Contacts of the helix formed by residues 113 - 131 (chain D) in PDB entry 3QAZ
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 THR 113 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40D LEU* 4.0 34.2 - - + +
42D PHE 3.9 9.2 - - - -
44D PHE* 3.7 1.6 - - - -
112D ALA* 1.3 75.2 - - - +
114D ILE* 1.3 60.0 + - - +
115D VAL* 3.0 10.8 + - - +
116D GLU* 2.9 39.4 + - + +
117D PHE* 2.8 29.3 + - - +
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Residues in contact with ILE 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D ILE* 3.2 37.0 - - + -
36D LEU* 5.7 0.2 - - + -
39D MET* 3.8 17.9 + - + +
40D LEU* 4.8 7.6 - - + -
42D PHE 4.2 2.0 + - - -
44D PHE* 3.3 31.7 - - + -
66D LEU* 4.1 18.6 - - + -
69D VAL* 3.3 29.8 - - + -
70D LEU* 4.4 2.9 - - + -
113D THR* 1.3 74.1 - - - +
115D VAL* 1.3 75.4 + - + +
117D PHE* 3.2 3.0 + - + +
118D LEU* 3.0 42.9 + - + +
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Residues in contact with VAL 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D LEU* 4.4 12.5 - - + +
28D ILE* 4.0 20.6 - - + -
29D ASN* 4.1 17.0 - - - +
36D LEU* 5.2 1.3 - - + -
40D LEU* 4.2 15.0 - - + -
113D THR* 3.0 8.2 + - - +
114D ILE* 1.3 91.9 - - + +
116D GLU* 1.3 70.4 + - + +
118D LEU* 3.9 8.0 + - + +
119D ASN* 3.4 29.4 + - - +
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Residues in contact with GLU 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D MET* 4.0 10.7 - - - +
111D THR 4.6 1.7 - - - +
112D ALA* 3.5 22.0 - - + +
113D THR* 2.9 40.6 + - + +
115D VAL* 1.3 80.7 - - + +
117D PHE* 1.3 63.7 + - - +
119D ASN* 3.4 9.1 - - - +
120D ARG* 3.4 13.7 + - - +
125F LYS* 6.2 0.4 - - - +
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Residues in contact with PHE 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D LEU* 6.3 1.6 - - + -
44D PHE* 3.3 32.5 - + + -
45D TYR 3.7 10.3 - - - -
46D MET* 4.5 13.9 - - + -
59D LEU* 3.9 9.9 - - + -
62D GLU* 3.3 44.9 - - + -
66D LEU* 4.6 13.9 - - + -
112D ALA* 4.5 1.3 - - - +
113D THR 2.8 19.7 + - - +
114D ILE* 3.2 10.1 - - + +
116D GLU* 1.3 74.5 - - - +
118D LEU* 1.3 90.1 + - + +
120D ARG* 3.1 14.0 + - - +
121D TRP* 3.5 40.6 + + + -
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Residues in contact with LEU 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D LEU* 4.3 18.8 - - + +
24D ILE* 4.2 17.0 - - + -
25D LEU* 3.7 40.6 - - + +
28D ILE* 4.2 10.3 - - + -
66D LEU* 4.5 18.2 - - + -
114D ILE* 3.0 29.3 + - + +
115D VAL* 4.2 3.4 - - + +
117D PHE* 1.3 89.7 - - + +
119D ASN* 1.3 64.6 + - - +
121D TRP* 2.9 7.4 + - - +
122D ILE* 2.7 36.9 + - + +
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Residues in contact with ASN 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D LEU* 3.6 25.3 - - - +
115D VAL* 3.4 18.7 + - - +
116D GLU* 3.4 14.6 - - - +
117D PHE 3.1 0.4 - - - -
118D LEU* 1.3 78.4 - - - +
120D ARG* 1.3 57.3 + - - +
122D ILE* 3.8 6.9 - - - +
123D THR* 2.8 35.7 + - - -
125F LYS* 3.1 39.2 - - - +
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Residues in contact with ARG 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D MET* 3.7 34.8 - - + +
47D PRO* 4.4 22.5 + - + +
48D LYS 5.3 1.6 + - - -
49D LYS* 5.0 2.8 - - - +
50D ALA* 3.6 40.9 + - - +
51D THR* 5.7 1.2 - - - +
116D GLU 3.4 2.2 + - - +
117D PHE 3.1 9.3 + - - +
118D LEU 3.1 0.8 - - - -
119D ASN* 1.3 77.4 - - - +
121D TRP* 1.3 56.9 + - + +
123D THR* 3.1 8.8 + - - +
124D PHE* 2.6 50.9 + - - +
103F TYR 5.0 11.1 + - - -
125F LYS* 6.2 0.9 - - - +
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Residues in contact with TRP 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D LEU* 4.0 17.7 - - + -
46D MET* 5.8 0.4 - - + +
47D PRO* 3.6 36.1 - - + +
50D ALA* 3.9 17.9 - - + -
55D HIS 3.6 20.9 - - - -
56D LEU* 3.8 29.2 - - + -
58D CYS* 3.4 8.9 + - + -
59D LEU* 3.2 50.1 - - + +
62D GLU* 5.1 0.2 - - - +
117D PHE* 3.5 39.0 + + + +
118D LEU* 2.9 7.4 + - - +
120D ARG* 1.3 75.6 - - + +
122D ILE* 1.3 65.0 + - - +
124D PHE* 3.6 19.3 - + + +
125D CYS* 3.0 28.2 + - - -
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Residues in contact with ILE 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D LEU* 3.2 26.6 - - + +
21D LEU* 3.6 22.2 - - + +
