Contacts of the helix formed by residues 25 - 34 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170C ARG* 4.1 33.7 - - + +
171C ASP* 5.0 11.7 - - + +
174C THR* 6.0 5.6 - - + -
23D LEU* 5.3 6.5 - - + +
24D MET* 1.3 77.5 - - - +
26D PRO* 1.4 76.0 - - + +
27D GLU* 4.4 11.4 - - + +
28D GLU* 2.9 28.6 + - + +
29D VAL* 3.4 9.6 + - - +
40D ASP* 3.2 23.8 - - + +
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Residues in contact with PRO 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D LEU* 1.4 83.3 - - + +
27D GLU* 1.3 64.6 + - - +
29D VAL* 2.9 2.8 + - + +
30D GLU* 2.8 28.6 + - - +
36D LYS* 4.0 17.5 - - + -
37D PRO* 3.7 41.4 - - + +
38D GLU 4.8 4.0 - - - +
39D SER* 3.8 7.6 - - - +
40D ASP* 3.5 28.9 - - - +
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Residues in contact with GLU 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C ARG* 2.7 34.9 + - - +
25D LEU* 4.9 10.2 - - + +
26D PRO* 1.3 80.0 - - - +
28D GLU* 1.3 61.8 + - + +
30D GLU* 4.3 14.5 - - - +
31D GLU* 3.9 16.8 + - - +
36D LYS* 5.0 4.1 - - - +
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Residues in contact with GLU 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169C GLY* 4.0 4.7 - - - -
170C ARG* 3.3 50.0 + - + +
171C ASP 4.8 0.7 + - - -
190C PRO* 5.1 4.7 - - - +
191C HIS 5.0 1.2 + - - -
195C LEU* 5.3 0.9 - - - +
196C SER* 5.4 3.3 - - - -
23D LEU 4.5 1.2 - - - +
24D MET* 3.0 42.6 - - + +
25D LEU* 2.9 34.6 + - + +
27D GLU* 1.3 77.2 - - + +
29D VAL* 1.3 65.9 + - - +
31D GLU* 3.8 12.6 - - - +
32D VAL* 3.7 17.2 - - - +
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Residues in contact with VAL 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195C LEU* 4.4 13.5 - - + -
24D MET* 4.2 17.3 - - + -
25D LEU 3.7 13.0 - - - +
26D PRO 2.9 4.8 + - - +
28D GLU* 1.3 77.6 - - - +
30D GLU* 1.3 70.4 + - - +
32D VAL* 3.0 12.8 + - - +
33D ILE* 3.1 18.9 + - + -
37D PRO* 4.4 6.1 - - + -
41D ILE* 4.2 24.5 - - + -
43D VAL* 5.0 0.2 - - + -
58D LEU* 3.7 14.8 - - + -
68D TRP* 3.7 32.3 - - + -
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Residues in contact with GLU 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D PRO 2.8 14.9 + - - +
27D GLU* 4.3 15.6 - - - +
29D VAL* 1.3 75.4 - - - +
31D GLU* 1.3 68.2 + - - +
32D VAL 2.8 1.9 + - - -
34D GLY* 2.9 24.8 + - - -
35D ASN 3.9 16.5 + - - +
36D LYS* 3.8 45.5 + - + +
37D PRO* 4.5 0.2 - - - +
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Residues in contact with GLU 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190C PRO* 5.6 2.8 - - - +
196C SER* 6.0 0.3 - - - -
199C ARG* 3.3 57.6 + - - +
27D GLU 3.9 9.8 + - - +
28D GLU* 3.8 18.3 - - - +
30D GLU* 1.3 81.0 - - - +
32D VAL* 1.3 58.5 + - + +
34D GLY* 4.6 1.9 + - - -
56I PRO* 5.3 0.7 - - - +
58I ASP* 5.3 1.4 - - - +
59I ASN* 3.3 24.4 - - - +
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Residues in contact with VAL 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195C LEU* 3.4 46.0 - - + +
196C SER* 4.9 1.6 - - - -
199C ARG* 3.5 32.3 - - + +
28D GLU 3.7 17.3 - - - +
29D VAL 3.0 4.6 + - - +
30D GLU 2.8 3.6 + - - -
31D GLU* 1.3 72.8 - - + +
33D ILE* 1.3 60.1 + - + +
34D GLY 3.6 0.7 - - - -
79D ASN* 3.8 23.4 + - - +
81D ILE* 3.6 12.2 - - + +
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Residues in contact with ILE 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195C LEU* 4.2 11.7 - - + -
29D VAL* 3.1 19.4 + - + +
32D VAL* 1.3 78.1 - - - +
34D GLY* 1.3 61.6 + - - +
35D ASN* 4.1 8.8 - - + +
58D LEU* 3.2 33.0 - - + -
68D TRP* 3.8 19.3 - - + -
69D ALA* 4.0 4.5 - - + -
71D VAL* 3.8 18.2 - - + -
81D ILE* 3.8 26.0 - - + +
83D MET* 3.8 26.2 - - - -
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Residues in contact with GLY 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D GLU* 2.9 15.0 + - - -
31D GLU 4.6 2.4 + - - -
32D VAL 3.6 1.4 - - - -
33D ILE* 1.3 79.3 - - - +
35D ASN* 1.3 70.5 + - - +
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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