Contacts of the helix formed by residues 54 - 64 (chain A) in PDB entry 4TMU
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 SER 54 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A GLY* 3.2 3.6 - - - -
53A LYS* 1.3 83.2 - - - +
55A LEU* 1.3 57.9 + - - +
57A TYR* 3.1 20.3 + - - -
58A GLN* 2.9 49.3 + - - +
81A GLN* 3.0 25.0 + - - -
146A ASP* 3.8 6.2 + - - -
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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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17A LEU* 4.4 13.0 - - + -
21A PHE* 3.4 47.8 - - + -
23A TYR* 3.8 32.5 - - + -
30A GLN* 4.9 13.9 - - - +
34A ILE* 4.1 3.4 - - + +
52A GLY* 3.3 22.8 + - - +
53A LYS 3.1 1.0 - - - -
54A SER* 1.3 77.6 - - - +
56A CYS* 1.3 62.9 + - - +
58A GLN* 3.8 7.9 - - - +
59A ILE* 3.1 34.2 + - + +
60A PRO* 3.7 0.3 - - - +
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Residues in contact with CYS 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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30A GLN* 5.6 9.9 - - - -
33A ILE* 4.2 13.2 - - + +
34A ILE* 3.9 17.8 - - - +
37A VAL* 4.9 0.3 - - - +
45A VAL* 4.4 7.9 - - - -
47A MET* 3.7 30.1 - - - -
52A GLY 4.8 1.8 - - - -
53A LYS* 3.0 23.9 + - - +
55A LEU* 1.3 77.8 - - - +
57A TYR* 1.3 57.5 + - - +
60A PRO* 3.2 17.7 - - - +
178A MET* 3.4 30.3 - - + +
180A LEU* 3.8 2.5 - - + -
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Residues in contact with TYR 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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54A SER* 3.1 20.5 + - - -
56A CYS* 1.3 79.8 - - - +
58A GLN* 1.3 76.2 + - + +
59A ILE 3.3 2.7 - - - -
60A PRO* 3.3 4.7 - - - +
61A ALA* 3.0 24.8 + - - +
68A THR* 4.9 1.6 - - + -
70A VAL* 3.6 28.4 - - + +
81A GLN* 2.8 30.2 + - - -
118A LEU* 4.4 4.0 - - + -
120A TYR* 3.0 21.9 + - - -
142A MET* 3.3 17.1 - - + +
144A ALA* 3.8 12.8 - - + -
146A ASP* 3.0 21.2 + - + -
178A MET* 3.9 9.0 - - - -
180A LEU* 3.5 30.5 - - + -
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Residues in contact with GLN 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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21A PHE* 3.8 20.5 - - + -
54A SER* 2.9 28.6 + - - +
55A LEU* 3.8 19.1 - - - +
57A TYR* 1.3 91.4 + - + +
59A ILE* 1.3 63.0 + - - +
61A ALA* 3.3 6.6 + - - +
62A LEU* 3.1 29.9 + - + +
81A GLN* 3.9 14.8 + - - +
85A LEU* 3.6 26.1 - - + +
118A LEU* 4.1 10.7 - - + +
120A TYR* 3.1 21.2 + - - -
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Residues in contact with ILE 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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13A ALA* 3.7 36.8 - - + +
16A VAL* 4.3 10.0 - - + +
17A LEU* 3.8 39.3 - - + -
21A PHE* 3.6 21.5 - - + -
26A PHE* 4.1 10.3 - - + -
34A ILE* 4.3 10.1 - - + -
55A LEU* 3.1 25.9 + - + +
58A GLN* 1.3 76.8 - - - +
60A PRO* 1.3 71.5 - - + +
62A LEU* 3.0 12.1 + - - +
63A VAL* 3.1 13.5 + - - +
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Residues in contact with PRO 60 (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 ILE* 4.2 10.8 - - + -
37A VAL* 3.8 25.6 - - + -
38A LEU* 3.7 28.3 - - + -
55A LEU 3.7 1.3 - - - +
56A CYS 3.2 26.9 - - - +
57A TYR* 3.3 12.1 - - - +
59A ILE* 1.3 99.9 - - + +
61A ALA* 1.3 54.7 + - - -
63A VAL* 3.9 3.1 - - + +
64A LYS* 2.9 37.6 + - - +
142A MET* 4.5 2.5 - - + -
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Residues in contact with ALA 61 (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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57A TYR 3.0 19.1 + - - +
58A GLN 3.5 6.5 - - - +
59A ILE 3.2 0.2 - - - -
60A PRO* 1.3 77.5 - - - +
62A LEU* 1.3 59.5 + - - +
63A VAL 3.4 0.2 - - - -
64A LYS* 3.5 6.0 - - - +
66A GLY 4.6 0.7 - - - +
68A THR* 3.1 37.9 + - + +
117A ARG* 3.2 28.5 + - - +
118A LEU* 3.9 18.4 - - + -
142A MET* 4.1 2.6 - - + +
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Residues in contact with LEU 62 (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 VAL* 3.9 32.0 - - + +
20A THR* 4.1 12.8 - - + +
21A PHE* 4.1 9.2 - - + -
58A GLN* 3.1 14.3 + - + +
59A ILE 3.0 9.0 + - - +
61A ALA* 1.3 79.7 - - - +
63A VAL* 1.3 60.3 + - - +
85A LEU* 5.5 0.4 - - + -
90A VAL* 3.8 44.2 - - + -
117A ARG* 3.1 36.7 + - + +
118A LEU* 4.5 4.0 - - + -
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Residues in contact with VAL 63 (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 GLN* 4.0 15.7 - - - +
12A LEU* 4.0 33.8 - - + +
13A ALA* 3.8 34.1 - - + +
16A VAL* 4.0 8.3 - - + -
38A LEU* 4.1 13.5 - - + -
59A ILE 3.1 14.0 + - - +
60A PRO* 3.3 5.8 + - + +
62A LEU* 1.3 78.0 - - - +
64A LYS* 1.3 67.3 + - - +
65A THR* 3.8 5.9 + - - +
117A ARG* 4.6 0.3 + - - -
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Residues in contact with LYS 64 (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 VAL* 3.1 44.9 + - - -
38A LEU* 3.9 24.5 + - + +
40A GLY* 4.8 2.8 - - - +
60A PRO 2.9 19.7 + - - +
61A ALA* 3.5 4.3 - - - +
62A LEU 3.7 0.2 - - - -
63A VAL* 1.3 77.7 - - - +
65A THR* 1.3 61.1 + - - +
117A ARG* 2.8 30.3 + - - -
141A ALA* 3.9 32.6 + - + +
142A MET* 4.4 7.2 - - + -
176A PRO* 4.0 18.2 - - - +
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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