Contacts of the helix formed by residues 44 - 59 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A SER* 4.1 1.8 - - - -
43A VAL* 1.3 81.6 - - - +
45A ARG* 1.3 79.1 + - + +
46A THR* 4.4 3.8 - - - +
47A THR* 3.0 9.2 + - - -
48A LEU 2.8 17.7 + - - -
9X A 2.8 60.1 + - + +
10X C 3.6 35.9 + - + +
11X G 6.0 0.2 - - - +
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Residues in contact with ARG 45 (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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34A GLU* 3.4 40.3 + - + +
35A ARG* 4.0 32.1 - - - +
38A SER* 3.7 19.7 + - - +
44A THR* 1.3 76.1 - - + +
46A THR* 1.3 58.9 + - - +
48A LEU* 2.4 32.9 + - - +
49A ARG* 2.8 18.6 + - - +
10X C 6.3 0.2 - - + -
11X G 5.5 5.1 + - - +
12X A 4.2 9.9 - - - +
6Y G 3.4 17.8 + - - -
7Y G 2.7 51.3 + - - -
8Y T 3.4 13.7 + - - -
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Residues in contact with THR 46 (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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44A THR* 3.2 2.5 - - - +
45A ARG* 1.3 75.2 - - - +
47A THR* 1.3 58.4 + - - +
48A LEU 2.6 1.6 + - - -
49A ARG* 2.6 38.1 + - + +
50A GLU* 3.1 21.5 + - + +
46B THR* 3.6 31.6 - - + -
50B GLU* 5.7 1.6 - - - +
8X T 6.3 2.5 - - + -
9X A 5.0 8.5 - - - +
10X C 3.3 33.3 + - - +
11X G 4.2 4.7 + - - -
8Y T 6.4 1.1 - - + -
9Y C 4.8 1.7 + - - +
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Residues in contact with THR 47 (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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8A PRO* 4.3 3.6 - - + -
9A ALA* 4.1 20.2 - - + +
43A VAL* 4.1 6.8 - - + +
44A THR* 3.0 13.9 + - - -
46A THR* 1.3 79.4 - - - +
48A LEU* 1.3 59.8 + - - +
50A GLU* 3.9 13.3 - - - +
51A VAL* 3.0 23.9 + - - +
8X T 3.1 43.0 - - - +
9X A 3.0 25.0 + - - +
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Residues in contact with LEU 48 (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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12A ALA* 5.4 2.2 - - + -
16A ILE* 3.8 20.9 - - + -
34A GLU* 3.2 34.1 - - + +
37A LEU* 4.0 10.1 - - + -
38A SER* 3.7 15.0 - - - +
41A ILE* 4.9 8.3 - - + -
43A VAL* 3.8 14.8 - - + +
44A THR 2.8 9.6 + - - +
45A ARG* 2.4 26.4 + - + +
47A THR* 1.3 71.6 - - - +
49A ARG* 1.3 49.3 + - + +
51A VAL* 2.8 13.1 + - + +
52A LEU* 2.7 61.8 + - + -
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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
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34A GLU* 2.8 36.0 + - - -
45A ARG* 2.8 29.7 + - - +
46A THR* 2.6 24.1 + - + +
48A LEU* 1.3 67.7 - - - +
50A GLU* 1.3 59.0 + - - +
52A LEU* 2.8 10.2 + - - +
53A GLN* 2.5 46.7 + - - +
63A ILE* 5.5 0.6 - - - +
50B GLU* 2.9 47.1 + - + +
7Y G 2.8 56.8 + - - +
8Y T 3.4 16.6 - - + +
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Residues in contact with GLU 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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9A ALA* 5.3 2.9 - - + +
46A THR* 3.1 18.7 + - + +
47A THR* 3.9 16.6 - - + +
49A ARG* 1.3 82.5 - - - +
51A VAL* 1.3 63.6 + - + +
53A GLN* 3.0 9.7 + - - +
54A ARG* 2.9 24.7 + - - +
46B THR* 6.0 0.2 - - - -
49B ARG* 2.9 58.0 + - + +
50B GLU* 4.7 10.8 - - + +
53B GLN* 3.8 27.9 + - + +
8X T 3.9 20.9 + - - +
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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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9A ALA* 3.7 30.5 - - + +
12A ALA* 4.1 12.8 - - + +
13A GLU* 3.4 37.2 - - + +
16A ILE* 4.5 4.7 - - + -
47A THR 3.0 20.0 - - - +
48A LEU* 2.8 10.7 + - + +
50A GLU* 1.3 77.0 - - - +
52A LEU* 1.3 63.4 + - - +
54A ARG* 3.0 23.9 - - - +
55A LEU* 3.0 24.1 + - + +
