Contacts of the helix formed by residues 73 - 86 (chain B) in PDB entry 5ZCJ
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B VAL* 3.6 3.1 - - - +
69B ARG* 6.1 0.2 - - - -
72B TRP* 1.3 75.5 - - - +
74B LEU* 1.3 61.4 + - - +
75B GLU* 3.6 11.3 + - - +
76B ASP* 3.1 34.0 + - - +
77B GLY* 2.8 26.2 + - - -
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Residues in contact with LEU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ARG* 4.0 21.5 - - - +
18B MET* 3.6 34.5 - - + -
26B HIS* 4.4 11.9 - - + +
28B CYS* 3.6 22.2 - - - -
67B VAL* 4.4 5.4 - - + -
69B ARG* 4.5 11.4 - - + +
73B SER* 1.3 75.0 - - - +
75B GLU* 1.3 63.8 + - - +
77B GLY* 3.9 0.3 - - - -
78B LEU* 2.9 30.1 + - - +
111B HIS* 3.6 35.2 - - + +
113B TYR* 3.3 20.2 - - - +
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Residues in contact with GLU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ARG* 3.0 30.2 + - - -
73B SER* 3.3 9.2 + - - +
74B LEU* 1.3 79.1 + - - +
76B ASP* 1.3 63.0 + - - +
78B LEU* 3.4 5.9 + - - +
79B ASN* 2.9 37.7 + - - +
91B LEU 4.5 8.5 - - - +
92B THR* 3.7 7.6 - - - -
93B GLU* 3.5 34.2 - - + +
113B TYR* 2.5 29.9 + - + +
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Residues in contact with ASP 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B TRP* 4.2 19.7 - - + -
73B SER* 3.1 27.2 + - - +
75B GLU* 1.3 78.6 - - - +
77B GLY* 1.3 58.2 + - - +
79B ASN* 3.8 7.9 + - - +
80B ARG* 3.0 28.8 + - - +
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Residues in contact with GLY 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B PHE 5.1 0.3 - - - +
67B VAL* 3.6 25.8 - - - +
72B TRP* 3.8 13.3 - - - +
73B SER 2.8 17.0 + - - -
76B ASP* 1.3 74.9 - - - +
78B LEU* 1.3 65.8 + - - +
80B ARG* 3.4 10.6 + - - +
81B VAL* 3.3 21.0 - - - +
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Residues in contact with LEU 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B CYS* 3.6 37.2 - - + +
29B HIS* 4.1 9.9 - - - +
30B ALA 4.3 0.2 - - - +
64B GLY* 4.3 3.4 - - - -
65B GLY 6.0 0.4 - - - +
67B VAL* 3.9 1.6 - - - +
74B LEU 2.9 18.8 + - - +
75B GLU* 3.7 5.4 - - - +
77B GLY* 1.3 76.0 - - - +
79B ASN* 1.3 59.3 + - - +
80B ARG 3.2 0.5 + - - -
81B VAL* 3.3 6.7 + - - +
82B LEU* 2.9 51.8 + - + +
91B LEU* 3.9 26.7 - - + -
113B TYR* 3.6 38.4 - - + -
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Residues in contact with ASN 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B GLU* 2.9 25.0 + - - +
76B ASP* 4.0 9.9 + - - +
78B LEU* 1.3 76.3 - - - +
80B ARG* 1.3 57.9 + - - +
82B LEU* 3.8 15.2 - - - +
83B GLY* 3.0 23.7 + - - -
89B LEU 4.3 3.1 - - - +
90B ARG* 3.5 22.5 - - + +
91B LEU* 2.8 49.9 + - - +
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Residues in contact with ARG 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B PHE 4.6 9.7 + - - -
72B TRP* 3.6 47.9 - - + +
76B ASP 3.0 17.4 + - - +
77B GLY* 3.5 8.0 + - - +
78B LEU 3.1 0.6 - - - -
79B ASN* 1.3 79.8 - - - +
81B VAL* 1.3 81.2 + - - +
83B GLY* 3.4 1.9 + - - -
84B LEU* 3.3 40.9 + - + +
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Residues in contact with VAL 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B GLY* 3.4 42.2 - - - +
65B GLY* 4.5 10.3 - - - +
66B PHE 4.7 8.1 - - - +
77B GLY 3.3 17.9 - - - +
78B LEU* 3.3 4.4 + - - +
80B ARG* 1.3 96.1 - - - +
82B LEU* 1.3 63.6 + - - +
84B LEU* 3.2 12.8 + - + +
85B GLY* 2.8 26.5 + - - -
134B ASP* 4.4 2.3 - - - +
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Residues in contact with LEU 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ALA* 4.3 6.5 - - + -
32B LEU* 6.0 0.4 - - + -
63B PRO* 3.8 24.7 - - + +
64B GLY 4.4 1.8 - - - +
78B LEU* 2.9 48.6 + - + +
79B ASN* 3.9 17.7 - - - +
81B VAL* 1.3 78.2 - - - +
83B GLY* 1.3 55.5 + - - +
85B GLY 4.5 0.2 - - - +
86B LEU* 2.7 57.1 + - + +
87B GLY 2.7 7.8 + - - -
89B LEU* 4.5 17.7 - - + +
91B LEU* 3.9 22.4 - - + -
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Residues in contact with GLY 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ASN 3.0 17.7 + - - -
80B ARG 3.4 2.4 + - - -
82B LEU* 1.3 76.9 - - - +
84B LEU* 1.3 61.1 + - - +
86B LEU 4.2 0.2 - - - -
87B GLY* 3.3 30.9 + - - -
89B LEU 5.0 1.5 + - - -
132B SER* 5.0 2.1 - - - -
133B ARG* 4.1 16.4 + - - -
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Residues in contact with LEU 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B ARG* 3.3 40.9 + - + +
81B VAL* 3.2 14.4 + - + +
83B GLY* 1.3 78.6 - - - +
85B GLY* 1.3 57.4 + - - +
132B SER* 3.3 2.1 - - - -
133B ARG* 3.1 42.7 + - + -
134B ASP* 3.1 39.4 + - + +
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Residues in contact with GLY 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B GLN* 5.9 1.3 - - - -
63B PRO* 6.5 0.7 - - - -
81B VAL 2.8 13.6 + - - -
84B LEU* 1.3 79.9 - - - +
86B LEU* 1.3 71.2 + - - +
129B ALA* 3.6 9.5 - - - +
132B SER* 3.1 15.3 + - - -
134B ASP* 3.1 20.8 + - - +
139B VAL* 4.7 8.5 - - - +
142B LEU* 5.1 2.3 - - - +
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Residues in contact with LEU 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LEU* 3.7 29.4 - - + -
51B LEU* 5.8 0.2 - - + -
53B GLN* 5.0 1.3 - - - +
63B PRO* 4.1 19.5 - - + -
82B LEU* 2.7 40.3 + - + +
83B GLY 4.2 0.4 - - - -
85B GLY* 1.3 83.9 - - - +
87B GLY* 1.3 55.8 + - - +
88B CYS* 3.3 2.8 + - - +
89B LEU* 5.0 11.0 - - + -
125B VAL* 4.2 15.7 - - + -
128B SER* 2.7 39.2 + - - +
129B ALA* 4.0 17.7 - - + +
132B SER* 4.4 4.1 - - - -
142B LEU* 4.0 21.3 - - + -
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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