Contacts of the helix formed by residues 22 - 36 (chain X) 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 LYS 22 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20X LYS 3.6 3.8 + - - -
21X ILE* 1.3 73.2 - - - +
23X LYS* 1.3 66.7 + - - +
24X GLU* 4.6 3.8 - - + +
25X GLU* 3.2 14.9 + - + +
26X LEU* 2.9 19.6 + - - +
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Residues in contact with LYS 23 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21X ILE 3.5 2.2 + - - -
22X LYS* 1.3 72.5 - - - +
24X GLU* 1.3 57.2 + - - +
26X LEU* 3.4 6.4 + - - +
27X LYS* 3.1 28.6 + - - +
45X ALA* 5.2 13.5 - - + +
46X LEU* 6.1 1.1 - - - -
47X LYS* 5.5 12.8 - - + +
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Residues in contact with GLU 24 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19W VAL* 5.9 0.9 - - - +
22X LYS* 3.4 3.3 - - + +
23X LYS* 1.3 79.0 - - - +
25X GLU* 1.3 57.2 + - - +
27X LYS* 4.0 5.3 - - - +
28X ARG* 3.1 26.2 + - - +
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Residues in contact with GLU 25 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21X ILE* 5.3 4.0 - - + -
22X LYS* 3.2 20.5 + - + +
24X GLU* 1.3 74.6 - - - +
26X LEU* 1.3 61.3 + - - +
28X ARG* 3.2 5.3 + - - +
29X SER* 2.9 31.5 + - - -
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Residues in contact with LEU 26 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21X ILE* 4.6 16.0 - - + +
22X LYS 2.9 14.1 + - - +
23X LYS* 3.6 11.4 - - - +
25X GLU* 1.3 73.6 - - - +
27X LYS* 1.3 61.3 + - - +
29X SER* 3.3 5.1 + - - -
30X LEU* 2.9 31.1 + - - +
45X ALA* 5.9 6.3 - - + -
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Residues in contact with LYS 27 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18W ALA 5.8 2.7 - - - +
19W VAL* 5.4 8.9 - - + +
23X LYS 3.1 13.4 + - - +
24X GLU* 4.0 7.0 - - - +
26X LEU* 1.3 81.6 - - - +
28X ARG* 1.3 57.1 + - - +
30X LEU* 3.3 6.3 + - - +
31X TYR* 2.9 28.2 + - - +
43X ILE* 4.9 18.4 - - + +
45X ALA* 5.8 8.9 - - + +
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Residues in contact with ARG 28 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19W VAL* 4.9 14.3 - - + +
24X GLU 3.1 18.0 + - - +
25X GLU* 3.2 6.0 + - - +
27X LYS* 1.3 76.4 - - - +
29X SER* 1.3 62.4 + - - +
31X TYR* 3.5 7.0 + - - +
32X ALA* 3.2 21.3 + - - +
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Residues in contact with SER 29 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147W PHE* 5.3 14.5 - - - +
25X GLU 2.9 16.0 + - - -
26X LEU* 4.0 4.5 - - - -
28X ARG* 1.3 74.8 - - - +
30X LEU* 1.3 62.0 + - - +
32X ALA* 3.2 6.3 + - - +
33X LEU* 2.8 32.7 + - - +
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Residues in contact with LEU 30 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26X LEU 2.9 17.5 + - - +
27X LYS* 3.6 8.1 - - - +
29X SER* 1.3 77.4 - - - +
31X TYR* 1.3 61.5 + - - +
33X LEU* 3.8 4.7 - - - +
34X PHE* 3.0 28.6 + - - +
43X ILE* 5.5 7.4 - - + -
55X ALA* 5.9 7.6 - - + -
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Residues in contact with TYR 31 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18W ALA* 5.8 7.4 - - + -
19W VAL* 5.3 9.4 - - + -
27X LYS 2.9 17.4 + - - +
28X ARG* 3.7 8.7 - - - +
30X LEU* 1.3 77.3 - - - +
32X ALA* 1.3 61.0 + - - +
34X PHE* 3.9 2.2 - - - +
35X SER* 3.1 26.0 + - - -
40X VAL* 5.2 13.0 - - + +
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Residues in contact with ALA 32 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94W ILE* 4.8 21.8 - - + +
28X ARG 3.2 14.6 + - - +
29X SER* 3.6 7.4 - - - +
31X TYR* 1.3 76.4 - - - +
33X LEU* 1.3 66.7 - - - +
35X SER* 3.2 19.4 + - - -
36X GLN* 4.2 2.1 + - - +
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Residues in contact with LEU 33 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147W PHE* 5.9 7.2 - - + -
29X SER 2.8 20.8 + - - +
30X LEU* 3.8 5.6 - - - +
32X ALA* 1.3 73.8 - - - +
34X PHE* 1.3 59.7 + - + +
35X SER 3.5 0.3 + - - -
36X GLN* 3.8 15.1 + - - +
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Residues in contact with PHE 34 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30X LEU 3.0 16.1 + - - +
31X TYR* 3.9 2.5 - - - +
33X LEU* 1.3 74.7 - - + +
35X SER* 1.3 62.4 + - - +
36X GLN 3.1 3.2 + - - -
37X PHE* 3.4 16.2 + - - +
38X GLY 3.6 8.4 - - - +
40X VAL* 5.3 11.0 - - + +
57X VAL* 5.3 13.7 - - + -
68X ALA* 5.7 9.2 - - + -
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Residues in contact with SER 35 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50W SER* 4.7 11.1 - - - -
70W LEU* 4.9 17.5 - - - -
72W ASN* 5.0 3.6 - - - -
31X TYR 3.1 18.1 + - - -
32X ALA* 3.2 10.8 + - - -
34X PHE* 1.3 75.3 - - - +
36X GLN* 1.3 64.5 + - - +
37X PHE 3.1 1.4 + - - -
38X GLY* 3.4 21.2 + - - +
39X HIS* 5.8 0.4 - - - +
40X VAL* 5.5 3.8 - - - +
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Residues in contact with GLN 36 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50W SER* 6.0 0.3 - - - -
72W ASN* 3.9 24.6 - - + +
73W ASN* 5.3 7.0 - - + +
96W THR* 4.8 14.8 - - - +
97W ASN* 6.1 3.1 - - + -
32X ALA 4.2 1.6 + - - +
33X LEU 3.8 12.8 + - - +
34X PHE 3.1 1.2 - - - -
35X SER* 1.3 79.7 - - - +
37X PHE* 1.3 56.2 + - - +
38X GLY 3.6 0.2 - - - -
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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