Contacts of the helix formed by residues 25 - 34 (chain N) 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 25 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170M ARG* 3.5 48.0 - - + +
171M ASP* 4.7 14.4 - - + +
174M THR* 6.1 4.3 - - + -
24N MET* 1.3 77.6 - - - +
26N PRO* 1.4 69.7 - - + +
27N GLU* 3.1 13.9 - - + +
28N GLU* 3.1 22.9 + - + +
29N VAL* 3.1 17.4 + - - +
40N ASP* 3.5 22.4 - - - +
41N ILE 5.1 0.2 - - - -
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Residues in contact with PRO 26 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25N LEU* 1.4 87.0 - - + +
27N GLU* 1.3 60.2 + - + +
29N VAL 3.8 1.1 - - - +
30N GLU* 3.2 30.5 + - - +
36N LYS* 3.6 24.9 - - + +
37N PRO* 3.5 42.3 - - + +
38N GLU 4.2 11.4 - - - +
39N SER 4.6 0.7 - - - +
40N ASP* 3.4 19.2 - - - +
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Residues in contact with GLU 27 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170M ARG* 3.2 29.0 + - - +
25N LEU* 3.1 11.0 - - + +
26N PRO* 1.3 84.2 - - + +
28N GLU* 1.3 62.2 + - + +
30N GLU* 4.5 7.0 - - - +
31N GLU* 4.1 14.0 + - - +
36N LYS* 5.3 3.8 - - - +
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Residues in contact with GLU 28 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169M GLY* 3.8 5.0 - - - -
170M ARG* 3.3 53.3 + - + +
171M ASP 4.6 0.5 + - - -
190M PRO* 4.7 9.7 - - - +
195M LEU* 5.9 0.7 - - - +
196M SER* 5.8 2.8 - - - -
23N LEU 4.6 0.5 - - - +
24N MET* 3.3 42.8 - - + +
25N LEU* 3.1 30.3 + - + +
27N GLU* 1.3 78.7 - - + +
29N VAL* 1.3 61.4 + - - +
31N GLU* 3.8 14.9 - - - +
32N VAL* 3.8 10.0 - - - +
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Residues in contact with VAL 29 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195M LEU* 5.0 9.2 - - + -
24N MET* 4.3 13.0 - - + -
25N LEU 3.1 19.8 + - - +
26N PRO* 3.6 1.3 + - + -
27N GLU 3.4 0.2 - - - -
28N GLU* 1.3 75.2 - - - +
30N GLU* 1.3 66.6 + - - +
31N GLU 3.2 1.8 - - - -
32N VAL* 3.0 14.4 + - - +
33N ILE* 3.1 17.5 + - + +
37N PRO* 4.1 11.4 - - + -
41N ILE* 4.3 20.9 - - + -
58N LEU* 3.8 20.2 - - + -
68N TRP* 3.8 33.2 - - + -
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Residues in contact with GLU 30 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26N PRO 3.2 16.5 + - - +
27N GLU* 4.5 6.0 - - - +
28N GLU 3.6 0.2 - - - -
29N VAL* 1.3 75.6 - - - +
31N GLU* 1.3 66.7 + - - +
34N GLY* 2.7 34.3 + - - +
35N ASN* 4.2 13.5 + - - +
36N LYS* 3.2 45.1 + - - +
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Residues in contact with GLU 31 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199M ARG* 4.6 18.9 + - - +
27N GLU 4.1 9.0 + - - +
28N GLU* 3.8 14.5 + - - +
29N VAL 3.2 0.2 - - - -
30N GLU* 1.3 80.3 - - - +
32N VAL* 1.3 66.4 + - + +
34N GLY* 4.8 1.2 + - - -
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Residues in contact with VAL 32 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195M LEU* 3.3 45.5 - - + +
196M SER* 5.0 2.9 - - - -
199M ARG* 3.8 30.3 - - + +
28N GLU 3.8 16.6 - - - +
29N VAL* 3.0 4.4 + - - +
30N GLU 2.8 2.2 + - - -
31N GLU* 1.3 79.7 - - + +
33N ILE* 1.3 62.1 + - + +
79N ASN* 4.1 19.5 + - - +
81N ILE* 3.4 17.7 - - + +
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Residues in contact with ILE 33 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195M LEU* 4.4 8.5 - - + -
29N VAL* 3.1 16.5 + - + +
32N VAL* 1.3 83.6 - - - +
34N GLY* 1.3 57.6 + - - +
35N ASN* 4.1 25.1 - - + +
58N LEU* 3.8 32.3 - - + -
68N TRP* 3.8 28.5 - - + -
69N ALA* 4.2 6.1 - - + -
71N VAL* 4.2 9.9 - - + -
81N ILE* 3.8 36.0 - - + +
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Residues in contact with GLY 34 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30N GLU* 2.7 28.7 + - - +
31N GLU 4.6 1.1 + - - -
32N VAL 3.9 0.4 - - - -
33N ILE* 1.3 73.4 - - - +
35N ASN* 1.4 72.1 + - - +
36N LYS 4.2 0.2 - - - -
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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