Contacts of the helix formed by residues 44 - 54 (chain B) in PDB entry 5FEY
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 CYS 44 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20B CYS* 3.4 10.2 - - + -
23B CYS* 4.1 0.4 - - - -
27B PHE* 3.5 22.2 - - + -
32B LEU* 3.7 27.1 - - + -
33B ARG 3.4 5.6 - - - -
43B ILE* 1.3 80.1 - - - +
45B ARG* 1.3 62.9 + - - +
46B GLN* 3.4 7.4 - - - -
47B CYS* 3.2 20.0 - - - -
48B LEU* 3.1 22.4 + - - +
101B ZN 2.4 34.5 - - - -
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Residues in contact with ARG 45 (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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30B GLU 3.4 20.3 + - - -
31B GLN* 3.3 35.9 + - - +
32B LEU 4.0 0.2 - - - -
33B ARG* 2.8 32.0 + - + +
35B LYS* 4.3 11.4 - - + -
44B CYS* 1.3 74.9 - - - +
46B GLN* 1.3 66.2 + - - +
48B LEU* 3.6 1.6 + - - -
49B GLU* 3.2 42.5 + - - +
73B LEU* 3.7 18.6 - - + +
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Residues in contact with GLN 46 (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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25B GLU* 4.5 7.3 - - - +
31B GLN* 3.4 39.7 + - + +
32B LEU* 3.5 27.2 - - + +
44B CYS* 3.3 2.7 - - - -
45B ARG* 1.3 80.2 - - - +
47B CYS* 1.3 66.2 + - - +
49B GLU* 3.2 26.0 + - - +
50B LYS* 3.4 21.0 + - - +
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Residues in contact with CYS 47 (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 CYS* 4.3 1.1 - - - -
22B ILE* 3.8 35.0 - - + -
23B CYS* 3.4 19.3 - - - -
43B ILE* 4.4 2.0 - - + -
44B CYS* 3.2 9.1 - - - +
46B GLN* 1.3 79.8 - - - +
48B LEU* 1.3 62.7 + - - +
50B LYS* 3.2 29.8 + - + +
51B LEU* 3.3 17.2 + - - +
101B ZN 2.5 33.9 - - - -
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Residues in contact with LEU 48 (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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35B LYS* 3.7 26.9 - - + -
37B LEU* 4.2 7.2 - - + -
43B ILE* 3.6 24.4 - - + +
44B CYS 3.1 17.9 + - - +
45B ARG 3.8 5.2 - - - +
46B GLN 3.2 0.2 - - - -
47B CYS* 1.3 78.1 - - - +
49B GLU* 1.3 57.1 + - - +
51B LEU* 3.3 1.9 + - - +
52B LEU* 2.8 27.2 + - - +
59B VAL* 3.7 33.2 - - + -
73B LEU* 3.6 28.0 - - + -
76B LEU* 3.6 22.9 - - + -
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Residues in contact with GLU 49 (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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45B ARG* 3.2 46.1 + - - +
46B GLN* 3.2 19.6 + - - +
48B LEU* 1.3 76.9 - - - +
50B LYS* 1.3 58.2 + - + +
52B LEU* 3.7 8.7 - - + +
53B ALA* 2.9 27.7 + - - +
73B LEU* 3.7 16.4 - - + +
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Residues in contact with LYS 50 (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 CYS* 6.0 2.0 - - - +
46B GLN* 3.4 17.7 + - - +
47B CYS* 3.2 22.6 + - - +
48B LEU 3.2 0.6 - - - -
49B GLU* 1.3 78.7 - - + +
51B LEU* 1.3 63.7 + - + +
53B ALA* 3.4 19.1 + - - +
54B SER* 3.7 10.0 + - - -
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Residues in contact with LEU 51 (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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22B ILE* 4.4 14.6 - - + -
43B ILE* 3.9 27.8 - - + -
47B CYS 3.3 9.4 + - - +
48B LEU 3.3 5.4 + - - +
50B LYS* 1.3 78.4 - - + +
52B LEU* 1.3 63.7 + - - +
54B SER* 3.6 8.0 + - - +
55B SER* 3.6 14.9 + - - -
58B GLY 4.4 4.9 - - - +
59B VAL* 4.1 19.2 - - + +
60B ARG* 4.0 22.3 + - + +
62B PRO* 4.5 10.3 - - + -
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Residues in contact with LEU 52 (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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48B LEU 2.8 17.2 + - - +
49B GLU* 3.7 8.7 - - + +
50B LYS 3.3 0.2 - - - -
51B LEU* 1.3 75.0 - - - +
53B ALA* 1.3 63.1 + - - +
54B SER 3.2 0.9 - - - -
55B SER* 3.2 24.9 - - - -
59B VAL* 3.7 20.2 - - + +
70B ILE* 3.6 30.1 - - + +
71B THR* 4.2 21.3 - - - +
72B SER* 4.4 3.6 - - - +
73B LEU* 3.7 25.4 - - + +
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Residues in contact with ALA 53 (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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49B GLU 2.9 14.5 + - - +
50B LYS* 3.4 13.7 - - - +
51B LEU 3.3 0.4 - - - -
52B LEU* 1.3 79.5 - - - +
54B SER* 1.3 58.9 + - - +
55B SER 3.3 0.8 + - - -
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Residues in contact with SER 54 (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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50B LYS 3.7 8.8 + - - -
51B LEU* 3.6 11.6 + - - -
52B LEU 3.2 0.4 - - - -
53B ALA* 1.3 77.2 - - - +
55B SER* 1.3 64.0 + - - +
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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