Contacts of the helix formed by residues 52 - 58 (chain E) in PDB entry 5TWV
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 GLN 52 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E ILE* 4.7 5.3 - - + +
51E GLU* 1.3 72.5 - - - +
53E GLY* 1.3 59.2 + - - +
54E ARG 3.3 2.2 - - - -
55E PHE* 3.2 16.7 + - + +
56E LEU* 3.0 23.9 + - - +
60F ILE* 5.8 8.3 - - + -
129F THR* 3.2 31.2 + - - +
130F SER* 3.4 12.1 - - - -
131F ASN* 4.3 2.4 + - - -
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Residues in contact with GLY 53 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E GLU* 3.4 7.2 - - - +
52E GLN* 1.3 75.6 - - - +
54E ARG* 1.3 61.2 + - - +
56E LEU* 3.2 4.8 + - - +
57E GLN* 2.9 30.4 + - - +
130F SER* 3.4 18.9 - - - +
131F ASN* 4.3 14.7 + - - -
132F PHE* 5.2 6.1 - - - -
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Residues in contact with ARG 54 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E GLU* 4.4 33.4 + - + +
52E GLN* 3.3 0.8 - - - +
53E GLY* 1.3 76.2 - - - +
55E PHE* 1.3 66.3 + - + +
57E GLN* 3.2 13.8 + - - +
58E ASP* 2.9 29.0 + - - +
39G LYS* 4.7 16.0 - - - +
176G ARG* 5.7 5.1 - - - +
179G GLU* 5.0 23.0 + - + +
180G THR* 6.3 3.8 - - + -
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Residues in contact with PHE 55 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E ILE* 4.8 9.2 - - + -
51E GLU 3.2 27.4 - - - -
52E GLN* 3.2 14.3 + - + +
54E ARG* 1.3 80.5 - - + +
56E LEU* 1.3 63.7 + - - +
58E ASP* 3.2 24.7 + - - +
62E THR* 4.6 8.8 - - + +
180G THR* 4.1 12.8 - - + -
205G LEU* 3.7 41.7 - - + -
206G ARG* 3.1 52.3 - - + +
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Residues in contact with LEU 56 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52E GLN 3.0 13.5 + - - +
53E GLY* 3.2 9.4 + - - +
55E PHE* 1.3 79.5 - - - +
57E GLN* 1.3 59.8 + - - +
58E ASP 3.4 0.2 + - - -
59E VAL* 3.3 24.1 + - + +
46F ILE* 5.1 20.6 - - + +
49F ILE* 6.4 2.0 - - + -
50F GLY* 6.5 1.1 - - - -
126F ASN* 5.3 2.9 - - + +
130F SER* 3.6 22.2 - - - +
132F PHE* 5.2 13.0 - - + -
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Residues in contact with GLN 57 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53E GLY 2.9 16.7 + - - +
54E ARG* 3.2 17.5 + - - +
56E LEU* 1.3 77.0 - - - +
58E ASP* 1.3 59.5 + - - +
59E VAL* 2.9 16.0 + - - +
68G TRP* 5.9 4.9 - - - -
176G ARG* 5.7 14.5 - - + +
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Residues in contact with ASP 58 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54E ARG 2.9 15.9 + - - +
55E PHE* 3.2 16.3 + - - +
57E GLN* 1.3 73.7 - - - +
59E VAL* 1.3 60.8 + - - +
60E PHE 3.6 2.5 - - - -
61E THR* 3.7 23.4 - - + +
62E THR* 3.9 4.7 - - - +
176G ARG* 4.0 33.4 - - + +
177G ARG* 5.9 2.0 - - - -
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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