Contacts of the helix formed by residues 50 - 59 (chain A) in PDB entry 1SIQ
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 ARG 50 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A PHE* 3.3 10.5 + - - -
49A HIS* 1.3 70.1 - - - +
51A GLU* 1.3 73.1 + - - +
53A ILE* 3.1 25.1 + - - +
54A SER* 3.6 16.3 + - - -
127A GLY 2.7 25.1 + - - -
128A GLU* 3.1 18.0 + - - +
130A LEU* 3.6 20.7 - - + +
174A MET* 3.4 36.0 + - + +
176A ASP* 3.1 27.5 + - - -
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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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38A ARG* 4.9 7.5 + - - +
49A HIS* 3.3 30.1 - - + +
50A ARG* 1.3 93.6 + - - +
52A ILE* 1.3 56.7 + - - +
54A SER* 2.8 13.2 + - - -
55A GLU* 2.8 45.0 + - + +
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Residues in contact with ILE 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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30A TYR* 4.4 2.0 - - - +
35A LEU* 4.0 19.3 - - + -
38A ARG* 3.7 21.5 - - - +
48A PHE* 4.2 11.2 - - + -
49A HIS* 2.9 34.1 + - + +
51A GLU* 1.3 77.4 - - - +
53A ILE* 1.3 57.1 + - - +
55A GLU* 3.5 10.2 + - - +
56A MET* 3.0 50.8 + - + +
93A TYR* 3.5 46.9 - - + +
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Residues in contact with ILE 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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48A PHE* 4.0 17.5 - - + -
50A ARG* 3.1 16.6 + - - +
52A ILE* 1.3 73.7 - - - +
54A SER* 1.3 60.5 + - - +
56A MET* 3.8 21.7 - - + -
57A GLY* 3.0 21.0 + - - -
62A LEU* 3.6 17.8 - - + +
96A ALA* 4.2 28.9 - - + +
97A MET* 5.2 0.7 - - - -
100A GLN* 4.3 15.7 - - + +
127A GLY* 3.7 23.5 - - - +
129A LEU 4.8 1.3 - - - +
130A LEU* 4.2 24.0 - - + -
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Residues in contact with SER 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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50A ARG* 3.6 21.8 + - - -
51A GLU* 2.8 15.3 + - - -
53A ILE* 1.3 75.4 - - - +
55A GLU* 1.3 67.8 + - - +
57A GLY* 2.9 3.1 + - - -
58A GLU* 2.9 33.9 + - - +
126A LYS 4.0 12.0 - - - +
127A GLY 4.0 4.4 + - - -
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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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30A TYR* 2.5 44.4 + - + +
34A ARG* 2.8 31.2 + - - -
38A ARG* 3.1 27.4 + - - -
51A GLU* 2.8 26.9 + - + +
52A ILE* 3.7 1.9 - - - +
54A SER* 1.3 78.1 - - - +
56A MET* 1.3 61.9 + - - +
58A GLU* 3.1 15.7 + - - +
59A LEU* 3.0 30.9 + - + +
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Residues in contact with MET 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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27A PHE* 4.2 13.9 - - + -
30A TYR* 4.2 19.5 - - + +
35A LEU* 5.5 0.4 - - - -
52A ILE* 3.0 38.7 + - + +
53A ILE* 3.8 22.9 - - + +
55A GLU* 1.3 75.0 - - - +
57A GLY* 1.3 61.3 + - - +
59A LEU* 3.4 10.1 + - - +
60A GLY 3.1 3.6 + - - -
61A VAL* 3.1 31.1 + - + +
62A LEU* 3.7 16.5 + - + -
86A LEU* 4.0 26.2 - - + -
93A TYR 4.8 5.6 - - - +
96A ALA* 5.4 0.7 - - + -
97A MET* 4.3 21.8 - - + +
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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 ILE 3.0 12.4 + - - -
54A SER 2.9 8.3 + - - -
56A MET* 1.3 75.5 - - - +
58A GLU* 1.3 59.4 + - - +
60A GLY* 2.9 19.2 + - - -
62A LEU* 3.7 6.5 - - - +
125A ALA 3.4 24.4 - - - +
126A LYS* 3.7 17.7 - - - +
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Residues in contact with GLU 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 SER* 2.9 26.3 + - - +
55A GLU* 3.1 16.1 + - - +
57A GLY* 1.3 75.5 - - - +
59A LEU* 1.3 67.0 + - + +
60A GLY* 3.2 1.4 + - - -
126A LYS* 4.5 2.4 + - - +
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Residues in contact with LEU 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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26A THR* 5.6 5.6 - - + +
27A PHE* 3.9 17.3 - - + -
30A TYR* 3.5 49.8 - - + -
55A GLU* 3.0 30.4 + - + +
56A MET* 3.7 9.9 - - - +
58A GLU* 1.3 82.6 - - + +
60A GLY* 1.3 61.3 + - - +
61A VAL* 3.5 11.3 + - + +
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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