Contacts of the helix formed by residues 61 - 69 (chain B) in PDB entry 3ZPL
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 MET 61 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60B ARG* 1.3 69.7 - - - +
62B THR* 1.3 65.6 + - - +
64B LEU* 3.1 3.8 + - - -
65B ALA 2.9 19.2 + - - -
72B ARG* 5.8 4.7 - - + -
75B LEU* 2.9 40.5 - - + +
76B SER* 4.7 0.9 - - - -
79B VAL* 3.9 24.7 - - + -
90B ARG* 4.8 3.8 - - - +
100B GLN* 3.1 26.7 + - + +
101B PHE 4.4 3.1 - - - +
102B ALA* 3.9 24.0 - - + -
5D A 3.5 23.8 + - - +
6D T 3.4 33.4 - - - +
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Residues in contact with THR 62 (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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60B ARG* 3.3 0.4 - - - -
61B MET* 1.3 73.0 - - - +
63B GLU* 1.3 56.5 + - - +
65B ALA* 3.2 8.5 + - - +
66B LYS* 2.9 28.5 + - + +
72B ARG* 3.1 45.5 + - - +
161B TRP* 4.0 19.7 - - + +
162B LEU* 5.1 1.6 - - + -
4D G 3.5 14.6 - - - +
5D A 2.4 30.9 + - - -
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Residues in contact with GLU 63 (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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59B LEU* 4.3 15.0 - - + -
60B ARG* 2.9 19.3 + - + +
62B THR* 1.3 76.0 - - - +
64B LEU* 1.3 64.7 + - - +
66B LYS* 3.1 9.6 + - - +
67B TYR* 3.1 36.6 + - + -
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Residues in contact with LEU 64 (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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47B LEU* 4.1 23.6 - - + +
50B LYS* 4.1 19.5 - - + -
51B LEU* 3.9 27.6 - - + -
59B LEU* 4.1 23.8 - - + +
60B ARG 2.9 11.0 + - - +
61B MET* 3.3 9.9 - - - +
63B GLU* 1.3 78.5 - - - +
65B ALA* 1.3 63.1 + - - +
67B TYR* 3.2 2.2 + - + +
68B ALA* 3.0 24.5 + - + +
75B LEU* 3.8 26.5 - - + -
79B VAL* 4.9 2.9 - - + -
102B ALA* 3.9 20.4 - - + -
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Residues in contact with ALA 65 (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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61B MET 2.9 12.2 + - - +
62B THR* 3.5 11.7 - - - +
64B LEU* 1.3 75.8 - - - +
66B LYS* 1.3 52.3 + - - +
68B ALA 3.3 0.5 + - - -
69B LYS* 2.7 31.7 + - - -
70B ILE* 3.2 36.5 + - + +
72B ARG* 4.3 13.0 - - + +
75B LEU* 3.5 14.4 - - + +
161B TRP* 3.8 10.3 - - + -
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Residues in contact with LYS 66 (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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62B THR* 2.9 17.0 + - + +
63B GLU* 3.1 10.1 + - - +
65B ALA* 1.3 76.4 - - - +
67B TYR* 1.3 62.1 + - + +
69B LYS* 3.0 38.4 + - - +
161B TRP* 3.7 45.6 - - + +
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Residues in contact with TYR 67 (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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17A ARG* 6.0 5.2 - - - -
21A GLU* 4.0 14.9 - - - +
50B LYS* 4.9 15.3 - - + -
59B LEU* 3.7 35.1 - - + +
63B GLU* 3.1 30.2 + - + -
64B LEU* 3.7 4.9 - - - +
66B LYS* 1.3 77.9 - - + +
68B ALA* 1.3 62.1 + - - +
69B LYS* 3.4 18.8 - - - +
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Residues in contact with ALA 68 (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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20A ILE* 5.8 2.8 - - - +
21A GLU* 5.7 0.3 - - - -
24A THR* 4.0 9.7 + - - +
43B VAL* 5.4 3.2 - - + +
46B GLY 6.2 0.9 - - - -
47B LEU* 3.7 26.7 - - + -
64B LEU* 3.0 16.9 + - + +
65B ALA 3.8 3.1 - - - +
67B TYR* 1.3 75.5 - - - +
69B LYS* 1.3 70.8 + - - +
70B ILE* 3.6 24.1 - - + +
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Residues in contact with LYS 69 (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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21A GLU* 3.6 45.4 + - + -
24A THR* 3.8 17.9 - - + +
25A LEU* 3.9 24.0 - - + +
28A ASP* 5.2 2.9 - - - +
65B ALA 2.7 13.8 + - - -
66B LYS* 3.0 27.1 + - - +
67B TYR* 3.3 14.8 - - - +
68B ALA* 1.3 78.4 - - - +
70B ILE* 1.3 59.1 + - - +
151B GLN* 2.8 34.7 + - - +
160B PRO* 3.7 16.4 - - - +
161B TRP* 3.8 14.7 - - + -
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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