Contacts of the helix formed by residues 37 - 56 (chain B) in PDB entry 1T6S
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 37 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25B LEU* 4.2 1.1 - - - -
35B LYS 4.3 6.1 - - - +
36B PHE* 1.3 75.9 - - - +
38B PRO* 1.3 74.7 - - - +
39B SER* 3.7 6.2 + - - -
40B GLU* 2.9 44.1 + - + +
41B LEU* 2.9 21.8 + - - +
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Residues in contact with PRO 38 (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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25B LEU* 4.3 24.9 - - + -
36B PHE 4.4 2.0 - - - +
37B THR* 1.3 86.5 - - - +
39B SER* 1.3 61.9 + - - +
41B LEU* 4.0 2.6 - - + +
42B GLN* 3.4 21.7 + - - +
68B TYR* 4.8 2.3 + - - -
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Residues in contact with SER 39 (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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37B THR* 3.1 6.0 + - - -
38B PRO* 1.3 81.5 - - - +
40B GLU* 1.3 64.8 + - - +
42B GLN* 3.4 6.2 + - - +
43B GLU* 3.1 29.5 + - - +
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Residues in contact with GLU 40 (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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5B ARG* 6.3 0.4 - - - +
8B LEU* 5.3 1.0 - - - +
34B HIS* 2.8 34.2 + - - -
35B LYS 3.9 3.5 - - - +
36B PHE* 3.5 14.9 - - + -
37B THR* 2.9 40.4 + - + +
39B SER* 1.3 78.0 - - - +
41B LEU* 1.3 61.9 + - - +
43B GLU* 3.3 14.1 + - - +
44B ALA* 3.1 20.9 + - + +
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Residues in contact with LEU 41 (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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12B LEU* 4.1 30.3 - - + -
25B LEU* 3.8 35.2 - - + -
28B LEU* 4.0 13.9 - - + -
36B PHE* 3.7 21.9 - - + -
37B THR 2.9 16.1 + - - +
38B PRO* 4.0 4.5 - - + +
40B GLU* 1.3 78.7 - - - +
42B GLN* 1.3 61.8 + - - +
44B ALA* 3.2 1.2 + - - +
45B VAL* 3.0 34.0 + - + +
68B TYR* 3.6 26.5 - - + +
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Residues in contact with GLN 42 (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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38B PRO 3.4 15.6 + - - +
39B SER* 3.8 6.1 - - - +
40B GLU 3.3 0.6 - - - -
41B LEU* 1.3 80.1 - - - +
43B GLU* 1.3 53.2 - - - +
45B VAL* 3.3 5.8 + - - +
46B ASP* 2.8 68.8 + - - +
63B ALA* 3.9 8.1 - - - +
68B TYR* 2.7 32.9 + - - +
414B NO3 3.1 27.9 + - - -
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Residues in contact with GLU 43 (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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5B ARG* 4.4 11.5 + - - +
39B SER* 3.1 20.4 + - - +
40B GLU* 3.4 15.9 - - - +
42B GLN* 1.3 74.9 - - - +
44B ALA* 1.3 64.1 + - - +
46B ASP* 3.4 12.6 + - + +
47B GLU* 3.2 21.1 + - - +
50B ARG* 4.6 5.9 + - - +
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Residues in contact with ALA 44 (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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5B ARG* 4.1 11.6 - - - +
9B LEU* 3.4 27.6 - - + +
12B LEU* 3.6 19.3 - - + -
36B PHE* 4.4 7.2 - - + -
40B GLU* 3.1 12.4 + - + +
41B LEU 3.2 8.5 + - - +
43B GLU* 1.3 73.4 - - - +
45B VAL* 1.3 66.1 + - - +
47B GLU* 3.2 4.7 + - - +
48B LEU* 3.2 26.7 + - - +
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Residues in contact with VAL 45 (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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12B LEU* 5.5 1.6 - - + -
16B ILE* 4.5 13.7 - - + -
41B LEU* 3.0 30.6 + - + +
42B GLN* 3.5 11.0 - - - +
44B ALA* 1.3 77.5 - - + +
46B ASP* 1.3 62.0 + - - +
48B LEU* 3.2 12.1 + - + +
49B ASN* 3.0 27.2 + - - +
61B ILE* 3.6 23.1 - - + -
68B TYR* 3.7 22.7 - - + -
414B NO3 3.4 25.6 - - - +
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Residues in contact with ASP 46 (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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42B GLN* 2.8 52.0 + - - +
43B GLU* 3.6 12.3 - - + +
44B ALA 3.2 0.2 - - - -
45B VAL* 1.3 77.0 - - - +
47B GLU* 1.3 57.5 + - - +
49B ASN* 3.3 8.8 + - - +
50B ARG* 2.8 53.4 + - - +
414B NO3 4.0 6.6 + - - -
