Contacts of the helix formed by residues 12 - 26 (chain L) in PDB entry 6FF7
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 ARG 12 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10L VAL* 3.6 5.1 - - + +
11L TRP* 1.3 80.9 - - - +
13L ASN* 1.3 61.3 + - - +
14L THR* 3.3 6.1 - - - +
15L GLU* 3.4 10.9 + - + +
16L ASP* 3.1 22.5 + - - +
388Z U 5.1 10.5 - - - +
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Residues in contact with ASN 13 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412 U 6.0 2.2 - - - +
717 ALA* 4.6 12.5 - - + +
12L ARG* 1.3 73.5 - - - +
14L THR* 1.3 59.6 + - - +
16L ASP* 3.6 9.1 - - + +
17L GLU* 2.9 32.4 + - - +
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Residues in contact with THR 14 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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677 GLY* 3.9 36.3 - - - -
687 SER* 4.9 1.1 - - - -
717 ALA* 4.8 3.9 - - - +
12L ARG* 3.3 5.3 - - - +
13L ASN* 1.3 79.7 - - - +
15L GLU* 1.3 57.4 + - - +
17L GLU* 4.7 1.0 - - - +
18L ILE* 3.7 18.5 + - - +
388Z U 5.7 4.5 - - - -
389Z U 6.3 4.5 - - - -
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Residues in contact with GLU 15 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11L TRP* 5.6 2.5 - - - -
12L ARG* 3.4 14.7 + - + +
13L ASN 3.3 0.2 - - - -
14L THR* 1.3 76.9 - - - +
16L ASP* 1.3 59.5 + - - +
17L GLU 3.4 0.4 - - - -
18L ILE* 3.4 6.8 + - - +
19L LEU* 2.9 29.9 + - - +
38L LEU* 5.9 6.7 - - + -
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Residues in contact with ASP 16 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11L TRP* 5.3 3.8 - - + +
12L ARG 3.1 16.6 + - - +
13L ASN* 3.2 11.8 + - + +
15L GLU* 1.3 77.0 - - - +
17L GLU* 1.3 57.6 + - - +
19L LEU* 3.3 7.3 + - - +
20L LYS* 2.9 26.9 + - - +
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Residues in contact with GLU 17 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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677 GLY* 5.7 1.1 - - - +
707 LEU* 3.5 32.2 - - + +
717 ALA* 4.8 4.7 - - + +
13L ASN 2.9 15.2 + - - +
14L THR 4.7 2.5 - - - +
16L ASP* 1.3 75.1 - - - +
18L ILE* 1.3 60.3 + - - +
20L LYS* 3.3 9.1 + - - +
21L ALA* 3.0 27.5 + - - +
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Residues in contact with ILE 18 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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677 GLY* 5.6 5.5 - - - +
14L THR 3.7 14.4 + - - +
15L GLU* 3.4 10.2 + - - +
16L ASP 3.3 0.2 - - - -
17L GLU* 1.3 78.0 - - - +
19L LEU* 1.3 57.2 + - - +
21L ALA* 3.3 7.8 + - - +
22L ALA* 2.9 28.8 + - - +
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Residues in contact with LEU 19 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15L GLU 2.9 17.4 + - - +
16L ASP* 3.3 8.3 + - - +
18L ILE* 1.3 72.5 - - - +
20L LYS* 1.3 61.5 + - - +
22L ALA* 3.7 7.9 - - - +
23L VAL* 2.9 30.5 + - - +
46L CYS* 6.2 4.5 - - + -
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Residues in contact with LYS 20 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16L ASP 2.9 14.0 + - - +
17L GLU* 3.4 12.8 - - + +
19L LEU* 1.3 76.6 - - - +
21L ALA* 1.3 55.8 + - - +
23L VAL* 3.4 5.9 + - - +
24L MET* 2.9 29.2 + - - +
54L LEU* 5.9 9.4 - - + +
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Residues in contact with ALA 21 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337 LEU* 5.7 6.3 - - + +
377 THR* 4.8 19.1 - - - -
17L GLU 3.0 15.8 + - - +
18L ILE* 3.7 7.6 - - - +
20L LYS* 1.3 76.5 - - - +
22L ALA* 1.3 57.3 + - - +
24L MET* 3.3 7.8 + - - +
25L LYS* 2.9 29.8 + - - +
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Residues in contact with ALA 22 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18L ILE 2.9 16.8 + - - +
19L LEU* 3.7 8.1 - - - +
20L LYS 3.2 0.2 - - - -
21L ALA* 1.3 75.8 - - - +
23L VAL* 1.3 59.0 + - - +
25L LYS* 4.8 3.4 - - - -
26L TYR* 3.1 33.5 + - + +
27L GLY 4.8 0.2 - - - +
34L ILE* 3.7 33.0 - - + +
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Residues in contact with VAL 23 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19L LEU 2.9 17.2 + - - +
20L LYS* 3.9 5.6 - - - +
22L ALA* 1.3 74.6 - - - +
24L MET* 1.3 63.9 + - - +
27L GLY* 3.3 34.2 + - - +
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Residues in contact with MET 24 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262C ILE* 4.3 18.5 - - - +
20L LYS 2.9 18.3 + - - +
21L ALA* 3.6 9.2 - - - +
22L ALA 3.3 0.4 - - - -
23L VAL* 1.3 77.6 - - - +
25L LYS* 1.3 61.4 + - - +
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Residues in contact with LYS 25 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486 A 4.9 4.4 - - - -
260C TYR* 5.2 7.6 - - - +
262C ILE* 5.8 1.4 - - - +
21L ALA 2.9 16.3 + - - +
22L ALA* 4.3 3.6 - - - +
24L MET* 1.3 80.1 - - - +
26L TYR* 1.3 66.4 + - + +
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Residues in contact with TYR 26 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486 A 3.6 33.0 + - + +
253C ASN 4.9 2.9 - - - +
260C TYR* 5.3 4.5 - - - +
22L ALA* 3.1 14.8 + - - +
25L LYS* 1.3 82.0 - - + +
27L GLY* 1.3 60.2 + - - +
30L GLN* 4.8 18.0 - - + +
33L ARG* 5.9 6.1 - - + -
34L ILE* 5.4 5.8 - - + +
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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