Contacts of the helix formed by residues 24 - 35 (chain D) in PDB entry 2VCK
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 TRP 24 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22D THR* 3.0 7.0 - - - +
23D ILE* 1.3 97.2 - - + +
25D GLN* 1.3 63.3 + - - +
26D ASN 3.3 2.5 - - - -
27D TYR* 3.0 21.6 + + - +
28D ILE* 2.9 34.9 + - + +
85D ASP* 3.1 47.0 + - - -
87D TYR* 4.1 13.9 - - + -
106D LEU* 3.3 50.8 + - + -
107D MSE 3.6 3.1 - - - -
108D LYS 4.0 5.1 - - - +
114D VAL* 3.6 20.0 - - + -
116D ILE* 3.5 31.2 - - + -
164D VAL* 3.6 23.3 - - + -
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Residues in contact with GLN 25 (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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21D LYS* 5.0 6.2 - - - +
22D THR* 3.3 37.7 + - + +
23D ILE 3.4 1.6 + - - -
24D TRP* 1.3 77.2 - - - +
26D ASN* 1.3 60.2 + - - +
28D ILE* 3.3 20.4 + - - +
29D ASP* 2.9 65.8 + - - +
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Residues in contact with ASN 26 (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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23D ILE 4.9 2.2 + - - -
24D TRP 3.3 1.2 - - - -
25D GLN* 1.3 76.9 - - - +
27D TYR* 1.3 60.4 + - - +
29D ASP* 3.8 11.1 - - - +
30D ALA* 3.0 27.7 + - - +
165D ASP* 2.8 32.7 + - - +
168D LEU* 3.7 25.8 - - + +
172D LYS* 5.3 0.2 - - - -
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Residues in contact with TYR 27 (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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24D TRP* 3.0 31.2 + + - +
26D ASN* 1.3 76.0 - - - +
28D ILE* 1.3 64.1 + - - +
30D ALA 3.3 1.0 + - - -
31D LEU* 3.0 19.9 + - - +
87D TYR* 5.9 1.1 - - - -
104D MSE 6.2 0.4 - - - -
106D LEU* 3.8 31.0 - - + -
116D ILE* 3.6 10.3 - - + +
118D PHE* 4.4 8.1 - + - -
164D VAL* 2.6 29.1 + - + -
165D ASP* 3.5 23.8 - - - -
167D TYR* 3.4 21.8 - - - +
168D LEU* 3.9 14.6 - - + -
171D PHE* 3.4 57.2 - + + -
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Residues in contact with ILE 28 (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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22D THR* 4.0 24.0 - - + -
24D TRP* 2.9 22.4 + - + +
25D GLN* 3.7 21.3 - - - +
27D TYR* 1.3 74.4 - - + +
29D ASP* 1.3 65.0 + - - +
31D LEU* 3.1 14.5 + - - +
32D PHE* 3.3 36.9 + - + -
66D ARG* 5.7 1.3 - - - +
76D GLU* 4.4 3.6 - - - +
78D HIS* 4.3 7.4 - - + +
87D TYR* 3.6 46.0 - - + +
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Residues in contact with ASP 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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25D GLN* 2.9 49.7 + - - +
26D ASN* 3.8 12.9 - - - +
28D ILE* 1.3 77.0 - - - +
30D ALA* 1.3 56.3 + - - +
32D PHE* 3.3 3.8 + - - -
33D GLU* 2.9 50.1 + - + +
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Residues in contact with ALA 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 ASN 3.0 20.0 + - - +
27D TYR 3.6 4.5 - - - +
28D ILE 3.3 0.2 - - - -
29D ASP* 1.3 76.9 - - - +
31D LEU* 1.3 64.8 + - - +
33D GLU* 3.4 12.1 + - - +
34D THR* 3.0 28.6 + - - -
168D LEU* 4.3 1.1 - - + -
171D PHE* 4.3 6.5 - - + -
172D LYS* 4.0 36.3 - - + -
175D LEU* 3.7 8.3 - - + -
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Residues in contact with LEU 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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27D TYR 3.0 13.5 + - - +
28D ILE 3.4 9.0 - - - +
30D ALA* 1.3 79.3 - - - +
32D PHE* 1.3 88.0 + - + +
34D THR* 3.4 3.3 + - - -
35D PHE* 3.0 25.8 + - + +
87D TYR* 3.9 14.8 - - + +
89D THR* 4.0 9.9 - - + -
91D LEU* 4.0 28.5 - - + -
104D MSE 3.9 28.3 - - + -
171D PHE* 4.5 4.7 - - + -
175D LEU* 3.7 28.2 - - + +
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Residues in contact with PHE 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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28D ILE* 3.3 31.9 + - + +
29D ASP* 4.4 2.7 - - - +
31D LEU* 1.3 98.6 - - + +
33D GLU* 1.3 60.3 + - - +
34D THR 3.3 0.7 - - - -
35D PHE 3.7 11.7 - - - +
36D PRO* 3.1 31.6 - - + +
38D LEU* 3.9 26.7 - - + +
66D ARG* 3.3 48.7 - - - +
74D ALA* 5.5 2.7 - - + -
76D GLU* 3.6 22.2 - - + -
87D TYR* 3.6 8.5 - - - -
89D THR* 5.3 3.6 - - + -
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Residues in contact with GLU 33 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29D ASP* 2.9 39.7 + - - +
30D ALA* 3.7 12.5 - - - +
32D PHE* 1.3 80.9 - - - +
34D THR* 1.3 61.3 + - - +
36D PRO* 3.7 10.9 - - - +
172D LYS* 5.2 7.4 + - - -
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Residues in contact with THR 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 ALA 3.0 16.8 + - - -
31D LEU 3.7 4.7 - - - -
33D GLU* 1.3 78.5 - - - +
35D PHE* 1.3 78.7 + - + +
36D PRO* 3.3 7.7 - - - +
37D GLN* 4.6 0.2 - - - +
172D LYS* 5.4 1.6 + - - +
175D LEU* 3.6 43.3 - - + +
176D THR* 4.7 2.5 + - - +
179D LYS* 3.8 30.8 + - + +
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Residues in contact with PHE 35 (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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31D LEU* 3.0 20.4 + - + +
32D PHE* 3.3 11.9 - - + +
34D THR* 1.3 92.1 - - + +
36D PRO* 1.3 62.8 - - - +
37D GLN* 3.1 19.3 + - - +
38D LEU* 3.2 30.8 + - + +
71D PHE* 3.8 27.8 - + - -
91D LEU* 3.9 14.6 - - + -
175D LEU* 4.2 12.3 - - + -
178D TYR* 3.6 32.8 - + - -
179D LYS* 3.6 37.5 - - + -
182D ILE* 4.3 9.4 - - + -
183D ASP* 5.5 1.1 - - - -
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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