Contacts of the helix formed by residues 13 - 19 (chain I) 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 GLY 13 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11I GLU* 4.2 3.6 - - - -
12I ARG* 1.3 83.3 - - - +
14I TRP* 1.3 55.6 + - - -
15I ALA 3.2 3.6 - - - +
16I ALA* 3.5 20.7 - - - +
17I ALA* 3.1 23.4 + - - +
57I PHE* 3.4 21.6 - - - -
58I ASP* 6.0 0.4 - - - -
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Residues in contact with TRP 14 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10I VAL* 4.0 18.8 - - + -
11I GLU* 3.0 31.4 - - + -
12I ARG 2.5 10.3 + - - -
13I GLY* 1.3 69.5 - - - -
15I ALA* 1.3 54.2 + - - +
17I ALA* 3.0 9.2 + - + +
18I LEU* 2.7 47.7 + - + +
52I ALA 4.8 0.4 + - - -
53I PHE* 3.2 49.8 + + + +
55I PHE 2.8 20.9 + - - -
56I PRO 3.8 0.4 + - - -
57I PHE* 3.3 44.0 - + - +
60I VAL* 4.3 10.3 - - + +
124I LEU* 3.7 35.0 - - + -
152I ALA* 4.0 18.2 - - + -
156I LEU* 4.3 7.0 - - + -
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Residues in contact with ALA 15 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6I LEU* 3.8 10.2 - - + +
7I SER* 4.1 26.9 - - - +
10I VAL* 3.7 10.9 - - + +
12I ARG* 3.1 28.8 - - + +
13I GLY 3.2 0.6 - - - +
14I TRP* 1.3 79.0 - - - +
16I ALA* 1.3 56.1 + - - +
18I LEU 3.4 0.7 + - - -
19I GLU* 3.0 29.5 + - - +
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Residues in contact with ALA 16 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13I GLY* 3.5 19.7 - - - +
14I TRP 3.3 0.2 - - - -
15I ALA* 1.3 79.7 - - - +
17I ALA* 1.3 61.3 + - - +
18I LEU 3.4 0.3 + - - -
19I GLU* 3.5 18.7 + - - +
20I PRO* 4.2 2.9 - - - +
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Residues in contact with ALA 17 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13I GLY 3.1 20.5 + - - +
14I TRP* 3.0 13.6 + - + +
16I ALA* 1.3 75.7 - - - +
18I LEU* 1.3 61.3 + - + +
20I PRO* 3.7 6.8 - - - +
57I PHE* 3.6 31.0 - - + -
151I CYS* 3.7 17.3 - - - -
155I ALA* 3.7 19.9 - - + +
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Residues in contact with LEU 18 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6I LEU* 3.6 26.4 - - + +
10I VAL* 4.8 4.0 - - + -
14I TRP* 2.7 41.8 + - + +
17I ALA* 1.3 73.1 - - - +
19I GLU* 1.3 68.3 + - - +
20I PRO* 3.1 4.3 - - - -
21I VAL* 2.7 41.0 + - + +
22I ALA 3.2 4.5 + - - -
25I VAL* 5.5 1.3 - - + -
50I LEU* 6.4 0.2 - - + -
53I PHE* 4.3 22.7 - - + -
148I VAL* 3.8 26.9 - - + +
151I CYS* 4.4 1.6 - - - -
152I ALA* 4.1 20.0 - - + +
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Residues in contact with GLU 19 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6I LEU* 4.1 6.5 - - - -
15I ALA 3.0 13.5 + - - +
16I ALA* 3.5 13.9 + - - +
18I LEU* 1.3 74.0 - - - +
20I PRO* 1.3 65.5 - - + +
22I ALA* 2.8 28.7 + - - +
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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