Contacts of the helix formed by residues 83 - 90 (chain A) in PDB entry 4PK7
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 83 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A LEU* 1.3 78.5 + - + +
85A PHE 3.4 1.7 - - - +
86A GLU* 3.1 27.8 + - - +
87A VAL* 3.0 32.8 + - + +
116A ASP* 5.0 8.5 - - - +
123A GLN* 5.1 8.3 + - - +
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Residues in contact with LEU 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A MET* 1.3 86.0 - - + +
85A PHE* 1.3 66.2 + - - +
87A VAL* 2.9 20.5 + - - +
88A VAL* 3.1 19.1 + - + +
98A VAL* 5.3 9.0 - - + -
102A TRP* 4.3 21.1 - - + -
116A ASP* 3.7 46.4 - - + +
117A LEU* 4.6 4.0 - - + -
120A PHE* 3.7 24.9 - - + -
178A PHE* 4.2 25.4 - - + -
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Residues in contact with PHE 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A MET 3.4 1.3 - - - +
84A LEU* 1.3 78.2 - - - +
86A GLU* 1.3 69.4 + - + +
88A VAL* 3.4 8.1 + - - +
89A LYS* 3.6 29.4 + - + +
90A MET* 6.0 3.8 - - + -
120A PHE* 3.8 18.7 - - + +
123A GLN* 3.6 55.6 - - + +
124A CYS* 4.0 16.4 - - - -
126A GLY* 6.3 0.2 - - - -
160A PRO* 5.0 7.2 - - + -
168A TRP* 5.1 8.7 - + - -
171A PHE* 4.0 25.7 - + - -
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Residues in contact with GLU 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A MET* 3.1 30.3 + - - +
85A PHE* 1.3 86.2 - - + +
87A VAL* 1.3 68.9 + - - +
90A MET* 3.0 67.5 + - + +
91A GLY 3.7 0.2 + - - -
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Residues in contact with VAL 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A MET* 3.0 27.3 + - + +
84A LEU* 2.9 14.9 + - - +
86A GLU* 1.3 79.5 - - - +
88A VAL* 1.3 57.4 + - + +
91A GLY* 3.1 27.2 + - - +
93A SER* 4.0 19.4 + - - +
95A MET* 5.9 0.2 - - - +
98A VAL* 4.2 27.4 - - + -
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Residues in contact with VAL 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A LEU* 3.1 17.2 + - + +
85A PHE 4.0 3.6 - - - +
86A GLU 3.2 0.2 - - - -
87A VAL* 1.3 77.6 - - + +
89A LYS* 1.3 64.0 + - - +
91A GLY 3.0 17.3 - - - +
92A LYS* 5.2 0.7 - - - +
95A MET* 4.0 24.7 - - + +
98A VAL* 5.4 2.7 - - + -
120A PHE* 3.9 23.1 - - + -
171A PHE* 4.9 7.6 - - + +
174A SER* 3.3 51.8 + - - +
175A PHE* 3.8 7.2 - - - +
178A PHE* 4.8 7.2 - - + -
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Residues in contact with LYS 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A PHE* 3.6 20.0 + - + +
88A VAL* 1.3 79.7 - - - +
90A MET* 1.3 100.7 + - + +
91A GLY 3.3 4.3 + - - +
92A LYS* 4.3 11.6 - - - +
167A GLN* 4.0 30.0 - - - +
168A TRP* 3.6 48.8 - - + -
170A LYS* 5.9 0.8 - - - +
171A PHE* 3.4 34.2 - - + +
174A SER* 5.1 0.9 - - - -
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Residues in contact with MET 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A PHE* 6.0 4.5 - - + -
86A GLU* 3.0 54.8 + - + +
89A LYS* 1.3 103.2 - - + +
91A GLY* 1.3 56.8 + - - +
92A LYS* 4.7 7.3 - - - +
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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