Contacts of the helix formed by residues 73 - 80 (chain I) in PDB entry 4E45
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 VAL 73 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49I ALA 4.7 1.3 - - - +
52I ARG* 3.6 51.0 + - + +
53I GLY 4.5 2.0 - - - +
56I GLN* 3.9 17.0 - - + +
69I GLN 3.6 12.1 - - - +
70I LEU* 3.1 31.3 + - + +
72I LYS* 1.3 77.7 - - - +
74I LEU* 1.3 59.8 + - - +
75I PRO 3.5 1.5 - - - -
76I GLN* 3.7 6.1 + - - +
77I LEU* 3.0 31.1 + - + +
744J LEU* 4.3 16.4 - - + -
745J PRO* 6.1 2.5 - - + -
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Residues in contact with LEU 74 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53H LEU* 3.6 27.8 - - + -
70I LEU* 3.3 10.6 + - + +
71I GLU* 3.2 20.4 + - + +
73I VAL* 1.3 76.0 - - - +
75I PRO* 1.3 76.7 - - + +
77I LEU* 3.1 10.5 + - + -
78I LEU* 2.9 55.4 + - + +
731J LEU* 4.3 32.8 - - + -
732J SER 4.5 2.9 - - - +
733J LEU* 3.6 21.8 - - + -
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Residues in contact with PRO 75 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75G PRO* 4.5 9.6 - - + -
79G LEU* 5.7 1.7 - - + +
71I GLU 3.4 11.4 - - - +
72I LYS 4.0 5.4 - - - +
73I VAL 3.8 1.8 - - - -
74I LEU* 1.3 95.3 - - + +
76I GLN* 1.3 57.1 + - - +
78I LEU* 4.0 2.6 - - + +
79I LEU* 3.0 37.8 + - + +
733J LEU* 3.8 36.3 - - + +
736J TRP* 6.4 0.4 - - + -
740J GLN* 4.0 17.9 - - + +
758J PHE* 3.9 23.8 - - + -
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Residues in contact with GLN 76 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52I ARG* 3.6 3.8 - - - +
73I VAL 3.7 6.1 + - - +
74I LEU 3.3 0.4 - - - -
75I PRO* 1.3 76.0 - - - +
77I LEU* 1.3 58.9 + - - +
79I LEU* 3.7 0.6 + - - -
80I ASP* 3.0 10.4 + - - +
740J GLN* 3.2 29.2 + - - +
742J HIS 3.0 23.6 + - - -
743J PRO* 3.6 2.8 - - - +
744J LEU* 2.9 40.2 + - + +
751J HIS* 3.4 14.9 + - + -
755J CYS* 3.6 19.1 - - - -
758J PHE* 4.4 7.9 - - + -
759J ILE* 3.6 18.1 - - + +
901J ZN 2.5 27.7 - - - -
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Residues in contact with LEU 77 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53H LEU* 5.2 2.0 - - + -
45I PHE* 4.3 20.2 - - + -
48I GLU* 3.6 34.5 - - + -
49I ALA* 3.6 31.6 - - + +
52I ARG* 3.4 17.7 - - - +
70I LEU* 5.5 0.7 - - + -
73I VAL* 3.0 24.1 + - + +
74I LEU* 3.1 21.5 + - + +
76I GLN* 1.3 74.5 - - - +
78I LEU* 1.3 66.6 + - + +
80I ASP* 3.0 14.0 + - - +
81I PHE* 3.4 25.3 + - + -
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Residues in contact with LEU 78 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79G LEU* 3.7 34.0 - - + +
53H LEU* 4.5 13.7 - - + -
57H GLN* 3.9 22.0 + - - +
45I PHE* 4.2 17.9 - - + -
74I LEU* 2.9 47.0 + - + +
75I PRO* 4.1 1.3 - - + +
77I LEU* 1.3 77.3 - - + +
79I LEU* 1.3 62.9 + - - +
81I PHE* 3.1 16.8 + - - +
733J LEU* 4.1 10.3 - - + -
754J ARG* 3.5 12.1 + - - -
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Residues in contact with LEU 79 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75G PRO* 4.5 4.7 - - + +
78G LEU* 3.8 28.5 - - + -
79G LEU* 3.8 23.6 - - + -
88H ARG* 4.3 0.5 - - - -
75I PRO* 3.0 23.8 + - + +
76I GLN* 4.2 1.1 - - - +
77I LEU 3.2 0.4 - - - -
78I LEU* 1.3 78.3 - - - +
80I ASP* 1.3 55.6 + - - +
81I PHE 3.2 1.3 + - - +
752J SER* 2.7 22.0 + - - -
754J ARG* 3.1 33.0 + - + +
755J CYS* 3.8 20.0 - - + +
758J PHE* 3.5 48.0 - - + -
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Residues in contact with ASP 80 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88H ARG* 4.7 3.6 - - - +
89H SER* 4.0 18.4 - - - -
92H LEU* 4.7 2.9 - - - +
52I ARG* 2.7 32.0 + - - +
76I GLN 3.0 2.7 + - - -
77I LEU 3.0 10.1 + - - +
79I LEU* 1.3 76.7 - - - +
81I PHE* 1.3 63.6 + - + +
749J VAL* 4.2 9.0 - - + +
750J ASP 3.7 7.0 - - - +
751J HIS* 2.8 15.6 + - - -
752J SER* 3.0 22.1 + - - -
755J CYS* 3.1 2.3 - - - +
901J ZN 1.8 38.1 - - - -
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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