Contacts of the helix formed by residues 76 - 86 (chain A) in PDB entry 5PNZ
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 ASP 76 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A PHE* 3.6 9.2 - - - +
56A ALA 3.6 0.9 - - - +
57A GLN 3.4 20.4 - - - +
58A PRO* 3.2 37.6 - - + +
75A MET* 1.3 81.3 + - - +
77A PHE* 1.3 64.2 + - - +
78A ALA* 2.9 25.8 + - - +
79A THR* 2.6 27.0 + - - -
80A MET* 3.1 22.9 + - - +
102A ILE* 3.6 13.0 - - - -
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Residues in contact with PHE 77 (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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43A LEU* 3.7 29.0 - - + +
46A LEU* 4.1 10.3 - - + -
47A GLN* 3.5 61.7 - - + +
50A ASP* 3.9 20.6 - - + -
55A PHE* 2.9 37.3 + - + +
56A ALA 4.1 0.9 - - - +
76A ASP* 1.3 73.2 - - - +
78A ALA* 1.3 58.6 + - - +
80A MET* 3.3 6.2 + - - +
81A ARG* 2.9 29.8 + - - +
99A PHE* 4.2 14.8 - + - -
102A ILE* 3.7 16.6 - - + +
123A LEU* 4.0 20.0 - - + -
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Residues in contact with ALA 78 (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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47A GLN* 5.4 0.2 - - - +
56A ALA 3.1 17.5 + - - +
57A GLN* 3.7 23.6 - - - +
58A PRO* 4.5 2.5 - - + -
76A ASP* 2.9 10.1 + - - +
77A PHE* 1.3 75.6 - - - +
79A THR* 1.3 63.4 + - - +
81A ARG* 3.2 10.5 + - - +
82A LYS* 3.1 22.2 + - - +
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Residues in contact with THR 79 (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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58A PRO* 4.4 7.6 - - - +
74A PRO 5.7 0.2 - - - +
75A MET* 3.8 23.8 - - + -
76A ASP* 2.6 33.0 + - - -
78A ALA* 1.3 74.5 - - - +
80A MET* 1.3 65.4 + - - +
82A LYS* 3.3 9.2 + - + +
83A ARG* 3.2 21.1 + - + +
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Residues in contact with MET 80 (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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43A LEU* 4.3 17.0 - - + -
75A MET* 3.7 13.5 - - - -
76A ASP 3.1 17.3 + - - +
77A PHE* 3.6 10.3 - - - +
78A ALA 3.3 0.2 - - - -
79A THR* 1.3 77.4 - - - +
81A ARG* 1.3 57.3 + - - +
83A ARG 3.2 1.0 + - - -
84A LEU* 2.9 29.9 + - - +
89A TYR* 3.5 28.4 - - + +
95A PHE* 3.6 57.2 - - + +
98A ASP* 3.9 2.9 - - + -
99A PHE* 3.9 18.2 - - + +
102A ILE* 3.8 23.8 - - - -
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Residues in contact with ARG 81 (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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40A ARG* 4.5 13.9 - - - +
43A LEU* 3.8 32.6 + - + +
44A ASP* 3.1 30.1 + - - +
47A GLN* 3.0 27.5 + - - +
77A PHE 2.9 15.8 + - - +
78A ALA* 3.2 9.3 + - - +
80A MET* 1.3 75.2 - - - +
82A LYS* 1.3 57.3 + - - +
84A LEU* 3.3 4.8 + - + +
85A GLU* 2.9 49.3 + - + +
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Residues in contact with LYS 82 (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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78A ALA 3.1 13.3 + - - +
79A THR* 3.5 12.6 - - + +
80A MET 3.3 0.2 - - - -
81A ARG* 1.3 77.2 - - - +
83A ARG* 1.3 61.6 + - - +
85A GLU* 3.4 4.9 + - - +
86A ALA* 3.3 22.0 + - - +
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Residues in contact with ARG 83 (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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79A THR* 3.2 11.2 + - + +
80A MET 3.7 7.2 - - - +
82A LYS* 1.3 79.2 - - - +
84A LEU* 1.3 61.6 + - - +
86A ALA* 3.2 10.5 + - - +
88A GLY* 2.8 57.4 + - - -
89A TYR* 3.4 30.5 - - + +
94A GLU* 3.2 29.1 + - - +
98A ASP* 3.4 23.6 + - - -
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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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36A THR* 3.3 38.0 - - + +
39A LEU* 3.6 31.4 - - + +
40A ARG* 3.6 36.8 - - + +
43A LEU* 4.1 19.5 - - + -
80A MET 2.9 17.7 + - - +
81A ARG* 3.5 7.4 - - + +
82A LYS 3.3 0.2 - - - -
83A ARG* 1.3 77.8 - - - +
85A GLU* 1.3 65.4 + - - +
87A GLN* 2.8 17.3 + - - -
88A GLY 4.6 0.9 - - - +
89A TYR* 3.8 21.3 - - + -
95A PHE* 5.0 2.2 - - + -
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Residues in contact with GLU 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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36A THR* 5.2 0.4 - - - -
40A ARG* 2.7 47.7 + - - +
81A ARG* 2.9 32.0 + - + +
82A LYS* 4.1 4.7 - - - +
83A ARG 3.3 0.4 - - - -
84A LEU* 1.3 83.4 - - - +
86A ALA* 1.3 56.7 + - - +
87A GLN* 3.2 7.3 + - - +
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Residues in contact with ALA 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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82A LYS 3.3 10.8 + - - +
83A ARG* 3.2 10.2 + - - +
84A LEU 3.1 1.0 - - - -
85A GLU* 1.3 77.4 - - - +
87A GLN* 1.3 70.4 + - - +
88A GLY* 3.2 4.2 + - - +
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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