Contacts of the helix formed by residues 19 - 29 (chain D) in PDB entry 2VHW
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 THR 19 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D ILE* 1.3 77.4 - - - +
20D PRO* 1.3 76.9 - - - +
21D ALA* 3.6 14.5 + - - +
22D GLY* 3.1 9.2 + - - -
23D VAL* 3.0 21.3 + - - +
45D ILE* 4.2 2.0 - - + -
50D PHE* 3.7 5.4 - - - -
310D THR* 3.7 20.0 - - + -
311D TYR* 3.7 34.3 - - + -
314D THR* 3.3 24.4 + - - +
315D ASN* 5.2 1.9 + - - -
318D MET* 4.9 4.9 - - - +
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Residues in contact with PRO 20 (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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223A TYR* 3.5 35.2 - - + +
19D THR* 1.3 87.2 - - - +
21D ALA* 1.3 56.6 + - - +
23D VAL* 3.2 3.8 + - + -
24D ALA* 2.9 27.9 + - - +
45D ILE* 3.8 33.7 - - + -
49D ASP* 4.1 16.8 - - + +
50D PHE* 3.7 4.7 - - + -
53D ALA* 3.4 21.0 - - + +
311D TYR* 4.1 9.4 - - + +
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Residues in contact with ALA 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A SER* 3.4 30.4 - - - +
223A TYR* 3.6 27.7 + - + +
224A GLU* 4.9 3.4 - - + +
19D THR* 3.1 10.8 + - - +
20D PRO* 1.3 77.4 - - - +
22D GLY* 1.3 57.4 + - - +
24D ALA* 3.5 2.9 + - - +
25D GLU* 3.1 27.0 + - - +
311D TYR* 6.0 2.9 - - + -
315D ASN* 6.0 0.9 - - - +
318D MET* 4.4 9.4 - - + +
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Residues in contact with GLY 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D ILE* 3.9 15.5 - - - -
19D THR* 3.1 11.7 + - - -
21D ALA* 1.3 75.8 - - - +
23D VAL* 1.3 59.3 + - - +
25D GLU* 3.8 2.1 - - - +
26D LEU* 3.0 34.9 + - - +
318D MET* 4.0 26.3 - - - +
322D LEU* 5.2 0.7 - - - +
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Residues in contact with VAL 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D ILE* 3.8 18.1 - - + +
19D THR 3.0 17.6 + - - +
20D PRO 3.5 6.7 - - - +
22D GLY* 1.3 75.8 - - - +
24D ALA* 1.3 62.2 + - - +
26D LEU* 3.4 1.9 + - - +
27D THR* 3.0 28.6 + - - +
33D VAL* 4.0 13.0 - - + -
35D ILE* 3.7 26.2 - - + -
50D PHE* 3.9 7.6 - - + -
53D ALA* 3.7 17.0 - - + +
54D GLY 4.0 1.8 - - - -
55D ALA* 3.5 33.4 - - + +
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Residues in contact with ALA 24 (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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222A ALA* 6.1 3.1 - - + -
223A TYR* 4.6 17.9 - - + +
20D PRO 2.9 17.3 + - - +
21D ALA* 3.7 5.8 - - - +
23D VAL* 1.3 76.6 - - - +
25D GLU* 1.3 56.9 + - - +
27D THR* 3.5 2.6 + - - +
28D ARG* 2.9 30.5 + - - +
53D ALA* 3.5 20.2 + - + +
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Residues in contact with GLU 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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221A SER* 6.0 3.0 - - - -
222A ALA* 5.0 12.5 + - - +
21D ALA 3.1 17.3 + - - +
22D GLY* 3.9 5.8 - - - +
23D VAL 3.3 0.4 - - - -
24D ALA* 1.3 72.6 - - - +
26D LEU* 1.3 66.1 + - - +
28D ARG* 2.9 34.3 + - - +
29D ARG* 2.8 51.9 + - - +
318D MET* 4.8 8.3 - - - -
322D LEU* 3.5 31.2 - - + -
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Residues in contact with LEU 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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3D VAL* 4.0 26.2 - - + -
18D ILE* 3.6 31.6 - - + -
22D GLY 3.0 13.4 + - - +
25D GLU* 1.3 75.3 - - - +
27D THR* 1.3 59.8 + - - +
29D ARG* 3.2 8.0 + - - -
30D GLY 3.4 0.3 + - - -
31D HIS* 3.1 38.3 + - + +
33D VAL* 3.7 20.4 - - + -
321D VAL* 4.1 13.7 - - + -
322D LEU* 3.9 21.3 - - + -
325D ALA* 3.6 30.5 - - + -
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Residues in contact with THR 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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23D VAL 3.0 16.9 + - - -
24D ALA* 3.8 3.8 - - - +
26D LEU* 1.3 74.1 - - - +
28D ARG* 1.3 64.4 + - - +
29D ARG 3.1 1.3 - - - -
30D GLY* 3.1 14.2 + - - -
31D HIS 3.6 16.6 + - - +
33D VAL* 3.9 9.4 + - - +
53D ALA 4.2 13.0 - - - +
54D GLY* 3.7 25.9 + - - +
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Residues in contact with ARG 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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222A ALA* 5.8 7.6 - - - -
24D ALA 2.9 18.6 + - - +
25D GLU* 2.9 37.0 + - - +
27D THR* 1.3 78.5 - - - +
29D ARG* 1.3 80.4 + - - +
30D GLY 3.3 1.4 + - - -
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Residues in contact with ARG 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 GLU* 2.8 37.1 + - - +
26D LEU 3.2 9.5 + - - +
27D THR 3.1 1.0 - - - -
28D ARG* 1.3 91.8 - - - +
30D GLY* 1.3 57.3 + - - +
31D HIS* 3.5 17.5 + - + -
322D LEU* 4.0 36.7 - - - +
323D GLU* 4.2 10.5 + - - -
326D ASP* 2.8 42.6 + - - +
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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