Contacts of the helix formed by residues 73 - 88 (chain A) in PDB entry 2ZR7
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 GLY 73 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A SER 3.7 0.6 - - - -
72A SER* 1.3 80.0 - - - +
74A LYS* 1.3 70.1 + - - +
75A THR 3.3 2.2 - - - -
76A THR* 3.3 16.5 + - - -
77A VAL* 3.2 24.6 + - - +
227A VAL* 4.2 4.0 - - - -
242A ASN* 6.3 0.2 - - - -
264A ILE* 4.3 12.7 - - - +
501A PO4 3.0 13.2 + - - -
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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
----------------------------------------------------------
66A ILE* 3.5 33.8 - - + +
68A GLY* 3.1 33.4 - - - +
69A PRO 2.8 28.5 - - - -
72A SER* 4.1 2.0 - - - -
73A GLY* 1.3 79.7 - - - +
75A THR* 1.3 62.2 + - - +
77A VAL* 3.2 4.9 + - - +
78A ALA* 3.1 18.4 + - - +
194A ILE* 4.8 12.4 - - + +
195A ASN 3.7 11.6 + - - +
196A GLN* 4.3 12.5 - - - +
227A VAL* 3.8 25.1 - - + +
501A PO4 2.6 41.8 + - - -
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Residues in contact with THR 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A LYS* 1.3 76.1 - - - +
76A THR* 1.3 62.4 + - - +
78A ALA* 3.0 3.3 + - - +
79A LEU* 2.7 48.8 + - - +
94A PHE* 5.8 4.0 - - + -
105A TYR* 5.8 1.0 - - - -
146A ASP* 3.9 23.3 - - - +
194A ILE* 4.0 21.1 - - + -
501A PO4 2.9 31.5 + - - +
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Residues in contact with THR 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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73A GLY* 3.3 19.9 + - - -
74A LYS 3.3 0.6 - - - -
75A THR* 1.3 81.8 + - - +
77A VAL* 1.3 58.7 + - - +
79A LEU* 3.2 7.0 + - - +
80A HIS* 2.9 43.7 + - + +
105A TYR* 3.0 38.4 + - + +
109A LEU* 4.6 2.0 - - + +
264A ILE* 4.3 23.7 - - + +
269A GLY* 4.6 4.3 - - - -
270A ILE* 4.5 3.6 - - + -
501A PO4 4.8 1.4 + - - -
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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
----------------------------------------------------------
44A THR* 4.6 21.1 - - + +
49A LEU* 4.7 10.1 - - + -
58A LEU* 5.7 3.8 - - + -
66A ILE* 4.0 20.2 - - + -
73A GLY 3.2 11.0 + - - +
74A LYS* 3.6 7.9 - - - +
76A THR* 1.3 77.8 - - + +
78A ALA* 1.3 64.6 + - - +
80A HIS* 3.0 10.4 + - - +
81A ALA* 2.9 22.0 + - + +
225A LEU* 5.2 3.6 - - + -
227A VAL* 5.2 8.5 - - + -
262A PHE* 3.8 31.9 - - + -
264A ILE* 5.4 0.4 - - + -
270A ILE* 4.1 11.0 - - + -
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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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66A ILE* 4.4 4.0 - - + +
74A LYS 3.1 8.9 + - - +
75A THR 3.0 7.7 + - - +
77A VAL* 1.3 79.9 - - - +
79A LEU* 1.3 61.2 + - + +
81A ALA* 3.2 15.6 - - - +
82A VAL* 3.3 14.3 + - - +
94A PHE* 6.3 1.3 - - + -
144A VAL* 4.3 8.1 - - + +
192A ILE* 3.6 41.0 - - + +
194A ILE* 4.3 14.6 - - + -
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Residues in contact with LEU 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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75A THR* 2.7 32.2 + - - +
76A THR* 3.5 4.5 - - - +
78A ALA* 1.3 71.2 - - + +
80A HIS* 1.3 59.5 + - - +
81A ALA 2.9 1.6 - - - -
82A VAL* 2.6 34.1 + - + +
83A ALA 3.0 9.4 + - - -