22D GLN* 3.7 29.2 - - + +
25D LEU* 3.5 34.8 - - + -
118D LEU* 2.7 26.6 + - + +
119D ASN* 3.8 6.7 - - - +
121D TRP* 1.3 72.2 - - - +
123D THR* 1.3 57.8 + - - +
125D CYS* 3.1 6.4 - - - +
126D GLN* 2.8 44.6 + - - +
211F SER* 5.2 4.5 - - - +
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Residues in contact with THR 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119D ASN* 2.8 24.8 + - - -
120D ARG* 3.6 10.5 - - - +
122D ILE* 1.3 74.5 - - - +
124D PHE* 1.3 65.3 + - - +
126D GLN* 3.1 12.8 + - - +
127D SER* 2.9 20.8 + - - -
103F TYR* 4.2 23.6 - - + +
125F LYS* 4.6 8.6 - - + +
127F GLN* 3.1 39.1 + - + +
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Residues in contact with PHE 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D LEU* 4.7 5.8 - - + -
50D ALA* 3.7 26.2 - - + -
51D THR* 3.9 14.8 - - - -
52D GLU 3.9 9.0 - - - -
53D LEU* 4.1 22.7 - - + -
55D HIS* 4.9 0.7 - - + -
56D LEU* 4.0 29.4 - - + -
120D ARG* 2.6 32.9 + - - +
121D TRP* 3.6 28.5 - + + +
123D THR* 1.3 68.7 - - - +
125D CYS* 1.3 83.5 + - - +
127D SER* 2.3 30.3 + - - -
128D ILE* 3.1 40.0 + - + +
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Residues in contact with CYS 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D LEU* 4.5 8.1 - - - -
17D LEU* 3.5 32.8 - - - -
18D LEU* 3.6 36.6 - - + -
21D LEU* 3.9 4.3 - - - -
121D TRP 3.0 14.2 + - - -
122D ILE 3.1 11.0 - - - +
124D PHE* 1.3 87.0 - - - +
126D GLN* 1.3 61.5 + - - +
128D ILE* 3.0 7.6 + - - +
129D ILE* 2.9 33.0 + - + +
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Residues in contact with GLN 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D LEU* 3.7 10.5 - - + +
22D GLN* 4.5 2.0 + - - -
122D ILE* 2.8 28.5 + - - +
123D THR* 3.1 24.1 + - - +
125D CYS* 1.3 75.1 - - - +
127D SER* 1.3 63.1 + - - +
130D SER 3.4 12.3 + - - -
103F TYR* 3.4 20.1 + - + -
127F GLN* 3.9 12.0 + - - +
128F ASN* 4.3 0.3 - - - +
207F PRO 2.5 28.7 + - - -
208F LEU 3.2 13.9 - - - +
209F CYS* 3.8 13.2 - - - +
210F GLY* 3.0 23.6 + - - +
211F SER* 3.9 11.3 + - - -
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Residues in contact with SER 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D ALA 5.4 0.9 + - - -
51D THR* 5.1 1.2 + - - -
123D THR 2.9 7.7 + - - -
124D PHE* 2.3 32.2 + - - -
126D GLN* 1.3 73.1 - - - +
128D ILE* 1.3 79.6 + - - +
130D SER* 2.9 16.1 + - - -
131D THR* 3.3 14.7 + - - -
103F TYR* 3.4 37.2 - - - -
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Residues in contact with ILE 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D LEU* 3.7 32.3 - - + -
51D THR 3.4 26.0 - - - +
53D LEU* 4.4 16.6 - - + +
124D PHE* 3.3 42.2 - - + +
125D CYS* 3.0 5.6 + - - +
127D SER* 1.3 86.7 + - - +
129D ILE* 1.3 57.5 + - - +
131D THR* 4.1 3.3 + - - -
132D LEU* 3.2 30.6 + - + +
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Residues in contact with ILE 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D GLN* 3.3 33.7 - - + +
14D LEU* 4.7 12.6 - - + -
15D GLU* 4.4 15.5 - - + +
18D LEU* 3.7 24.5 - - + -
125D CYS* 2.9 20.3 + - + +
127D SER 2.9 0.6 + - - -
128D ILE* 1.3 75.4 - - - +
130D SER* 1.3 66.8 + - - +
132D LEU* 3.5 10.7 + - - +
159F HIS* 3.3 22.6 + - + +
208F LEU* 3.3 43.5 - - + +
209F CYS* 4.3 0.4 - - - -
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Residues in contact with SER 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126D GLN 3.4 3.2 + - - -
127D SER 2.9 2.5 + - - -
129D ILE* 1.3 73.9 - - - +
131D THR* 1.3 56.2 + - - +
132D LEU 2.7 15.7 + - - -
133D THR* 2.8 21.1 + - - -
102F LEU* 5.9 0.5 - - - +
103F TYR* 3.3 43.0 + - - -
157F LEU* 5.9 2.9 - - - +
159F HIS* 4.3 4.3 - - - -
160F CYS* 4.9 2.1 - - - -
205F PHE* 5.7 0.7 - - - -
209F CYS* 3.9 14.3 - - - +
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Residues in contact with THR 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D SER 3.3 10.8 + - - -
128D ILE* 4.1 3.4 - - - -
130D SER* 1.3 78.7 + - - +
132D LEU* 1.3 57.1 + - - +
133D THR 3.3 5.4 + - - -
103F TYR* 5.8 1.9 - - - -
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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
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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