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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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16A ILE* 3.8 20.2 - - + -
31A LEU* 4.8 14.4 - - + -
34A GLU* 3.9 28.5 - - + +
37A LEU* 5.2 0.7 - - + -
48A LEU* 2.7 47.6 + - + +
49A ARG* 2.8 10.7 + - - +
51A VAL* 1.3 73.0 - - - +
53A GLN* 1.3 51.0 + - + +
55A LEU* 3.4 2.5 - - - +
56A ALA* 2.8 35.2 + - - +
61A LEU* 3.0 31.6 - - + +
63A ILE* 4.1 14.6 - - + +
69A THR* 4.9 6.5 - - + +
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Residues in contact with GLN 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* 2.5 26.0 + - - +
50A GLU* 3.4 4.7 - - - +
52A LEU* 1.3 71.8 - - - +
54A ARG* 1.3 62.6 + - - +
56A ALA* 3.0 17.7 + - - +
57A ARG* 3.1 12.1 + - - +
63A ILE* 4.0 10.7 - - - +
1241A CL 3.0 33.7 - - - +
50B GLU* 3.5 41.4 + - + +
54B ARG* 4.0 29.4 + - + +
7Y G 3.9 18.6 + - - -
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Residues in contact with ARG 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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9A ALA* 4.2 24.4 - - - +
10A GLY* 5.2 3.0 - - - +
13A GLU* 2.9 39.1 + - - +
50A GLU* 2.9 22.4 + - - +
51A VAL* 3.0 22.5 - - - +
53A GLN* 1.3 75.9 - - - +
55A LEU* 1.3 61.8 + - - +
57A ARG* 3.5 5.2 + - - +
58A ASP* 3.3 22.6 + - - +
53B GLN* 3.9 36.7 + - + +
54B ARG* 4.4 12.5 - - - +
57B ARG* 3.0 36.6 - - - +
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Residues in contact with LEU 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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13A GLU* 3.9 18.8 - - + +
16A ILE* 4.2 27.1 - - + -
17A ILE* 4.0 19.3 - - + -
20A ILE* 6.0 0.2 - - + -
51A VAL* 3.0 40.3 + - + +
52A LEU* 3.4 5.2 - - - +
54A ARG* 1.3 75.9 - - - +
56A ALA* 1.3 69.4 + - - +
57A ARG 2.8 1.3 - - - -
58A ASP* 2.6 24.0 + - - +
59A GLY 3.2 8.0 + - - -
60A TRP* 3.1 41.4 + - + +
61A LEU* 4.5 11.2 - - + -
57B ARG* 5.3 0.4 - - - +
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Residues in contact with ALA 56 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A LEU 2.8 13.9 + - - +
53A GLN* 3.1 15.5 - - - +
55A LEU* 1.3 75.9 - - - +
57A ARG* 1.3 61.5 + - - +
59A GLY* 3.6 8.8 + - - -
61A LEU* 3.6 28.4 - - + +
62A THR* 5.3 0.4 - - - -
63A ILE* 3.8 30.1 - - + +
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Residues in contact with ARG 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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53A GLN 3.1 6.4 + - - +
54A ARG* 3.5 11.9 - - - +
55A LEU 2.6 4.4 + - - -
56A ALA* 1.3 76.1 - - - +
58A ASP* 1.3 70.8 + - - +
59A GLY* 3.3 0.5 + - - -
81A ASN* 5.1 0.3 + - - -
13B GLU* 3.5 15.3 + - - -
54B ARG* 2.5 69.4 + - - +
55B LEU* 5.3 0.4 - - - +
57B ARG* 4.0 12.8 - - + -
58B ASP* 2.9 45.2 + - - +
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Residues in contact with ASP 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 ARG 3.3 5.2 + - - +
55A LEU* 2.6 17.5 + - - +
57A ARG* 1.3 80.6 - - - +
59A GLY* 1.3 58.2 + - - +
60A TRP* 3.8 18.8 + - + +
78A SER* 3.0 17.5 + - - -
79A GLY 4.6 0.3 + - - -
81A ASN* 3.1 39.9 + - - +
82A ILE* 5.6 5.2 - - + +
85A THR* 5.8 3.8 - - - +
57B ARG* 2.5 53.0 + - - +
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Residues in contact with GLY 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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55A LEU 3.2 2.0 + - - -
56A ALA 3.6 6.0 + - - -
57A ARG 3.2 1.7 - - - -
58A ASP* 1.3 80.9 - - - +
60A TRP* 1.3 71.7 - - - +
61A LEU 4.2 3.6 - - - +
72A ASN* 3.8 3.1 - - - +
74A PHE* 4.4 5.3 - - - +
77A THR* 2.7 31.7 + - - +
78A SER* 2.8 15.9 - - - -
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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
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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