Contacts of the helix formed by residues 67 - 76 (chain U) in PDB entry 5JPQ
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 ALA 67 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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354S PHE* 4.2 20.6 - - + -
9U TYR* 4.2 22.5 - - + +
63U GLU 3.9 4.7 + - - +
64U GLU* 3.1 27.8 + - - +
66U VAL* 1.3 77.0 - - - +
68U HIS* 1.3 59.4 + - - +
69U LEU 3.6 0.3 + - - -
70U PRO* 4.0 13.1 - - - +
71U LEU* 4.5 3.8 + - - +
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Residues in contact with HIS 68 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288S ALA* 4.4 22.0 - - + +
289S LYS* 4.4 14.8 - - + +
350S ARG* 5.8 4.5 - - + +
64U GLU 4.5 2.7 + - - +
65U ILE 5.8 1.6 - - - +
66U VAL 3.0 1.4 + - - -
67U ALA* 1.3 76.5 - - - +
69U LEU* 1.3 60.1 + - - +
70U PRO 3.5 0.2 - - - -
71U LEU* 3.4 9.8 + - - +
72U LEU* 2.9 29.7 + - + +
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Residues in contact with LEU 69 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54U VAL* 6.2 4.0 - - + -
56U ILE* 5.8 7.6 - - + -
66U VAL* 3.0 20.0 + - + +
68U HIS* 1.3 75.2 - - - +
70U PRO* 1.4 59.4 - - - +
72U LEU* 3.8 6.4 - - - +
73U CYS* 2.8 35.5 + - + +
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Residues in contact with PRO 70 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9U TYR* 4.8 13.5 - - + +
11U LYS* 5.8 8.1 - - + -
66U VAL 4.4 1.4 - - - -
67U ALA 4.0 9.7 - - - +
68U HIS 3.5 0.6 - - - -
69U LEU* 1.4 78.4 - - - +
71U LEU* 1.3 63.3 + - - +
73U CYS* 3.8 4.5 - - + +
74U ASP* 3.2 23.0 + - - +
80U TYR* 5.9 4.3 - - + -
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Residues in contact with LEU 71 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67U ALA 4.5 2.6 + - - +
68U HIS* 3.4 14.6 + - - +
69U LEU 3.3 0.4 - - - -
70U PRO* 1.3 78.3 - - - +
72U LEU* 1.3 62.4 + - - +
74U ASP* 3.5 5.4 + - - +
75U GLU* 3.4 20.1 + - - +
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Residues in contact with LEU 72 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289S LYS* 5.9 7.4 - - + +
46U VAL* 4.9 15.5 - - + +
47U GLU 6.1 0.4 - - - +
68U HIS* 2.9 21.9 + - + +
69U LEU* 3.8 6.5 - - - +
71U LEU* 1.3 73.3 - - - +
73U CYS* 1.3 62.0 + - - +
75U GLU* 3.4 8.0 + - - +
76U LYS* 3.3 23.6 + - - +
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Residues in contact with CYS 73 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46U VAL* 5.3 7.4 - - + +
54U VAL* 5.5 5.6 - - + -
69U LEU* 2.8 21.6 + - + +
70U PRO* 3.8 5.4 - - + +
72U LEU* 1.3 73.1 - - - +
74U ASP* 1.3 57.4 + - - +
76U LYS* 4.0 1.8 - - - +
77U LYS* 2.8 7.3 + - - -
78U ILE* 2.7 54.7 + - + +
80U TYR* 4.7 14.1 - - + +
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Residues in contact with ASP 74 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70U PRO 3.2 16.7 + - - +
71U LEU* 3.9 5.6 - - - +
72U LEU 3.3 0.4 - - - -
73U CYS* 1.3 75.3 - - - +
75U GLU* 1.3 63.8 - - - +
77U LYS* 3.4 12.7 + - - +
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Residues in contact with GLU 75 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71U LEU 3.4 10.8 + - - +
72U LEU* 3.6 11.2 - - - +
73U CYS 3.4 0.2 - - - -
74U ASP* 1.3 80.1 - - - +
76U LYS* 1.3 58.4 + - + +
77U LYS* 3.6 1.7 + - - +
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Residues in contact with LYS 76 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46U VAL* 4.1 21.1 - - - +
49U GLY* 5.5 5.2 - - - -
72U LEU 3.3 13.5 + - - +
73U CYS* 4.5 2.5 - - - +
75U GLU* 1.3 77.6 - - + +
77U LYS* 1.3 69.2 + - - +
78U ILE* 3.3 9.2 + - + +
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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