Contacts of the helix formed by residues 53 - 74 (chain B) in PDB entry 4TXQ
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 53 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B GLN* 4.2 14.2 + - - +
50B ASP* 2.6 30.2 + - - -
52B LYS* 1.3 76.1 - - - +
54B PRO* 1.3 70.2 - - + +
55B GLU* 3.8 15.3 - - + +
56B CYS* 2.9 19.9 + - - +
57B ARG* 2.9 24.6 + - - +
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Residues in contact with PRO 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B LYS 3.1 8.3 - - - +
53B THR* 1.3 86.9 - - + +
55B GLU* 1.3 63.8 + - - +
57B ARG* 3.9 6.4 - - + +
58B LYS* 3.0 25.8 + - - +
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Residues in contact with GLU 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B PRO* 5.6 1.3 - - + +
9B PRO* 4.3 9.8 - - - +
10B LEU 4.7 0.9 - - - +
11B PRO* 3.7 34.1 - - + +
12B ALA 5.1 1.1 + - - -
13B GLN* 4.3 9.4 + - - +
53B THR* 3.4 10.6 - - + +
54B PRO* 1.3 77.6 - - - +
56B CYS* 1.3 58.3 + - - +
58B LYS* 3.6 6.0 + - - +
59B PHE* 3.1 26.0 + - - +
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Residues in contact with CYS 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B PRO* 3.9 9.2 - - - -
13B GLN* 3.7 31.6 - - - -
14B PHE* 3.6 22.2 - - + -
50B ASP* 3.6 38.6 - - - +
53B THR* 2.9 16.8 + - - +
55B GLU* 1.3 77.1 - - - +
57B ARG* 1.3 60.1 + - - +
59B PHE* 3.0 3.6 + - - +
60B LEU* 2.9 35.3 + - - +
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Residues in contact with ARG 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B SER* 3.0 34.8 - - - +
52B LYS* 3.8 9.0 - - - +
53B THR 2.9 18.0 + - - +
54B PRO* 3.9 6.5 - - + +
56B CYS* 1.3 72.3 - - - +
58B LYS* 1.3 57.7 - - - +
60B LEU* 3.3 4.4 + - - +
61B SER* 2.9 31.6 + - - -
184D GLU* 5.6 8.1 - - + -
185D GLN 5.3 5.8 - - - +
188D LEU* 3.9 19.2 - - + +
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Residues in contact with LYS 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B PRO* 5.0 8.7 - - + -
54B PRO 3.0 18.7 + - - +
55B GLU* 3.7 7.0 - - - +
57B ARG* 1.3 77.5 - - - +
59B PHE* 1.3 61.2 + - - +
61B SER* 3.5 9.2 + - - +
62B LYS* 3.2 41.0 + - + +
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Residues in contact with PHE 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LEU* 3.9 23.5 - - + +
8B PRO* 3.5 42.3 - - + +
9B PRO 3.9 1.3 - - - +
10B LEU* 3.5 31.4 - - + -
11B PRO* 3.7 20.9 - - + -
14B PHE* 3.8 18.8 - + - -
17B ILE* 5.0 2.7 - - + -
21B LEU* 3.7 15.9 - - + -
55B GLU 3.1 14.3 + - - +
56B CYS 3.0 9.0 + - - +
58B LYS* 1.3 77.4 - - - +
60B LEU* 1.3 63.0 + - + +
62B LYS* 3.2 5.4 + - - +
63B LEU* 2.9 43.4 + - + +
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Residues in contact with LEU 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B PHE* 3.8 21.3 - - + -
17B ILE* 5.8 0.2 - - + -
42B ALA 4.8 0.7 - - - +
43B MET* 3.4 41.5 - - + +
46B GLY* 4.0 11.9 - - - +
47B MET* 3.8 21.3 - - - -
50B ASP 3.6 23.6 - - - +
51B SER* 4.3 7.0 - - - -
56B CYS 2.9 19.5 + - - +
57B ARG 3.7 4.3 - - - +
59B PHE* 1.3 81.6 - - + +
61B SER* 1.3 53.5 + - - +
63B LEU* 3.2 10.2 + - + -
64B MET* 2.7 35.5 + - - +
188D LEU* 3.9 8.1 - - + -
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Residues in contact with SER 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B ARG 2.9 18.6 + - - -
58B LYS* 3.6 13.0 - - - +
60B LEU* 1.3 77.2 - - - +
62B LYS* 1.3 58.7 - - - +
64B MET* 3.1 4.6 + - - +
65B ASP* 2.9 33.7 + - - +
187D GLU* 5.5 0.9 + - - -
188D LEU* 3.6 19.0 - - - +
191D ARG* 3.8 13.0 + - - +
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Residues in contact with LYS 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B LEU 6.0 2.2 - - - +
5B ALA* 6.0 4.0 - - + +
6B PRO 5.3 3.4 - - - +
7B LEU* 3.4 23.7 - - + +
8B PRO* 3.9 19.5 - - + -
58B LYS* 3.2 24.2 + - + +
59B PHE 3.2 5.7 + - - +
61B SER* 1.3 76.3 - - - +
63B LEU* 1.3 65.6 + - - +
65B ASP* 3.2 21.1 + - - +
66B GLN* 3.1 18.7 + - - +
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Residues in contact with LEU 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LEU* 3.5 14.0 - - + +
17B ILE* 5.4 0.4 - - + -
21B LEU* 4.1 11.2 - - + -
39B ARG* 4.0 29.4 - - + +
42B ALA* 4.1 10.5 - - + +
43B MET* 3.6 40.2 - - + +
59B PHE* 2.9 31.9 + - + +
60B LEU* 3.5 12.3 - - + +
62B LYS* 1.3 75.8 - - - +
64B MET* 1.3 64.1 + - - +
66B GLN* 3.0 21.4 + - - +
67B LEU* 2.9 22.7 + - + +