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Residues in contact with GLU 47 (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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5B ARG* 2.9 33.4 + - - +
6B GLN* 4.0 12.1 + - - +
9B LEU* 3.3 25.0 - - + +
43B GLU 3.2 10.7 + - - +
44B ALA 3.2 8.7 + - - +
46B ASP* 1.3 76.2 - - - +
48B LEU* 1.3 65.6 + - - +
50B ARG* 3.0 20.4 + - + +
51B ASP* 3.0 30.9 + - - +
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Residues in contact with LEU 48 (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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9B LEU* 3.9 44.9 - - + +
10B ARG* 5.6 0.9 - - + -
12B LEU* 4.5 8.3 - - + -
13B GLU* 4.0 22.4 - - + +
16B ILE* 5.3 1.6 - - + -
44B ALA 3.2 13.9 + - - +
45B VAL* 3.2 10.3 + - + +
47B GLU* 1.3 77.7 - - - +
49B ASN* 1.3 64.2 + - - +
51B ASP* 2.9 21.5 + - + +
52B TYR* 2.9 40.7 + - + +
61B ILE* 3.8 22.4 - - + -
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Residues in contact with ASN 49 (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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45B VAL* 3.0 26.7 + - - +
46B ASP* 3.6 10.5 + - - +
48B LEU* 1.3 75.3 - - - +
50B ARG* 1.3 62.9 + - - +
52B TYR* 3.3 16.8 + - - +
53B GLU* 3.0 23.4 + - - +
60B ARG* 3.4 17.8 + - - +
61B ILE* 2.7 49.8 + - - +
414B NO3 4.1 8.7 + - - -
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Residues in contact with ARG 50 (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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43B GLU* 4.6 7.5 + - - +
46B ASP* 2.8 40.4 + - - +
47B GLU* 3.0 22.7 + - + +
49B ASN* 1.3 77.9 - - - +
51B ASP* 1.3 57.8 + - - +
53B GLU* 3.3 8.4 + - + +
54B ALA* 2.9 28.6 + - - +
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Residues in contact with ASP 51 (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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9B LEU* 5.0 2.1 - - - +
47B GLU* 3.0 31.1 + - - +
48B LEU* 2.9 18.0 + - + +
50B ARG* 1.3 74.3 - - - +
52B TYR* 1.3 65.1 + - + +
54B ALA* 3.6 7.7 - - - +
55B THR* 2.8 40.0 + - + +
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Residues in contact with TYR 52 (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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13B GLU* 2.7 33.2 + - - +
48B LEU* 2.9 36.0 + - + +
49B ASN* 3.4 29.6 - - - +
50B ARG 3.3 0.2 - - - -
51B ASP* 1.3 77.4 - - + +
53B GLU* 1.3 65.3 + - - +
55B THR* 5.2 0.2 - - - -
56B GLY* 3.1 4.3 + - - -
57B ARG* 2.9 48.7 + - + +
59B PHE* 3.7 32.3 - + - +
60B ARG* 3.8 7.2 - - - +
61B ILE* 3.8 8.8 - - + +
70B PHE* 3.3 37.1 - + - -
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Residues in contact with GLU 53 (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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49B ASN 3.0 13.4 + - - +
50B ARG* 3.5 11.4 - - + +
52B TYR* 1.3 78.6 - - - +
54B ALA* 1.3 63.6 + - - +
56B GLY* 3.4 8.7 + - - -
60B ARG* 2.9 31.1 + - - +
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Residues in contact with ALA 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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50B ARG 2.9 16.9 + - - +
51B ASP* 3.6 11.7 - - - +
52B TYR 3.3 0.2 - - - -
53B GLU* 1.3 80.5 - - - +
55B THR* 1.3 63.9 + - + +
56B GLY 3.6 0.2 + - - -
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Residues in contact with THR 55 (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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51B ASP* 2.8 27.4 + - + +
52B TYR* 4.0 0.3 - - - -
54B ALA* 1.3 79.0 - - + +
56B GLY* 1.3 61.0 + - - +
57B ARG* 3.5 39.4 + - - +
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Residues in contact with GLY 56 (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 TYR 3.1 5.6 + - - -
53B GLU 3.4 7.2 + - - -
54B ALA 3.3 3.8 + - - -
55B THR* 1.3 80.1 - - - +
57B ARG* 1.3 73.7 + - - +
58B THR* 3.9 6.8 + - - +
60B ARG* 6.0 0.4 - - - -
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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
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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