Contacts of the helix formed by residues 44 - 63 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A GLU* 3.0 7.1 + - + +
43A LEU* 1.3 88.6 - - - +
45A GLY* 1.3 56.0 + - - +
46A GLY 3.5 1.3 - - - -
47A LEU* 3.0 8.1 + - - +
48A TRP* 2.8 64.4 + - + -
126A ARG* 4.1 5.6 - - - -
127A CYS* 2.0 55.9 - - + -
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Residues in contact with GLY 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU* 4.6 4.0 - - - +
39A GLN 5.2 1.8 - - - -
41A GLU* 2.8 19.1 + - - -
42A GLU* 4.8 1.3 - - - -
43A LEU 3.6 0.8 - - - -
44A CYS* 1.3 78.0 - - - +
46A GLY* 1.3 62.9 + - - +
48A TRP* 3.2 23.8 + - - +
49A ARG* 3.2 13.3 + - - +
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Residues in contact with GLY 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A GLU 6.2 0.4 - - - -
43A LEU 5.4 1.0 + - - -
44A CYS 3.5 0.4 - - - -
45A GLY* 1.3 73.2 - - - +
47A LEU* 1.3 51.0 + - - +
49A ARG* 3.4 3.6 + - - +
50A LEU* 2.8 42.9 + - - +
111A GLN* 3.9 26.7 - - - -
115A LEU* 4.8 4.5 - - - -
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Residues in contact with LEU 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A CYS* 4.9 2.2 - - - -
6A PHE* 5.4 4.5 - - + -
43A LEU 4.6 3.7 + - - +
44A CYS* 3.0 15.1 + - - +
46A GLY* 1.3 73.2 - - - +
48A TRP* 1.3 60.5 + - - +
50A LEU* 3.4 4.0 + - - +
51A VAL* 3.0 31.8 + - - +
81A PHE* 4.7 7.6 - - + -
82A VAL* 4.4 17.7 - - + -
87A PHE* 3.7 25.8 - - + -
115A LEU* 3.8 29.1 - - + +
119A ILE* 4.8 7.4 - - + -
124A PHE* 3.6 35.7 - - + -
127A CYS* 3.8 15.5 - - + -
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Residues in contact with TRP 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU* 3.7 27.1 - - + -
39A GLN* 3.4 46.4 - - + -
41A GLU* 3.9 15.3 - - + -
44A CYS* 2.8 31.9 + - + +
45A GLY* 3.5 16.4 - - - +
47A LEU* 1.3 71.6 - - - +
49A ARG* 1.3 57.7 + - - +
51A VAL* 3.3 8.5 + - - +
52A LEU* 3.1 31.4 + - - +
87A PHE* 4.4 4.7 - + - -
126A ARG 5.0 1.8 - - - -
127A CYS* 2.7 31.2 + - + -
129A GLU 3.5 15.0 - - - -
130A LEU* 3.4 33.8 - - + +
131A GLN* 3.6 23.8 - - + -
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Residues in contact with ARG 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU* 4.3 8.9 - - + +
45A GLY 3.2 9.2 + - - +
46A GLY* 3.7 2.9 - - - +
48A TRP* 1.3 76.0 - - - +
50A LEU* 1.3 53.6 + - - +
52A LEU* 3.3 12.3 + - + +
53A ALA* 2.7 36.0 + - - +
104A LEU* 5.5 1.2 - - - +
107A GLU* 5.8 0.7 - - - +
111A GLN* 3.0 32.3 - - - +
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Residues in contact with LEU 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A GLY 2.8 17.2 + - - +
47A LEU 3.7 5.2 - - - +
48A TRP 3.3 0.2 - - - -
49A ARG* 1.3 72.1 - - - +
51A VAL* 1.3 56.2 + - - +
53A ALA* 3.7 2.6 - - - +
54A GLN* 2.7 35.4 + - - +
79A ILE* 3.8 29.1 - - + +
81A PHE* 4.4 10.1 - - + -
82A VAL* 4.0 12.7 - - + +
108A THR* 3.8 21.8 - - + +
111A GLN* 3.4 23.8 - - + +
112A LEU* 4.1 18.2 - - + -
115A LEU* 3.5 31.6 - - + -
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Residues in contact with VAL 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A LEU 3.0 22.4 + - - +
48A TRP* 3.4 10.3 - - - +
50A LEU* 1.3 77.2 - - - +
52A LEU* 1.3 61.5 - - + +
54A GLN* 3.3 5.5 - - - +
55A ARG* 3.0 26.2 + - + +
82A VAL* 3.8 19.3 - - + -
87A PHE* 3.5 56.1 - - + -
130A LEU* 5.2 7.0 - - + -
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Residues in contact with LEU 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A THR 6.1 0.7 - - - +
34A VAL* 5.8 2.0 - - - -
35A ALA* 3.7 34.1 - - + +
38A LEU* 4.1 12.6 - - + -
48A TRP 3.1 16.2 + - - +
49A ARG* 3.5 9.6 - - + +
51A VAL* 1.3 78.2 - - + +
53A ALA* 1.3 63.6 + - - +
55A ARG* 3.1 18.5 + - + +
56A TRP* 3.1 20.8 + - + +
59A ARG* 4.2 0.7 + - - -
90A PRO* 4.4 10.5 - - + -
94A LEU* 4.8 0.7 - - + -
96A PHE* 4.1 25.1 - - + -
104A LEU* 5.7 0.7 - - + -
130A LEU* 4.2 20.2 - - + -
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Residues in contact with ALA 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ARG 2.7 20.8 + - - +
50A LEU* 3.7 8.3 - - - +
52A LEU* 1.3 71.2 - - - +
54A GLN* 1.3 61.3 + - - +
56A TRP* 3.0 15.6 + - - +
57A MET* 3.1 20.3 + - + +
79A ILE* 4.1 8.3 - - + -
104A LEU* 4.0 24.0 - - + +
