Contacts of the helix formed by residues 73 - 84 (chain A) in PDB entry 4ZGY
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 73 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A ASN* 2.5 26.6 + - - -
72A ASP* 1.3 76.5 + - - +
74A LYS* 1.3 66.2 + - - +
75A ALA 4.5 0.2 - - - -
76A ILE* 3.1 18.2 + - - +
77A VAL* 3.1 14.4 + - - +
391A VAL* 4.2 7.6 - - - +
402A ARG* 4.2 7.6 + - - +
405A ILE* 3.9 15.2 - - - +
407A TYR* 3.0 28.4 + - - -
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Residues in contact with LYS 74 (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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72A ASP 3.5 4.1 + - - -
73A SER* 1.3 72.0 - - - +
75A ALA* 1.3 57.2 + - - +
77A VAL* 3.6 5.3 + - - +
78A LYS* 2.9 37.9 + - + +
97A LEU* 4.7 16.2 - - + -
101A LEU* 4.0 29.5 - - + +
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Residues in contact with ALA 75 (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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45A LEU* 4.8 6.7 - - + -
73A SER* 3.2 1.0 - - - -
74A LYS* 1.3 77.5 - - - +
76A ILE* 1.3 60.4 + - - +
78A LYS* 3.5 15.6 + - - +
79A THR* 2.9 34.3 + - - -
407A TYR* 3.6 41.5 - - + -
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Residues in contact with ILE 76 (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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45A LEU* 4.3 1.8 - - + -
48A ILE* 3.5 27.6 - - + -
66A TYR* 3.9 16.4 - - + +
71A ASN* 4.0 12.3 - - - +
73A SER* 3.1 26.9 + - - +
75A ALA* 1.3 77.2 - - - +
77A VAL* 1.3 58.0 + - - +
79A THR* 3.2 7.5 + - - -
80A LEU* 2.9 37.6 + - + +
280A VAL* 3.7 23.6 - - + -
284A PHE* 3.6 26.0 - - + -
407A TYR* 3.7 12.6 - - + +
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Residues in contact with VAL 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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66A TYR* 4.5 7.2 - - + -
68A VAL* 4.3 23.1 - - + -
71A ASN 4.5 5.4 - - - +
72A ASP 4.4 3.6 - - - -
73A SER 3.1 16.3 + - - +
74A LYS* 4.0 2.2 - - - +
76A ILE* 1.3 75.5 - - - +
78A LYS* 1.3 57.7 + - - +
80A LEU* 4.7 0.7 - - - -
81A ALA* 2.9 30.2 + - + +
87A PHE* 3.4 31.3 - - + -
97A LEU* 4.3 11.7 - - + -
98A VAL* 4.1 16.4 - - + -
101A LEU* 3.6 22.7 - - + -
103A VAL* 5.9 0.2 - - + -
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Residues in contact with LYS 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A LEU* 5.7 4.9 - - - +
74A LYS* 2.9 25.6 + - + +
75A ALA* 3.7 12.9 + - - +
76A ILE 3.2 0.2 - - - -
77A VAL* 1.3 75.1 - - - +
79A THR* 1.3 65.2 + - - +
81A ALA* 3.3 6.5 + - - +
82A ALA* 2.9 28.7 + - + +
101A LEU* 4.1 16.5 - - + +
417A MET* 4.6 16.3 - - + +
421A GLN* 5.7 3.8 - - - -
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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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45A LEU* 3.7 25.2 - - + +
48A ILE* 4.5 17.0 - - + -
49A LEU* 3.9 27.8 - - + -
75A ALA 2.9 23.3 + - - -
76A ILE* 3.2 6.5 + - - -
78A LYS* 1.3 78.6 + - - +
80A LEU* 1.3 60.7 + - + +
82A ALA* 3.2 5.0 + - - +
83A THR* 3.0 26.4 + - - -
409A MET* 4.8 3.6 - - + -
417A MET* 3.7 25.6 - - - +
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Residues in contact with LEU 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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48A ILE* 3.8 18.2 - - + -
49A LEU* 6.3 0.9 - - + -
52A HIS* 5.0 2.0 - - + -
66A TYR* 3.4 47.6 - - + -
76A ILE* 2.9 25.5 + - + +
77A VAL 4.1 2.9 - - - +
79A THR* 1.3 77.0 - - + +
81A ALA* 1.3 62.2 + - - +
83A THR* 3.1 15.9 - - + +
84A GLY 3.1 4.3 + - - -
85A THR* 3.0 42.3 + - + +
87A PHE* 4.0 5.2 - - + -
279A TYR* 3.7 36.3 - - + -
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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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77A VAL* 2.9 20.5 + - + +
78A LYS* 3.5 8.5 - - - +
80A LEU* 1.3 72.9 - - - +
82A ALA* 1.3 68.2 + - - +
84A GLY* 3.0 4.2 + - - -
87A PHE* 3.6 10.9 - - + -
101A LEU* 5.3 7.4 - - + +
103A VAL* 4.0 20.6 - - + -
107A ARG* 2.9 30.2 + - - +
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Residues in contact with ALA 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 LYS* 2.9 14.3 + - + +
79A THR 3.4 8.5 - - - +
81A ALA* 1.3 78.4 - - - +
83A THR* 1.3 61.4 + - - +
84A GLY* 3.2 1.7 + - - -
417A MET* 3.9 20.6 - - + -
420A PHE* 3.4 24.3 - - + +
421A GLN* 4.2 25.4 - - + +
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Residues in contact with THR 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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49A LEU* 4.7 9.6 - - - +
52A HIS* 3.0 41.4 + - + +
79A THR 3.0 11.7 + - - -
80A LEU* 3.1 29.6 - - + +
81A ALA 3.2 0.2 - - - -
82A ALA* 1.3 75.6 - - - +
84A GLY* 1.3 58.1 + - - +
85A THR* 3.5 20.9 - - + -
417A MET* 5.9 0.4 - - - -
420A PHE* 3.7 37.5 - - - -
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Residues in contact with GLY 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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52A HIS* 5.3 1.6 - - - -
63A THR* 5.3 5.9 - - - +
64A PRO* 6.0 0.2 - - - +
80A LEU 3.1 0.8 + - - -
81A ALA 3.0 8.0 + - - -
82A ALA 3.1 2.1 - - - -
83A THR* 1.3 80.9 - - - +
85A THR* 1.3 65.8 + - - +
107A ARG* 3.4 20.2 + - - -
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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