Contacts of the helix formed by residues 50 - 55 (chain E) in PDB entry 2ZHX
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 LEU 50 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6E LEU* 6.0 0.4 - - + -
9E LEU* 4.2 24.7 - - + +
10E VAL* 4.1 20.8 - - + +
18E LEU* 5.9 1.3 - - + -
25E VAL* 4.4 20.6 - - + -
46E GLY 4.8 1.2 + - - -
47E SER 5.0 1.8 + - - -
48E ASN 3.2 0.2 - - - -
49E VAL* 1.3 86.6 - - + +
51E ARG* 1.3 54.7 + - - +
52E ALA* 3.1 3.8 - - - -
53E PHE* 2.7 50.7 + - + +
54E THR* 3.7 6.1 + - - -
130E LEU* 3.6 28.0 - - + -
145E TRP* 4.4 9.9 - - + -
148E VAL* 5.6 2.7 - - + -
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Residues in contact with ARG 51 (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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203A GLY* 2.9 26.5 + - - +
204A SER 4.0 1.6 + - - -
205A ARG* 3.7 31.7 - - - +
209A ARG* 4.4 3.8 - - - +
47E SER 4.7 3.3 + - - -
48E ASN* 3.0 32.3 + - - +
50E LEU* 1.3 75.5 - - - +
52E ALA* 1.3 65.9 + - - +
54E THR* 2.8 27.8 + - - +
55E PHE* 3.7 10.5 - - + -
77E VAL* 3.0 45.6 + - - +
78E GLY 3.7 2.7 - - - +
79E LEU* 3.5 27.9 - - + +
114E ASP* 5.7 0.2 + - - -
116E THR* 3.0 37.7 + - - +
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Residues in contact with ALA 52 (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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14E TRP* 4.5 1.4 + - - -
49E VAL 5.6 1.8 - - - +
50E LEU* 4.5 2.5 - - - +
51E ARG* 1.3 79.2 - - - +
53E PHE* 1.3 63.0 + - + +
54E THR 3.4 2.9 + - - -
55E PHE* 4.0 15.5 + - - +
78E GLY 3.6 6.4 + - - +
79E LEU* 3.5 20.9 - - + +
124E LEU* 3.9 29.1 - - + +
125E LEU 4.3 12.3 - - - +
126E LEU* 4.6 13.7 - - + -
130E LEU* 5.7 3.6 - - + -
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Residues in contact with PHE 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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10E VAL* 3.6 20.7 - - + +
11E GLU* 3.1 21.7 + - - +
14E TRP* 3.2 49.7 - + + +
18E LEU* 4.3 15.3 - - + -
50E LEU* 2.7 53.4 + - + +
52E ALA* 1.3 74.9 - - + +
54E THR* 1.3 59.5 + - - +
55E PHE 3.5 1.1 - - - -
124E LEU* 4.9 2.0 - - + -
126E LEU* 3.8 28.3 - - + -
130E LEU* 4.0 11.2 - - + -
148E VAL* 5.0 7.6 - - + -
149E THR* 5.0 2.0 - - + -
152E ALA* 3.7 28.0 - - + -
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Residues in contact with THR 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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198A SER* 4.0 10.2 - - - +
202A PHE* 3.4 41.4 - - + +
203A GLY* 3.7 11.1 - - - +
205A ARG* 4.9 6.6 + - - +
9E LEU 4.6 8.7 + - - -
10E VAL* 5.1 1.8 - - - +
11E GLU* 3.3 17.5 - - + +
47E SER 5.7 0.2 + - - -
50E LEU 3.7 3.5 + - - -
51E ARG* 2.8 32.2 + - - +
53E PHE* 1.3 72.1 - - - +
55E PHE* 1.3 64.9 + - - +
56E PRO 3.9 0.5 - - - -
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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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198A SER 4.8 0.7 - - - -
200A GLY* 3.9 15.5 - - - -
202A PHE 3.8 15.9 - - - -
203A GLY* 3.4 29.2 - - - -
204A SER 4.1 0.7 - - - -
11E GLU* 4.4 0.2 - - - -
14E TRP* 3.0 21.8 + - - -
51E ARG* 3.7 27.4 - - + -
52E ALA* 4.0 9.9 + - - +
53E PHE 4.0 0.2 - - - -
54E THR* 1.3 76.3 - - - +
56E PRO* 1.4 76.5 - - + +
60E VAL* 6.0 0.4 - - + -
79E LEU* 4.5 4.0 - - + -
116E THR* 4.2 13.9 - - + -
119E ALA* 3.6 35.9 - - + +
120E GLN* 3.7 32.8 - - + -
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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