Contacts of the helix formed by residues 44 - 59 (chain B) in PDB entry 1H9T
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 44 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38B SER* 3.6 1.6 - - - -
43B VAL* 1.3 77.1 - - - +
45B ARG* 1.3 70.9 + - - +
46B THR* 3.9 8.5 - - - +
47B THR* 2.8 11.8 + - - -
48B LEU 2.6 20.6 + - - -
9Y C 2.8 42.2 + - + +
10Y G 3.4 46.8 + - + +
11Y T 4.9 6.1 - - + -
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Residues in contact with ARG 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B GLU* 2.6 36.9 + - + +
35B ARG* 3.2 47.9 - - - +
38B SER* 3.3 17.1 + - - +
44B THR* 1.3 74.6 - - + +
46B THR* 1.3 72.9 + - - +
48B LEU* 2.7 8.4 + - - -
49B ARG* 2.6 35.5 + - + +
6X G 3.2 9.5 + - - -
7X G 2.7 50.1 + - - -
8X T 3.8 8.8 + - + +
11Y T 5.1 16.4 - - + +
12Y A 4.6 3.8 - - - +
13Y C 4.4 3.0 - - - +
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Residues in contact with THR 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A THR* 3.6 30.7 - - + -
44B THR* 4.0 6.2 - - - +
45B ARG* 1.3 89.9 - - - +
47B THR* 1.3 57.9 + - - +
49B ARG* 2.7 30.5 + - - +
50B GLU* 3.1 13.5 + - - +
9X A 5.0 1.3 + - - +
8Y T 5.6 5.2 - - + -
9Y C 4.0 17.5 - - + +
10Y G 3.0 37.0 + - - +
11Y T 4.3 4.9 + - - -
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Residues in contact with THR 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B PRO* 3.8 14.1 - - + -
9B ALA* 3.7 32.8 - - + +
43B VAL* 3.9 5.6 - - + -
44B THR* 2.8 15.4 + - - -
46B THR* 1.3 77.2 - - - +
48B LEU* 1.3 69.0 + - - +
50B GLU* 3.5 14.4 + - + +
51B VAL* 3.1 18.6 + - + +
8Y T 3.1 28.3 - - - +
9Y C 3.1 18.2 + - - +
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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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12B ALA* 5.5 2.0 - - + -
16B ILE* 3.8 19.5 - - + -
34B GLU* 3.7 12.6 - - + +
37B LEU* 3.9 14.8 - - + -
38B SER* 3.3 38.4 - - - +
41B ILE* 5.3 3.1 - - + -
43B VAL* 3.9 14.6 - - + -
44B THR 2.6 15.1 + - - +
45B ARG* 2.7 12.0 + - + +
47B THR* 1.3 71.5 - - - +
49B ARG* 1.3 68.3 + - + +
51B VAL* 2.5 23.4 + - + +
52B LEU* 2.9 49.5 + - + +
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Residues in contact with ARG 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A GLU* 2.9 48.9 + - + +
34B GLU* 2.6 43.8 + - - -
45B ARG* 2.6 43.4 + - + +
46B THR* 2.7 11.6 + - - +
48B LEU* 1.3 73.6 - - + +
50B GLU* 1.3 64.5 + - - +
52B LEU* 3.1 11.3 + - - +
53B GLN* 3.0 36.6 + - - +
63B ILE* 5.4 1.4 - - - +
7X G 2.3 61.1 + - - +
8X T 3.5 16.4 - - + +
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Residues in contact with GLU 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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46A THR* 5.7 1.2 - - - +
49A ARG* 2.9 57.3 + - + +
50A GLU* 4.6 11.2 - - + +
53A GLN* 3.5 32.2 + - + +
9B ALA* 5.3 3.3 - - + +
46B THR* 3.1 13.3 + - + +
47B THR* 3.8 14.9 - - - +
48B LEU 2.8 2.6 + - - -
49B ARG* 1.3 80.7 - - - +
51B VAL* 1.3 64.8 + - + +
53B GLN* 3.2 13.5 + - - +
54B ARG* 3.2 21.9 + - - +
7Y G 5.3 0.2 - - - +
8Y T 4.0 20.3 + - - +
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Residues in contact with VAL 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ALA* 3.8 31.6 - - + +
12B ALA* 4.2 11.0 - - + +
13B GLU* 3.1 38.1 - - + +
16B ILE* 4.8 3.1 - - + -
47B THR 3.1 17.9 - - - +
48B LEU* 2.5 16.1 + - + +
50B GLU* 1.3 71.5 - - - +
52B LEU* 1.3 63.2 + - - +
54B ARG* 2.9 14.6 - - - +
55B LEU* 2.8 36.2 + - + +
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Residues in contact with LEU 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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16B ILE* 3.8 19.3 - - + -
