 10.3 + - - -
38B LEU* 3.5 36.8 + - + +
45B GLY* 3.0 26.1 + - - +
46B GLY* 3.7 4.5 - - - +
47B LEU 3.3 0.2 - - - -
48B TRP* 1.3 72.4 - - - +
50B LEU* 1.3 54.7 + - - +
52B LEU* 3.3 10.5 + - + +
53B ALA* 2.7 35.9 + - - +
104B LEU* 5.5 1.0 - - - +
107B GLU* 5.9 0.4 - - - +
111B GLN* 3.1 36.1 - - - +
-1C HIS* 3.4 32.4 - - - +
0C MET 4.1 12.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 50 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B GLY 2.9 17.8 + - - +
47B LEU* 3.7 5.8 - - - +
49B ARG* 1.3 71.8 - - - +
51B VAL* 1.3 57.9 + - - +
53B ALA* 3.7 2.1 - - - +
54B GLN* 2.7 36.1 + - - +
79B ILE* 3.8 29.1 - - + +
81B PHE* 4.4 9.0 - - + -
82B VAL* 4.1 13.6 - - + +
108B THR* 3.9 23.1 - - + +
111B GLN* 3.4 22.9 - - + +
112B LEU* 4.0 17.9 - - + -
115B LEU* 3.5 32.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B LEU 3.0 20.5 + - - +
48B TRP* 3.4 9.6 - - - +
50B LEU* 1.3 76.5 - - - +
52B LEU* 1.3 61.6 + - + +
54B GLN* 3.3 4.7 - - - +
55B ARG* 3.0 35.4 + - + +
82B VAL* 3.8 21.1 - - + -
83B THR* 6.6 0.2 - - + -
87B PHE* 3.6 55.6 - - + -
130B LEU* 5.2 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 52 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B THR 6.1 0.7 - - - +
34B VAL* 6.3 1.6 - - - -
35B ALA* 3.8 33.9 - - + +
38B LEU* 4.1 12.3 - - + -
48B TRP 3.1 16.2 + - - +
49B ARG* 3.5 10.8 - - + +
51B VAL* 1.3 78.0 - - + +
53B ALA* 1.3 63.1 + - - +
55B ARG* 3.1 16.1 + - - +
56B TRP* 3.1 28.8 + - + +
59B ARG* 4.2 0.9 + - - -
90B PRO* 4.5 10.5 - - + -
94B LEU* 4.8 0.4 - - + -
96B PHE* 4.0 26.0 - - + -
104B LEU* 5.7 0.4 - - + -
130B LEU* 4.2 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ARG 2.7 21.3 + - - +
50B LEU* 3.7 8.1 - - - +
52B LEU* 1.3 71.2 - - - +
54B GLN* 1.3 62.2 + - - +
56B TRP* 3.0 15.7 + - - +
57B MET* 3.1 19.2 + - + +
79B ILE* 4.1 8.7 - - + -
104B LEU* 4.0 23.9 - - + +
108B THR* 3.3 26.5 - - - +
111B GLN* 4.8 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B LEU 2.7 19.3 + - - +
51B VAL 3.3 6.1 - - - +
53B ALA* 1.3 73.8 - - - +
55B ARG* 1.3 72.8 + - - +
57B MET* 3.1 13.0 + - - +
58B GLU* 3.2 30.1 + - - +
76B ASN* 2.9 25.9 + - - +
79B ILE* 3.5 35.8 - - + +
80B HIS* 3.3 16.3 + - - -
82B VAL* 3.7 12.1 - - + +
83B THR* 3.6 19.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B VAL* 3.0 22.3 + - + +
52B LEU* 3.1 19.6 + - + +
54B GLN* 1.3 82.8 + - - +
56B TRP* 1.3 60.4 + - - +
58B GLU* 3.6 8.7 + - - +
59B ARG* 3.4 45.8 + - - +
89B PRO* 6.2 0.2 - - - +
90B PRO* 5.0 15.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B TYR* 4.5 6.1 - + - -
31B PRO 3.9 6.7 - - - -
32B VAL* 3.5 24.2 - - + -
33B THR* 3.0 61.8 + - + +
52B LEU* 3.1 15.2 + - + +
53B ALA 3.0 13.0 + - - +
55B ARG* 1.3 73.8 - - - +
57B MET* 1.3 58.4 + - - +
58B GLU 3.2 2.2 - - - -
59B ARG* 3.2 44.3 + - + +
60B LEU* 2.9 56.0 + - + +
104B LEU* 3.9 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LEU* 4.7 0.2 - - - -
53B ALA 3.1 20.3 + - - +
54B GLN 3.1 7.4 + - - +
56B TRP* 1.3 74.8 - - - +
58B GLU* 1.3 57.8 + - - +
60B LEU* 3.7 10.5 + - + +
61B LYS* 3.2 32.9 + - - +
72B LEU* 4.2 28.4 - - - +
75B VAL* 3.8 20.9 - - + -
76B ASN* 3.7 28.0 - - + +
79B ILE* 4.1 18.6 - - + -
104B LEU* 5.0 10.1 - - + -
105B LEU* 3.4 33.2 - - + -
108B THR* 5.2 7.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B GLN* 3.2 31.4 + - - +
55B ARG* 3.7 9.6 - - - +
56B TRP 3.2 0.2 - - - -
57B MET* 1.3 74.3 - - - +
59B ARG* 1.4 65.7 + - + +
61B LYS* 3.2 32.3 + - - +
62B THR* 3.5 12.8 + - - +
76B ASN* 3.1 25.2 + - - +
80B HIS* 3.9 10.7 + - - -
307F ARG* 4.5 1.4 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
33B THR* 5.2 0.6 + - - -
52B LEU 4.2 1.2 + - - -
55B ARG* 3.4 34.4 + - - +
56B TRP* 3.2 74.2 + - + +
58B GLU* 1.4 77.7 - - + +
60B LEU* 1.3 59.3 + - - +
62B THR* 2.5 29.0 + - - -
63B VAL* 3.9 7.5 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
27A LEU* 4.6 9.0 - - + +
30B TYR* 3.5 41.7 - - + +
32B VAL* 4.7 4.7 - - + -
56B TRP* 2.9 36.8 + - + +
57B MET* 3.9 11.9 - - + +
59B ARG* 1.3 75.4 - - - +
61B LYS* 1.3 64.2 + - - +
63B VAL* 3.2 8.8 + - + +
64B ALA* 3.2 22.0 + - - +
72B LEU* 3.4 27.0 - - + +
101B ILE* 3.3 30.1 - - + -
104B LEU* 5.7 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B MET 3.2 27.0 + - - +
58B GLU* 3.2 23.0 + - - +
60B LEU* 1.3 75.2 - - - +
62B THR* 1.3 60.8 + - + +
64B ALA* 3.4 17.5 + - - +
69B GLN* 4.3 14.8 - - + +
72B LEU* 3.5 24.7 - - + +
73B GLU* 2.5 44.1 + - - +
76B ASN* 3.6 17.9 - - + +
307F ARG* 4.8 3.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B GLU 3.6 14.6 - - - +
59B ARG* 2.5 23.2 + - - -
61B LYS* 1.3 78.1 - - + +
63B VAL* 1.3 65.9 + - - +
64B ALA 3.5 1.6 - - - +
----------------------------------------------------------
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