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Residues in contact with MET 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B MET* 3.4 35.6 - - + -
60B LEU 2.7 16.5 + - - +
61B SER* 3.4 7.2 - - - +
63B LEU* 1.3 77.2 - - - +
65B ASP* 1.3 63.1 + - - +
67B LEU* 3.2 4.2 + - + +
68B GLU* 2.9 30.9 + - - +
188D LEU* 4.1 4.5 - - + +
191D ARG* 3.5 45.5 - - + +
192D LEU* 3.5 37.9 - - + +
195D LEU* 4.1 20.2 - - - -
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Residues in contact with ASP 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B LEU* 3.2 31.3 - - + +
61B SER* 2.9 20.2 + - - +
62B LYS* 3.3 28.3 - - - +
63B LEU 3.2 0.2 - - - -
64B MET* 1.3 76.2 - - - +
66B GLN* 1.3 60.4 + - - +
68B GLU* 3.7 5.3 + - - +
69B ALA* 3.2 18.2 + - - +
191D ARG* 2.7 33.0 + - - +
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Residues in contact with GLN 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 3.3 29.5 - - + +
4B LEU* 3.5 18.3 - - + +
5B ALA 4.4 8.9 + - - +
6B PRO* 5.0 1.6 - - - +
7B LEU* 3.5 46.5 - - + +
39B ARG* 3.0 27.7 + - - +
62B LYS 3.1 10.4 + - - +
63B LEU* 3.0 10.0 + - - +
65B ASP* 1.3 75.0 - - - +
67B LEU* 1.3 54.2 + - - +
69B ALA* 3.3 1.7 + - - +
70B LEU* 2.7 38.5 + - - +
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Residues in contact with LEU 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B TYR* 3.6 26.4 - - + +
39B ARG* 3.6 33.0 - - + +
40B LEU* 3.6 16.6 - - + +
43B MET* 3.6 37.0 - - + -
63B LEU* 2.9 18.1 + - + +
64B MET* 3.2 10.5 + - - +
66B GLN* 1.3 75.1 - - - +
68B GLU* 1.3 57.9 + - - +
70B LEU* 4.4 2.7 - - - -
71B LYS* 2.8 33.1 + - - +
195D LEU* 3.6 28.5 - - + -
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Residues in contact with GLU 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B MET* 2.9 22.9 + - - +
65B ASP* 4.0 5.2 - - - +
67B LEU* 1.3 74.7 - - - +
69B ALA* 1.3 63.1 + - - +
71B LYS* 3.9 1.6 - - - +
72B LYS* 3.2 33.2 + - + +
191D ARG* 2.9 61.7 + - - +
195D LEU* 4.2 14.4 - - + -
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Residues in contact with ALA 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MET* 4.1 16.8 + - - +
4B LEU* 3.8 21.1 - - + -
65B ASP 3.2 15.9 + - - +
66B GLN 3.9 1.1 - - - +
68B GLU* 1.3 77.5 - - - +
70B LEU* 1.3 66.3 + - - +
72B LYS* 4.1 6.3 - - - +
73B GLN* 3.1 26.8 + - - +
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Residues in contact with LEU 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MET* 3.9 19.3 - - + -
28B ASP* 4.4 3.6 - - - +
32B PRO* 4.3 11.9 - - + +
35B ALA 4.3 0.2 - - - -
36B TYR* 3.8 31.2 - - + +
39B ARG* 3.5 33.4 - - - +
66B GLN 2.7 21.8 + - - +
67B LEU* 3.7 2.9 - - - +
69B ALA* 1.3 74.7 - - - +
71B LYS* 1.3 57.8 + - - +
73B GLN* 3.5 15.3 - - - +
74B LEU* 2.8 54.4 + - + +
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Residues in contact with LYS 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B TYR* 3.7 27.1 - - + +
67B LEU 2.8 16.6 + - - +
68B GLU* 3.9 4.5 - - - +
70B LEU* 1.3 74.2 - - - +
72B LYS* 1.3 61.2 + - + +
74B LEU* 3.1 7.7 + - - +
75B GLY* 2.9 26.4 + - - -
80B ILE* 4.0 21.0 - - + +
195D LEU* 2.8 36.2 + - + +
198D GLN* 2.7 35.8 + - - +
199D VAL* 3.8 16.4 - - - -
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Residues in contact with LYS 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B GLU* 3.2 21.4 + - + +
69B ALA* 4.1 5.6 - - - +
71B LYS* 1.3 76.2 - - + +
73B GLN* 1.3 58.4 + - - +
75B GLY* 2.8 22.5 + - - -
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Residues in contact with GLN 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MET* 3.4 34.6 + - - +
32B PRO* 6.0 2.4 - - - +
69B ALA 3.1 14.2 + - - +
70B LEU* 3.5 15.2 - - - +
72B LYS* 1.3 79.5 - - - +
74B LEU* 1.3 67.3 + - + +
75B GLY 3.2 2.0 + - - -
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Residues in contact with LEU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B PRO* 3.7 40.4 - - + +
33B VAL* 4.2 2.0 - - + +
36B TYR* 4.1 4.5 - - + -
70B LEU* 2.8 43.1 + - + +
71B LYS 3.1 5.6 + - - +
73B GLN* 1.3 83.6 - - + +
75B GLY* 1.3 58.2 + - - +
76B ASP 3.3 2.7 - - - -
77B ASN* 2.9 40.0 + - + +
80B ILE* 3.6 39.9 - - + +
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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
------------------------------------------------------------
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