Contacts of the helix formed by residues 16 - 27 (chain B) in PDB entry 3FVS
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 ASN 16 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A THR* 4.6 2.2 - - - +
67A PHE* 4.5 3.6 - - - -
274A GLN* 3.1 45.6 + - - +
278A PHE* 4.1 15.5 - - - -
14B ASP 3.4 2.1 + - - +
15B TYR* 1.3 82.0 - - - +
17B PRO* 1.4 65.8 - - - +
18B TRP* 2.9 30.7 + - - +
19B VAL* 3.3 43.0 - - + +
20B GLU* 4.4 0.9 + - - +
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Residues in contact with PRO 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B TYR* 3.7 40.1 - - + +
16B ASN* 1.4 85.8 - - - +
18B TRP* 1.3 80.2 + - + +
20B GLU* 3.3 6.7 + - + +
21B PHE* 3.3 43.9 + - + -
126B ASP* 4.5 9.9 - - + +
364B ARG* 4.0 4.7 - - - +
383B ILE* 4.2 17.0 - - + -
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Residues in contact with TRP 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278A PHE* 3.9 31.0 - + + -
16B ASN* 2.9 17.0 + - - +
17B PRO* 1.3 84.8 - - + +
19B VAL* 1.3 59.3 + - + +
21B PHE* 3.7 13.1 - + + +
22B VAL* 2.9 41.4 + - + +
34B GLY 4.8 2.9 - - - -
101B TYR* 4.9 0.4 + - - -
125B PHE* 5.9 2.7 - + - -
126B ASP* 3.0 33.5 + - - -
379B ILE* 3.8 36.6 - - + -
383B ILE* 3.6 18.4 - - + -
384B PHE* 4.2 7.0 - + - -
398B ARG* 3.9 25.4 - - - -
423B GOL 3.6 35.6 + - - -
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Residues in contact with VAL 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A THR* 4.1 19.7 - - + -
67A PHE* 4.2 12.8 - - + -
16B ASN* 3.3 43.4 + - + +
18B TRP* 1.3 77.1 - - + +
20B GLU* 1.3 58.1 + - + +
22B VAL* 3.6 4.0 + - - +
23B LYS* 3.0 30.8 + - - +
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Residues in contact with GLU 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B TYR* 4.8 7.5 + - + +
16B ASN 5.2 1.3 - - - +
17B PRO* 3.3 9.7 + - + +
18B TRP 3.3 0.4 - - - -
19B VAL* 1.3 81.6 - - + +
21B PHE* 1.3 91.9 + - - +
23B LYS* 3.3 6.3 + - - +
24B LEU* 2.9 29.3 + - + +
360B GLU* 5.6 0.3 - - - +
364B ARG* 4.0 13.5 + - - -
368B LYS* 5.0 19.1 + - - +
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Residues in contact with PHE 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B PRO* 3.3 30.2 + - + -
18B TRP* 3.7 25.8 - + + +
20B GLU* 1.3 98.8 - - - +
22B VAL* 1.3 62.9 + - + +
24B LEU* 4.1 3.8 - - - +
25B ALA* 3.2 24.8 + - - +
364B ARG* 4.3 11.4 - - + -
367B VAL* 6.0 4.0 - - + -
371B ILE* 5.3 2.9 - - - +
377B VAL* 5.5 2.3 - - + +
379B ILE* 4.0 27.8 - - + -
380B PRO* 3.6 30.3 - - + -
383B ILE* 3.7 31.0 - - + -
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Residues in contact with VAL 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A LYS* 3.2 36.3 - - + +
18B TRP* 2.9 30.1 + - + +
19B VAL* 4.0 4.9 - - - +
21B PHE* 1.3 79.2 - - + +
23B LYS* 1.3 63.8 + - - +
25B ALA* 3.9 5.4 - - - +
26B SER* 3.2 23.2 + - - -
35B GLN* 6.2 7.6 - - + +
423B GOL 5.6 7.6 - - - -
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Residues in contact with LYS 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B VAL 3.0 20.1 + - - +
20B GLU* 3.6 7.0 - - - +
21B PHE 3.3 0.2 - - - -
22B VAL* 1.3 77.8 - - - +
24B LEU* 1.3 63.1 + - - +
26B SER* 2.6 25.6 + - - +
27B GLU* 2.8 37.2 + - - +
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Residues in contact with LEU 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B GLU* 2.9 22.1 + - + +
21B PHE* 4.1 4.7 - - - +
23B LYS* 1.3 76.0 - - - +
25B ALA* 1.3 58.7 + - - +
27B GLU* 2.9 29.0 + - - +
28B HIS* 3.3 46.3 - - - +
368B LYS* 3.9 34.1 - - + +
371B ILE* 3.8 30.3 - - + -
372B LYS* 4.7 10.3 - - + -
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Residues in contact with ALA 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B PHE 3.2 16.0 + - - +
22B VAL* 3.9 6.3 - - - +
24B LEU* 1.3 78.8 - - - +
26B SER* 1.3 60.2 + - - +
27B GLU 3.1 1.1 + - - -
28B HIS 3.4 17.8 + - - +
30B VAL* 3.5 10.6 - - - +
32B ASN* 3.7 25.6 - - - +
371B ILE* 4.6 8.7 - - + +
377B VAL* 3.9 26.0 - - + -
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Residues in contact with SER 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A LYS* 6.0 2.9 - - - -
22B VAL* 3.2 14.7 + - - -
23B LYS* 2.6 24.0 + - - +
24B LEU 3.2 0.2 - - - -
25B ALA* 1.3 77.7 - - - +
27B GLU* 1.3 64.0 + - - +
28B HIS 3.4 2.6 + - - +
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Residues in contact with GLU 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B LYS* 2.8 52.7 + - - +
24B LEU* 2.9 23.3 + - - +
26B SER* 1.3 83.3 - - - +
28B HIS* 1.3 75.0 + - + +
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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