Contacts of the helix formed by residues 43 - 57 (chain A) in PDB entry 3SHD
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 43 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A LEU* 4.1 1.3 - - - -
42A GLU* 1.3 72.6 - - - +
44A LEU* 1.3 58.4 + - + +
45A VAL* 3.2 32.3 - - + +
46A GLU* 2.8 28.1 + - - -
47A ALA* 2.6 34.7 + - - +
142A GLY* 5.4 2.2 - - - -
143A ASP* 3.4 29.6 + - + +
146A TRP* 3.9 16.6 + - - -
150A LYS* 4.9 5.5 + - - +
70I GLN* 3.0 13.3 + - - +
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Residues in contact with LEU 44 (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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6A VAL* 4.0 9.9 - - + -
8A VAL* 3.6 16.6 - - + +
38A LEU* 3.8 22.4 - - + +
42A GLU 3.8 2.0 + - - -
43A THR* 1.3 73.0 - - + +
45A VAL* 1.3 63.9 + - - +
47A ALA* 3.1 8.7 - - - +
48A ALA* 2.8 20.6 + - - +
82A PHE* 3.9 44.2 - - + -
84A PHE* 4.5 5.4 - - + -
141A ILE* 3.7 40.6 - - + +
68I MET* 4.0 10.5 - - + -
70I GLN* 3.3 11.8 + - - +
80I LEU* 4.7 4.5 - - + -
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Residues in contact with VAL 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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43A THR* 3.2 21.3 - - + -
44A LEU* 1.3 73.4 - - - +
46A GLU* 1.3 65.2 + - - +
48A ALA* 2.9 7.0 + - - +
49A ALA* 2.8 20.7 + - - +
61A GLN* 4.2 14.6 - - + +
62A PRO* 3.7 28.6 - - + +
84A PHE* 4.6 5.1 - - + -
138A LEU* 4.7 26.9 - - + -
141A ILE* 4.5 15.5 - - + -
142A GLY* 5.5 3.6 - - - -
143A ASP* 5.0 2.2 - - - +
150A LYS* 6.4 0.9 - - - -
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Residues in contact with GLU 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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41A ASP 4.5 3.3 - - - +
42A GLU* 3.9 18.1 - - + +
43A THR* 2.8 40.1 + - - +
45A VAL* 1.3 75.3 - - + +
47A ALA* 1.3 49.9 + - - +
49A ALA* 3.0 10.1 + - - +
50A ARG* 2.7 35.7 + - - +
61A GLN* 4.8 6.5 - - - +
146A TRP* 4.7 6.5 + - - -
149A THR 4.3 5.2 - - - +
150A LYS* 4.2 28.7 - - - +
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Residues in contact with ALA 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 VAL* 3.7 16.6 - - + -
37A HIS 4.8 0.2 - - - +
38A LEU* 3.6 17.0 - - + -
42A GLU* 3.5 27.6 - - - +
43A THR 2.6 15.0 + - - +
44A LEU* 3.1 11.2 - - - +
46A GLU* 1.3 70.3 - - - +
48A ALA* 1.3 52.3 + - - +
50A ARG* 2.7 28.9 + - - +
51A GLU* 2.8 19.8 + - - +
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Residues in contact with ALA 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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8A VAL* 3.3 15.8 - - + +
10A CYS* 3.8 21.0 - - - -
44A LEU 2.8 14.4 + - - +
45A VAL 2.9 7.8 + - - +
47A ALA* 1.3 71.0 - - - +
49A ALA* 1.3 63.5 + - - +
51A GLU* 4.5 1.5 - - - +
52A LEU* 3.2 23.4 + - - +
62A PRO* 4.0 7.6 - - + -
84A PHE* 3.7 29.6 - - + -
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Residues in contact with ALA 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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45A VAL 2.8 14.4 + - - +
46A GLU* 3.4 9.2 - - - +
48A ALA* 1.3 74.1 - - - +
50A ARG* 1.3 62.8 + - - +
52A LEU* 3.5 3.9 + - - +
53A TRP* 3.2 21.5 + - - +
58A ILE 5.0 0.5 - - - +
60A ALA 4.0 21.4 - - - +
61A GLN* 3.9 24.7 - - - +
62A PRO* 4.1 7.4 - - + +
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Residues in contact with ARG 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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37A HIS 3.2 21.8 + - - -