31B LEU* 4.8 14.6 - - + -
34B GLU* 4.2 22.7 - - + +
37B LEU* 4.9 2.5 - - + -
48B LEU* 2.9 45.3 + - + -
49B ARG* 3.8 10.5 - - - +
51B VAL* 1.3 77.6 - - - +
53B GLN* 1.3 57.6 + - + +
55B LEU* 3.3 7.6 + - - +
56B ALA* 2.8 30.5 + - - +
61B LEU* 3.3 27.3 - - + +
63B ILE* 3.8 20.4 - - + +
69B THR* 5.4 4.3 - - + +
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Residues in contact with GLN 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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50A GLU* 3.8 31.3 + - + +
54A ARG* 3.9 42.7 + - + +
49B ARG* 3.0 39.9 + - - +
50B GLU 3.4 6.1 - - - +
52B LEU* 1.3 73.3 - - - +
54B ARG* 1.3 68.9 + - - +
55B LEU 2.8 2.5 + - - -
56B ALA* 2.9 23.1 + - - +
57B ARG* 3.1 6.2 + - - +
63B ILE* 4.2 13.9 - - - +
7X G 4.0 11.3 + - - -
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Residues in contact with ARG 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A GLN* 4.0 35.6 + - - +
54A ARG* 4.4 11.6 - - - +
57A ARG* 2.5 57.7 + - - +
1241A CL 4.0 19.8 - - - +
9B ALA* 4.2 22.6 - - - +
10B GLY* 5.3 3.8 - - - +
13B GLU* 2.9 21.5 + - - +
50B GLU* 3.2 18.4 + - - +
51B VAL* 2.9 25.3 - - - +
53B GLN* 1.3 74.9 - - - +
55B LEU* 1.3 63.2 + - - +
57B ARG* 3.3 9.4 + - - +
58B ASP* 3.4 7.3 + - - +
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Residues in contact with LEU 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ARG* 5.8 0.2 - - - +
13B GLU* 3.8 14.8 - - + +
16B ILE* 3.8 28.3 - - + -
17B ILE* 3.7 28.0 - - + -
20B ILE* 6.3 0.2 - - + -
51B VAL* 2.8 41.5 + - + +
52B LEU* 3.3 9.4 - - - +
53B GLN 2.8 0.6 + - - -
54B ARG* 1.3 74.3 - - - +
56B ALA* 1.3 69.1 + - - +
57B ARG 2.9 1.4 + - - -
58B ASP* 2.9 17.0 + - - +
59B GLY 3.1 6.8 + - - -
60B TRP* 3.6 36.7 + - + +
61B LEU* 4.4 11.0 - - + -
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Residues in contact with ALA 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 LEU 2.8 15.6 + - - +
53B GLN* 3.1 14.1 - - - +
55B LEU* 1.3 71.2 - - - +
57B ARG* 1.3 60.9 + - - +
59B GLY* 2.8 24.1 + - - -
61B LEU* 4.4 22.0 - - + +
62B THR* 5.1 1.6 - - - +
63B ILE* 4.3 19.7 - - + +
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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
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13A GLU* 2.7 31.9 + - - -
17A ILE* 5.5 3.4 - - - +
54A ARG* 3.0 46.3 - - - +
55A LEU* 5.3 2.6 - - - +
57A ARG* 4.0 13.2 - - + -
58A ASP* 2.5 46.3 + - - +
81A ASN* 5.5 6.6 + - - +
53B GLN 3.1 5.3 + - - +
54B ARG* 3.5 11.2 - - - +
55B LEU 2.9 2.0 + - - -
56B ALA* 1.3 83.5 - - - +
58B ASP* 1.3 63.4 + - - +
59B GLY* 2.9 2.1 + - - -
81B ASN* 5.0 0.3 + - - -
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Residues in contact with ASP 58 (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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57A ARG* 2.9 52.4 + - - +
13B GLU* 5.1 1.9 - - - +
54B ARG 3.4 2.6 + - - +
55B LEU* 2.9 14.4 + - - +
57B ARG* 1.3 75.3 - - - +
59B GLY* 1.3 57.2 + - - +
60B TRP* 3.8 19.5 + - - +
78B SER* 2.8 21.7 + - - -
81B ASN* 3.4 41.9 + - - +
82B ILE* 4.6 4.4 - - + +
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Residues in contact with GLY 59 (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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55B LEU 3.1 1.0 + - - -
56B ALA 2.8 17.0 + - - -
57B ARG 2.8 2.2 - - - -
58B ASP* 1.3 80.5 - - - +
60B TRP* 1.3 70.0 - - - +
61B LEU 3.4 4.2 - - - +
62B THR* 4.8 0.2 + - - -
72B ASN* 4.2 0.2 - - - -
74B PHE* 5.2 0.7 - - - -
77B THR* 2.9 36.5 + - - -
78B SER* 3.5 2.9 - - - -
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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