Contacts of the helix formed by residues 24 - 35 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23G THR* 1.3 70.3 - - - +
25G PHE* 1.3 62.2 + - - +
27G LEU* 3.2 14.4 + - + +
28G LYS* 3.2 32.3 + - - +
44G LEU* 3.9 13.9 - - + +
51G LEU* 3.9 23.3 - - + +
52G ASP 3.3 28.5 - - - +
53G ASP* 3.7 3.8 + - - -
55G LYS 2.8 16.7 + - - +
57G LEU* 4.3 16.5 - - + +
60G CYS* 3.5 25.8 - - - -
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Residues in contact with PHE 25 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23G THR* 3.0 4.6 - - - +
24G VAL* 1.3 77.6 - - - +
26G GLU* 1.3 70.1 + - + +
28G LYS* 3.0 16.1 + - + +
29G ARG* 3.1 52.4 + - + +
39G PRO* 3.5 24.9 - - + -
53G ASP* 3.0 52.2 + - + +
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Residues in contact with GLU 26 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21G SER 4.7 0.2 - - - +
22G SER* 3.3 17.3 + - - +
23G THR* 2.6 48.4 + - - +
25G PHE* 1.3 82.3 - - + +
27G LEU* 1.3 57.9 + - - +
29G ARG* 3.0 29.7 - - + +
30G ILE* 3.1 14.4 + - + +
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Residues in contact with LEU 27 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5G LEU* 4.0 22.2 - - + -
7G ILE* 3.4 32.3 - - + -
16G THR* 4.5 8.7 - - + -
18G ALA* 5.4 5.4 - - + -
22G SER* 4.9 2.2 + - - +
23G THR 3.2 8.3 + - - +
24G VAL* 3.2 12.3 + - + +
25G PHE 3.1 0.2 - - - -
26G GLU* 1.3 73.0 - - - +
28G LYS* 1.3 66.7 + - - +
29G ARG 3.0 1.6 - - - -
30G ILE* 3.2 14.7 + - + +
31G VAL* 3.0 26.6 + - - +
44G LEU* 3.9 18.8 - - + -
51G LEU* 6.4 1.3 - - + -
57G LEU* 3.8 28.9 - - + -
62G PHE* 6.0 0.2 - - + -
75G VAL* 4.6 13.0 - - + -
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Residues in contact with LYS 28 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24G VAL* 3.2 17.5 + - - +
25G PHE* 3.0 8.2 + - + +
27G LEU* 1.3 79.7 - - - +
29G ARG* 1.3 56.7 + - - +
31G VAL* 3.3 1.2 + - - -
32G GLU* 2.9 24.6 + - - +
39G PRO* 3.3 30.1 - - + +
40G ASP* 5.6 0.2 - - - +
42G GLN* 2.9 60.6 + - - +
43G ARG* 4.2 1.8 - - - +
44G LEU* 3.7 28.9 - - + +
50G LEU* 5.6 1.2 - - - +
51G LEU 4.7 4.2 + - - -
53G ASP* 3.3 40.2 + - - +
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Residues in contact with ARG 29 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25G PHE* 3.1 47.4 + - + +
26G GLU* 3.0 16.6 - - + +
27G LEU 3.0 0.2 - - - -
28G LYS* 1.3 74.8 - - - +
30G ILE* 1.3 65.7 + - + +
32G GLU* 2.8 58.3 + - - +
33G GLY* 3.1 10.4 + - - -
39G PRO* 3.7 15.4 - - - +
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Residues in contact with ILE 30 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G ILE* 5.8 0.4 - - + -
16G THR* 4.3 15.0 - - + +
17G ASP 4.5 15.7 - - - +
18G ALA* 5.1 6.5 - - + -
26G GLU* 3.1 13.9 + - + +
27G LEU* 3.2 19.3 + - + +
29G ARG* 1.3 76.6 - - + +
31G VAL* 1.3 62.3 + - + +
33G GLY* 3.3 3.6 + - - -
34G ILE* 3.3 38.1 + - + +
18H TYR* 4.1 12.8 - - + +
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Residues in contact with VAL 31 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G ILE* 3.8 33.2 - - + -
14G ILE* 5.0 3.8 - - + -
27G LEU* 3.0 20.7 + - + +
28G LYS* 3.4 2.0 - - - +
29G ARG 3.1 0.2 - - - -
30G ILE* 1.3 73.8 - - - +
32G GLU* 1.3 59.2 + - - +
34G ILE* 3.1 6.4 + - - +
35G LEU* 2.8 47.7 + - + +
37G ARG* 5.5 0.2 - - + -
42G GLN* 3.2 33.9 - - - +
44G LEU* 4.9 5.6 - - + -
77G LEU* 4.1 19.7 - - + -
79G PHE* 4.6 3.4 - - + -
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Residues in contact with GLU 32 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28G LYS 2.9 11.8 + - - +
29G ARG* 2.8 41.3 + - - +
31G VAL* 1.3 77.2 - - - +
33G GLY* 1.3 59.0 + - - +
36G LYS* 2.8 33.7 + - - +
37G ARG 3.1 31.2 - - - +
38G PRO* 3.1 26.6 - - + +
39G PRO* 3.3 8.1 - - + +
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Residues in contact with GLY 33 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29G ARG 3.1 9.3 + - - -
30G ILE* 3.3 4.2 + - - -
31G VAL 3.3 0.4 - - - -
32G GLU* 1.3 79.6 + - - +
34G ILE* 1.3 59.8 + - - +
36G LYS* 3.2 27.8 - - - -
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Residues in contact with ILE 34 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14G ILE* 3.6 39.0 - - + -
30G ILE* 3.3 21.5 + - + +
31G VAL* 3.1 7.3 + - - +
33G GLY* 1.3 78.7 - - - +
35G LEU* 1.3 66.0 + - + +
36G LYS* 3.2 14.4 + - - +
18H TYR* 3.4 52.5 - - + +
30H ILE* 3.8 20.9 - - + -
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Residues in contact with LEU 35 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9G ARG* 5.6 1.6 - - - -
12G THR* 4.3 25.8 - - + -
14G ILE* 4.0 19.1 - - + -
31G VAL* 2.8 18.3 + - + +
34G ILE* 1.3 80.9 - - + +
36G LYS* 1.3 75.1 + - - +
37G ARG* 3.4 6.9 + - + +
77G LEU* 3.8 18.6 - - + -
79G PHE* 3.6 35.1 - - + -
30H ILE* 5.0 6.5 - - + -
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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