Contacts of the helix formed by residues 77 - 85 (chain A) in PDB entry 4PTJ
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 SER 77 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A LEU* 3.4 14.0 - - - +
75A VAL* 3.7 0.8 - - - +
76A LYS* 1.3 87.4 - - - +
78A VAL* 1.3 58.3 + - - +
79A ASP* 2.8 24.3 + - - -
80A GLU* 3.1 17.9 + - - +
81A ALA 2.9 24.1 + - - -
202A NAP 3.8 9.4 - - - -
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Residues in contact with VAL 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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62A LEU* 4.6 2.9 - - + -
77A SER* 1.3 70.3 - - - +
79A ASP* 1.3 69.8 + - + +
81A ALA* 3.2 6.6 + - - +
82A ILE* 3.1 42.3 + - + +
102A GLN* 3.9 39.0 - - + +
103A PHE* 3.8 29.6 - - + -
106A LYS* 5.6 6.3 - - + -
202A NAP 3.9 6.8 + - - +
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Residues in contact with ASP 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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77A SER* 2.8 22.7 + - - -
78A VAL* 1.3 77.9 - - + +
80A GLU* 1.3 60.7 + - - +
82A ILE* 3.6 7.3 + - - +
83A ALA* 3.1 23.6 + - - +
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Residues in contact with GLU 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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74A TRP 4.2 3.6 - - - +
75A VAL* 3.7 24.0 - - + +
76A LYS* 2.9 36.5 + - - +
77A SER* 3.1 19.3 + - - +
79A ASP* 1.3 76.7 - - - +
81A ALA* 1.3 59.4 + - - +
83A ALA* 3.3 5.7 + - + +
84A ALA* 2.9 30.5 + - + +
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Residues in contact with ALA 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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41A ILE* 3.9 21.7 - - + +
60A ILE* 4.1 7.7 - - + +
62A LEU* 4.2 8.3 - - + -
75A VAL* 3.6 27.2 - - + +
77A SER 2.9 13.3 + - - +
78A VAL* 3.2 7.2 + - - +
80A GLU* 1.3 77.0 - - - +
82A ILE* 1.3 62.8 + - - +
84A ALA* 3.4 10.7 + - - +
85A CYS* 3.4 18.9 + - - -
103A PHE* 4.4 4.9 - - + -
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Residues in contact with ILE 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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2A ILE* 3.7 24.9 - - + -
41A ILE* 4.7 2.2 - - + -
78A VAL* 3.1 33.3 + - + +
79A ASP* 4.1 6.1 - - - +
81A ALA* 1.3 74.9 - - - +
83A ALA* 1.3 63.1 + - - +
85A CYS* 3.2 21.4 + - - +
86A GLY 3.7 4.3 + - - +
91A ILE* 3.9 19.8 - - + +
103A PHE* 3.9 17.9 - - + -
106A LYS* 5.4 6.3 - - + -
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Residues in contact with ALA 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 ASP 3.1 18.1 + - - +
80A GLU* 3.3 8.7 + - + +
82A ILE* 1.3 77.2 - - - +
84A ALA* 1.3 57.0 + - - +
86A GLY* 2.9 22.7 + - - -
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Residues in contact with ALA 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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58A LYS* 2.8 32.1 + - + +
60A ILE* 4.0 14.6 - - + -
73A THR* 4.4 11.4 - - + -
75A VAL* 4.2 16.4 - - + -
80A GLU* 2.9 17.3 + - + +
81A ALA 3.7 6.5 - - - +
82A ILE 3.2 0.4 - - - -
83A ALA* 1.3 75.4 - - - +
85A CYS* 1.3 50.5 + - - +
86A GLY* 3.7 0.7 + - - -
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Residues in contact with CYS 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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39A PRO* 3.7 19.4 - - + +
41A ILE* 3.9 18.4 - - - -
58A LYS* 4.3 8.3 + - - +
60A ILE* 3.3 28.7 - - - -
81A ALA 3.4 10.5 - - - -
82A ILE 3.3 11.2 - - - +
83A ALA 3.0 0.2 - - - -
84A ALA* 1.3 78.3 - - - +
86A GLY* 1.3 62.5 + - - +
87A ASP 3.0 4.7 + - - -
88A VAL* 3.3 23.3 - - + +
91A ILE* 3.8 28.0 - - + -
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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