108A THR* 3.3 26.5 - - + +
111A GLN* 4.8 0.9 - - - +
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Residues in contact with GLN 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A LEU 2.7 19.5 + - - +
51A VAL 3.3 6.7 - - - +
53A ALA* 1.3 74.6 - - - +
55A ARG* 1.3 68.9 + - - +
57A MET* 3.1 13.4 + - - +
58A GLU* 3.0 31.7 + - - +
76A ASN* 3.0 26.3 + - - +
79A ILE* 3.5 34.5 - - + +
80A HIS* 3.3 15.5 + - - -
82A VAL* 3.7 11.4 - - + +
83A THR* 3.7 20.6 - - - +
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Residues in contact with ARG 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A VAL* 3.0 14.2 + - + +
52A LEU* 3.1 15.2 + - + +
54A GLN* 1.3 82.3 + - - +
56A TRP* 1.3 60.2 + - - +
58A GLU* 3.6 8.3 + - - +
59A ARG* 3.4 43.7 + - - +
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Residues in contact with TRP 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A TYR* 4.5 6.5 - + - -
31A PRO 3.9 6.5 - - - -
32A VAL* 3.5 25.1 - - + -
33A THR* 3.0 64.1 + - + +
52A LEU* 3.1 15.0 + - + +
53A ALA 3.0 11.5 + - - +
55A ARG* 1.3 74.9 - - - +
57A MET* 1.3 59.1 + - + +
58A GLU 3.1 2.2 - - - -
59A ARG* 3.2 43.0 + - + +
60A LEU* 2.9 56.5 + - + +
104A LEU* 3.9 22.4 - - + -
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Residues in contact with MET 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A LEU* 4.7 0.7 - - - -
53A ALA 3.1 18.5 + - - +
54A GLN 3.1 7.8 + - - +
56A TRP* 1.3 75.7 - - - +
58A GLU* 1.3 58.2 + - - +
60A LEU* 3.9 10.9 - - + +
61A LYS* 3.2 25.6 + - - +
72A LEU* 4.3 30.4 - - - +
75A VAL* 3.8 22.2 - - + -
76A ASN* 3.7 31.3 + - + +
79A ILE* 4.1 18.6 - - + -
104A LEU* 5.1 9.9 - - + -
105A LEU* 3.3 33.4 - - + -
108A THR* 5.1 8.3 - - + +
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Residues in contact with GLU 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A GLN* 3.0 38.9 + - - +
55A ARG* 3.7 9.0 - - - +
56A TRP 3.1 0.6 - - - -
57A MET* 1.3 75.0 - - - +
59A ARG* 1.3 65.3 + - + +
60A LEU 3.2 0.2 - - - -
61A LYS* 3.3 17.0 + - - +
62A THR* 3.6 16.4 - - - +
76A ASN* 3.2 20.3 + - - +
80A HIS* 3.8 11.4 + - - -
307E ARG* 4.6 1.0 + - - -
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Residues in contact with ARG 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A THR* 5.1 0.8 + - - -
52A LEU 4.2 1.0 + - - -
55A ARG* 3.4 25.8 + - - +
56A TRP* 3.2 74.2 + - + +
58A GLU* 1.3 77.1 - - + +
60A LEU* 1.3 60.8 + - - +
62A THR* 2.5 28.9 + - - -
63A VAL* 3.9 7.3 + - - +
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Residues in contact with LEU 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A TYR* 3.4 41.1 - - + +
32A VAL* 4.7 4.3 - - + -
56A TRP* 2.9 37.5 + - + +
57A MET* 3.9 11.0 - - + +
58A GLU 3.2 0.2 - - - -
59A ARG* 1.3 74.9 - - - +
61A LYS* 1.3 64.8 + - - +
63A VAL* 3.2 9.5 + - + +
64A ALA* 3.2 22.5 + - - +
72A LEU* 3.5 27.1 - - + +
101A ILE* 3.3 31.4 - - + -
104A LEU* 5.8 0.9 - - + -
27B LEU* 4.6 9.8 - - + +
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Residues in contact with LYS 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A MET 3.2 19.1 + - - +
58A GLU* 3.3 11.4 + - - +
60A LEU* 1.3 74.9 - - - +
62A THR* 1.3 61.2 + - + +
64A ALA* 3.4 7.7 + - - -
69A GLN* 3.1 38.1 + - + +
72A LEU* 3.5 17.9 - - + +
73A GLU* 5.6 3.6 - - + +
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Residues in contact with THR 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A GLU 3.6 14.6 - - - +
59A ARG* 2.5 22.8 + - - -
61A LYS* 1.3 78.6 - - + +
63A VAL* 1.3 63.8 + - - +
64A ALA 3.5 1.9 - - - +
69A GLN* 4.9 4.0 + - - +
62C THR* 3.3 43.2 + - - +
63C VAL* 4.0 21.0 - - + +
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Residues in contact with VAL 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A TYR* 4.0 20.0 - - - +
59A ARG 4.1 7.2 - - - +
60A LEU* 3.5 13.2 - - + +
62A THR* 1.3 90.0 + - - +
64A ALA* 1.3 60.7 + - - +
27B LEU* 4.1 10.3 - - + -
28B GLN* 3.8 25.8 + - + +
29B ASP* 4.6 19.7 - - - +
62C THR* 4.6 13.7 - - + +
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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) + - + + + + + -
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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