Contacts of the helix formed by residues 24 - 35 (chain D) in PDB entry 1VCB
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 VAL 24 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23D THR* 1.3 71.6 - - - +
25D PHE* 1.3 64.0 + - - +
27D LEU* 3.2 13.8 + - + +
28D LYS* 3.2 29.8 + - - +
44D LEU* 3.9 13.9 - - + +
51D LEU* 3.9 22.2 - - + +
52D ASP 3.2 28.7 - - - +
53D ASP* 3.7 6.5 + - - -
55D LYS 2.8 16.5 + - - +
57D LEU* 4.3 16.9 - - + +
60D CYS* 3.6 25.4 - - - -
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Residues in contact with PHE 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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23D THR* 3.0 5.5 - - - +
24D VAL* 1.3 78.0 - - - +
26D GLU* 1.3 65.1 + - + +
28D LYS* 3.0 21.1 + - - +
29D ARG* 3.1 52.8 + - + +
39D PRO* 3.4 25.1 - - + -
53D ASP* 3.0 50.7 + - + +
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Residues in contact with GLU 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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21D SER 4.7 0.2 - - - +
22D SER* 3.3 17.6 + - - +
23D THR* 2.6 48.0 + - - +
25D PHE* 1.3 83.0 - - + +
27D LEU* 1.3 57.8 + - - +
29D ARG* 3.0 29.9 - - + +
30D ILE* 3.2 15.0 + - + +
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Residues in contact with LEU 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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5D LEU* 4.0 22.9 - - + -
7D ILE* 3.4 31.6 - - + -
16D THR* 4.5 8.5 - - + -
18D ALA* 5.4 5.6 - - + -
22D SER* 4.9 1.9 + - - +
23D THR 3.2 8.1 + - - +
24D VAL* 3.2 12.0 + - - +
25D PHE 3.1 0.4 - - - -
26D GLU* 1.3 73.6 - - - +
28D LYS* 1.3 64.3 + - - +
29D ARG 3.0 1.6 - - - -
30D ILE* 3.2 15.7 + - + +
31D VAL* 3.0 26.5 + - + +
44D LEU* 3.9 18.4 - - + -
51D LEU* 6.4 1.1 - - + -
57D LEU* 3.9 28.5 - - + -
62D PHE* 6.0 0.4 - - + -
75D VAL* 4.6 13.5 - - + -
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Residues in contact with LYS 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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24D VAL* 3.2 16.9 + - - +
25D PHE* 3.0 9.0 + - + +
27D LEU* 1.3 79.3 - - - +
29D ARG* 1.3 57.4 + - - +
31D VAL* 3.3 1.0 + - - -
32D GLU* 2.9 24.6 + - - +
39D PRO* 3.4 29.5 - - + +
40D ASP* 5.6 0.2 - - - +
42D GLN* 2.9 62.9 + - - +
43D ARG* 4.2 1.4 - - - +
44D LEU* 3.7 29.6 - - + +
50D LEU* 5.6 1.0 - - - +
51D LEU 4.7 4.2 + - - -
53D ASP* 3.2 41.1 + - - +
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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 PHE* 3.1 46.7 + - + +
26D GLU* 3.0 15.7 - - + +
27D LEU 3.0 0.2 - - - -
28D LYS* 1.3 74.6 - - - +
30D ILE* 1.3 68.2 + - + +
32D GLU* 2.7 59.8 + - - +
33D GLY* 3.1 9.9 + - - -
39D PRO* 3.7 15.6 - - - +
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Residues in contact with ILE 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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7D ILE* 5.7 1.1 - - + -
16D THR* 4.3 20.2 - - + +
17D ASP 4.5 15.7 - - - +
18D ALA* 5.1 6.7 - - + -
26D GLU 3.2 13.1 + - - +
27D LEU* 3.2 19.5 + - + +
29D ARG* 1.3 77.5 - - + +
31D VAL* 1.3 62.7 + - + +
33D GLY* 3.4 3.5 + - - +
34D ILE* 3.3 36.8 + - + +
18E TYR* 4.5 5.6 - - + +
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Residues in contact with VAL 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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7D ILE* 3.8 34.3 - - + -
14D ILE* 5.0 4.5 - - + -
27D LEU* 3.0 21.2 + - + +
28D LYS* 3.4 1.8 - - - +
30D ILE* 1.3 72.8 - - - +
32D GLU* 1.3 58.7 + - - +
34D ILE* 3.1 7.6 + - - +
35D LEU* 2.8 47.9 + - + +
37D ARG* 5.5 0.2 - - + -
42D GLN* 3.3 33.2 - - - +
44D LEU* 4.9 5.6 - - + -
77D LEU* 4.1 20.2 - - + -
79D PHE* 4.6 2.7 - - + -
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Residues in contact with GLU 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 LYS 2.9 11.0 + - - +
29D ARG* 2.7 43.3 + - - +
31D VAL* 1.3 76.5 - - - +
33D GLY* 1.3 59.6 + - - +
36D LYS* 2.8 33.4 + - - +
37D ARG 3.1 30.3 - - - +
38D PRO* 3.1 26.7 - - + +
39D PRO* 3.3 7.0 - - + +
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Residues in contact with GLY 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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29D ARG 3.1 9.0 + - - -
30D ILE* 3.4 4.2 + - - -
31D VAL 3.3 0.2 - - - -
32D GLU* 1.3 80.7 + - - +
34D ILE* 1.3 58.5 + - - +
36D LYS* 3.2 27.0 - - - -
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Residues in contact with ILE 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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7D ILE* 6.4 0.2 - - + -
14D ILE* 3.6 39.0 - - + -
30D ILE* 3.3 24.6 + - + +
31D VAL* 3.1 6.1 + - - +
33D GLY* 1.3 79.0 - - - +
35D LEU* 1.3 68.8 + - + +
36D LYS* 3.2 14.4 + - - +
18E TYR* 3.6 48.9 - - + +
30E ILE* 3.9 21.5 - - + -
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Residues in contact with LEU 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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9D ARG* 5.6 1.3 - - - +
12D THR* 4.3 26.7 - - + -
14D ILE* 3.9 21.5 - - + -
31D VAL* 2.8 16.7 + - + +
34D ILE* 1.3 79.5 - - + +
36D LYS* 1.3 74.0 + - - +
37D ARG* 3.5 7.6 + - + +
77D LEU* 3.8 18.8 - - + -
79D PHE* 3.6 35.0 - - + -
30E ILE* 5.1 5.6 - - + -
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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