39A GLU* 3.6 25.4 + - - -
42A GLU* 2.3 44.3 + - - +
46A GLU 2.7 16.7 + - - +
47A ALA* 2.7 12.9 + - - +
49A ALA* 1.3 69.9 - - - +
51A GLU* 1.3 90.6 + - - +
53A TRP* 2.9 8.9 + - + +
54A GLU* 2.9 58.3 + - + +
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Residues in contact with GLU 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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8A VAL* 4.8 4.5 - - + -
34A PRO* 4.7 3.0 - - - +
35A ALA* 3.4 7.1 - - - +
36A GLY* 3.6 25.1 - - - +
37A HIS 3.8 3.6 - - - +
47A ALA 2.8 19.7 + - - +
48A ALA 4.5 1.8 - - - +
50A ARG* 1.3 100.1 + - - +
52A LEU* 1.3 61.1 + - - +
54A GLU* 3.8 6.6 - - - +
55A GLU* 3.0 29.8 + - - +
154A MN 2.3 29.3 + - - -
155A MN 2.2 32.3 + - - -
156A SO4 2.6 4.6 + - - -
157A SO4 3.1 2.8 + - - -
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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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10A CYS* 5.0 5.4 - - - -
12A VAL* 4.4 15.3 - - + -
19A LEU* 4.4 2.0 - - + -
34A PRO* 3.5 34.9 - - + +
48A ALA 3.2 20.1 + - - +
49A ALA* 3.6 5.6 - - - +
50A ARG 3.1 0.8 - - - -
51A GLU* 1.3 74.5 - - - +
53A TRP* 1.3 62.2 + - - +
56A THR* 2.4 54.5 + - + +
58A ILE* 3.6 37.2 - - + +
60A ALA* 4.2 16.4 - - + +
86A ILE* 4.3 18.4 - - + -
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Residues in contact with TRP 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 ALA 3.2 9.2 + - - +
50A ARG* 2.9 10.1 + - + +
52A LEU* 1.3 77.0 - - - +
54A GLU* 1.3 73.6 + - + +
57A GLY* 2.5 41.9 + - - -
58A ILE 3.4 20.8 + - - +
59A SER* 3.8 17.8 + - - +
97A HIS* 3.3 51.5 + + + -
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Residues in contact with GLU 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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39A GLU* 5.3 0.9 - - - +
50A ARG* 2.9 54.1 + - + +
51A GLU* 3.8 19.7 - - - +
53A TRP* 1.3 93.1 - - + +
55A GLU* 1.3 61.4 + - + +
97A HIS* 2.8 30.1 + - - +
98A ASP* 3.3 27.7 + - + +
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Residues in contact with GLU 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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21A VAL* 3.5 15.0 - - + +
34A PRO* 3.1 10.4 - - + +
35A ALA 3.1 19.4 + - - -
51A GLU* 3.0 21.3 + - - +
52A LEU 4.3 0.4 - - - +
54A GLU* 1.3 75.8 - - + +
56A THR* 1.3 63.4 + - + +
96A PRO* 3.7 6.4 - - - +
98A ASP* 5.2 2.2 - - + -
101A ILE* 3.3 48.0 - - + +
104A CYS* 3.8 0.2 - - - -
154A MN 2.6 13.3 + - - +
157A SO4 2.1 52.5 + - - -
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Residues in contact with THR 56 (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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19A LEU* 3.5 26.9 - - + -
21A VAL* 4.0 2.7 - - + -
34A PRO* 3.8 11.7 - - + -
52A LEU* 2.4 31.8 + - + +
54A GLU 3.4 0.8 + - - -
55A GLU* 1.3 80.8 - - - +
57A GLY* 1.3 60.2 + - - +
58A ILE* 2.8 26.0 + - - +
94A THR* 3.5 6.1 - - - -
95A GLN 2.6 35.2 + - - -
96A PRO* 4.0 1.8 - - - -
104A CYS* 3.9 17.9 - - - -
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Residues in contact with GLY 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 TRP* 2.5 37.4 + - - -
56A THR* 1.3 72.2 + - - +
58A ILE* 1.3 62.4 + - - +
59A SER 3.6 1.6 + - - -
93A PRO 5.1 3.1 - - - +
94A THR* 5.3 0.6 - - - -
95A GLN* 3.3 16.1 + - - +
97A HIS* 3.6 13.7 + - - -
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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