Contacts of the helix formed by residues 24 - 35 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22J SER 4.2 0.2 + - - -
23J THR* 1.3 70.7 - - - +
25J PHE* 1.3 63.2 + - - +
27J LEU* 3.1 15.2 + - + +
28J LYS* 3.2 29.1 + - - +
44J LEU* 3.9 13.6 - - + +
51J LEU* 3.9 23.1 - - + +
52J ASP 3.3 27.6 - - - +
53J ASP* 4.0 5.8 - - - -
55J LYS 2.8 16.7 + - - +
57J LEU* 4.3 16.9 - - + +
60J CYS* 3.5 25.6 - - - -
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Residues in contact with PHE 25 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23J THR* 3.0 4.4 - - - +
24J VAL* 1.3 78.2 - - - +
26J GLU* 1.3 70.1 + - + +
28J LYS* 3.0 16.8 + - + +
29J ARG* 3.1 52.6 + - + +
39J PRO* 3.5 26.0 - - + -
53J ASP* 3.1 51.6 + - + +
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Residues in contact with GLU 26 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22J SER* 3.3 17.6 + - - +
23J THR* 2.6 46.8 + - - +
25J PHE* 1.3 83.5 - - + +
27J LEU* 1.3 58.9 + - - +
29J ARG* 3.0 28.2 - - + +
30J ILE* 3.1 14.5 + - - +
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Residues in contact with LEU 27 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5J LEU* 4.0 24.7 - - + -
7J ILE* 3.4 32.3 - - + -
16J THR* 4.5 8.1 - - + -
18J ALA* 5.4 4.7 - - + -
22J SER* 4.9 2.2 + - - +
23J THR 3.2 7.6 + - - +
24J VAL* 3.1 12.7 + - + +
26J GLU* 1.3 75.3 - - - +
28J LYS* 1.3 65.1 + - - +
29J ARG 3.0 1.8 - - - -
30J ILE* 3.2 15.5 + - + +
31J VAL* 3.1 26.8 + - - +
44J LEU* 4.0 17.5 - - + -
51J LEU* 6.4 1.3 - - + -
57J LEU* 3.8 28.7 - - + -
62J PHE* 6.0 0.4 - - + -
75J VAL* 4.6 13.5 - - + -
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Residues in contact with LYS 28 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24J VAL* 3.2 17.1 + - - +
25J PHE* 3.0 8.7 + - + +
27J LEU* 1.3 79.7 - - - +
29J ARG* 1.3 56.3 + - - +
31J VAL* 3.3 1.0 + - - -
32J GLU* 2.9 24.8 + - - +
39J PRO* 3.3 28.3 - - + +
40J ASP* 5.6 0.4 - - - +
42J GLN* 2.9 62.1 + - - +
43J ARG* 4.2 1.6 - - - +
44J LEU* 3.7 29.7 - - + +
50J LEU* 5.6 1.0 - - - +
51J LEU 4.7 4.2 + - - -
53J ASP* 3.2 40.6 + - - +
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Residues in contact with ARG 29 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25J PHE* 3.1 45.7 + - + +
26J GLU* 3.0 16.4 - - + +
28J LYS* 1.3 74.4 - - - +
30J ILE* 1.3 66.4 + - + +
32J GLU* 2.8 58.6 + - - +
33J GLY* 3.1 10.4 + - - -
39J PRO* 3.7 14.7 - - + +
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Residues in contact with ILE 30 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7J ILE* 5.8 0.9 - - + -
16J THR* 4.4 14.4 - - + +
17J ASP 4.5 15.9 - - - +
18J ALA* 5.1 5.8 - - + -
26J GLU* 3.1 14.0 + - + +
27J LEU* 3.2 19.5 + - + +
29J ARG* 1.3 76.8 - - + +
31J VAL* 1.3 61.4 + - + +
33J GLY* 3.5 3.0 + - - -
34J ILE* 3.3 28.9 + - + +
18K TYR* 3.9 21.5 - - + +
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Residues in contact with VAL 31 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7J ILE* 3.8 33.7 - - + -
14J ILE* 5.0 4.5 - - + -
27J LEU 3.1 15.9 + - - +
28J LYS* 3.4 1.6 - - - +
29J ARG 3.1 0.2 - - - -
30J ILE* 1.3 73.0 - - - +
32J GLU* 1.3 61.4 + - - +
34J ILE* 3.1 6.2 + - - +
35J LEU* 2.8 45.1 + - + +
37J ARG* 5.5 0.2 - - + -
42J GLN* 3.2 33.7 - - - +
44J LEU* 4.9 5.6 - - + -
77J LEU* 4.0 20.6 - - + -
79J PHE* 4.6 2.9 - - + -
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Residues in contact with GLU 32 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28J LYS 2.9 11.8 + - - +
29J ARG* 2.8 41.6 + - - +
31J VAL* 1.3 76.1 - - - +
33J GLY* 1.3 58.6 + - - +
36J LYS* 2.7 34.6 + - - +
37J ARG 3.1 29.2 - - - +
38J PRO* 3.1 25.7 - - + +
39J PRO* 3.2 6.9 - - + +
42J GLN* 4.3 0.2 - - - +
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Residues in contact with GLY 33 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29J ARG 3.1 10.1 + - - -
30J ILE* 3.5 4.4 + - - -
31J VAL 3.3 0.4 - - - -
32J GLU* 1.3 80.7 + - - +
34J ILE* 1.3 58.5 + - - +
36J LYS* 3.2 28.4 - - - -
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Residues in contact with ILE 34 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7J ILE* 6.5 0.2 - - + -
14J ILE* 3.6 38.4 - - + -
30J ILE* 3.3 21.7 + - + +
31J VAL* 3.1 6.5 + - - +
33J GLY* 1.3 78.3 - - - +
35J LEU* 1.3 65.1 + - + +
36J LYS* 3.2 14.0 + - - +
18K TYR* 3.3 54.7 - - + +
30K ILE* 3.6 25.1 - - + -
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Residues in contact with LEU 35 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9J ARG* 5.7 1.3 - - - -
12J THR* 4.3 25.8 - - + -
14J ILE* 4.0 21.1 - - + -
31J VAL* 2.8 15.4 + - + +
34J ILE* 1.3 83.2 - - + +
36J LYS* 1.3 74.1 + - - +
37J ARG* 3.4 7.8 + - - +
77J LEU* 3.8 19.3 - - + -
79J PHE* 3.6 35.5 - - + -
20K LYS* 6.6 0.2 - - - -
30K ILE* 4.9 6.1 - - + -
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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