94A PHE* 4.2 27.6 - - + -
101A LEU* 4.6 16.6 - - + -
102A ASP 5.4 0.2 - - - +
105A TYR* 4.1 28.0 - - + -
106A ALA* 4.3 17.5 - - + -
109A LEU* 4.5 9.0 - - + -
111A VAL* 4.0 17.5 - - + +
116A LEU* 6.0 3.6 - - + -
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Residues in contact with HIS 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A THR 3.3 20.6 - - - +
45A GLY* 5.2 6.1 - - - -
76A THR* 2.9 22.2 + - + +
77A VAL* 3.4 7.4 - - - +
79A LEU* 1.3 74.8 - - - +
81A ALA* 1.3 61.9 + - - +
83A ALA* 3.3 8.5 + - - +
84A ASN* 3.2 30.5 + - - +
109A LEU* 3.5 40.4 + - + +
268A GLN 5.4 0.2 - - - -
270A ILE* 2.9 62.6 + - + +
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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
----------------------------------------------------------
42A ILE* 3.5 16.2 - - + +
43A PRO 4.6 4.9 - - - +
44A THR* 4.7 4.9 + - - +
58A LEU* 4.3 15.0 - - + -
77A VAL* 2.9 11.5 + - + +
78A ALA* 3.2 16.2 - - - +
79A LEU 2.9 0.6 - - - -
80A HIS* 1.3 78.4 - - - +
82A VAL* 1.3 56.2 - - - +
84A ASN 3.5 0.7 + - - -
85A ALA* 3.0 28.9 + - - +
142A ILE* 3.8 16.1 - - + +
192A ILE* 4.2 7.2 - - + -
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Residues in contact with VAL 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 3.4 15.5 - - - +
79A LEU* 2.6 21.3 + - + +
81A ALA* 1.3 70.2 - - - +
83A ALA* 1.3 67.3 + - - +
85A ALA* 3.3 3.0 + - - +
86A GLN* 2.8 42.6 + - - +
92A ALA* 3.5 29.2 - - + -
94A PHE* 5.6 1.8 - - + -
111A VAL* 3.9 15.9 - - + -
116A LEU* 4.9 6.3 - - + -
142A ILE* 4.0 17.9 - - + +
144A VAL* 4.5 16.8 - - + -
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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
----------------------------------------------------------
79A LEU 3.0 10.0 + - - +
80A HIS* 3.4 13.0 - - - +
82A VAL* 1.3 77.7 - - - +
84A ASN* 1.3 55.7 + - - +
86A GLN* 3.4 2.3 - - - +
87A ALA* 2.7 39.0 + - - +
109A LEU 3.7 15.9 - - - +
110A GLY* 3.6 34.2 - - - +
111A VAL* 3.8 8.2 - - + +
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Residues in contact with ASN 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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42A ILE* 3.9 5.8 - - + -
43A PRO* 2.5 47.0 + - + +
44A THR 3.8 1.4 - - - -
45A GLY* 3.7 15.8 - - - +
80A HIS* 3.2 18.2 + - - +
81A ALA 3.9 2.9 - - - +
83A ALA* 1.3 81.2 - - - +
85A ALA* 1.3 67.8 + - - +
86A GLN 3.1 1.0 + - - -
87A ALA* 3.1 17.3 + - - +
88A ALA* 3.2 14.7 + - - +
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Residues in contact with ALA 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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42A ILE* 3.9 20.5 - - + +
81A ALA 3.0 15.3 + - - +
82A VAL 3.8 1.3 - - - +
84A ASN* 1.3 75.8 - - - +
86A GLN* 1.3 59.3 + - + +
88A ALA* 3.5 9.5 + - - +
90A GLY* 3.0 25.6 + - - -
141A ASP* 4.7 9.2 - - + +
142A ILE* 3.4 33.7 - - + -
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Residues in contact with GLN 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 VAL* 2.8 30.9 + - + +
83A ALA 3.4 2.2 - - - +
85A ALA* 1.3 74.3 - - - +
87A ALA* 1.3 54.8 + - - +
88A ALA 2.6 17.4 + - - -
89A GLY* 2.7 15.9 + - - -
90A GLY 3.4 20.6 + - - +
92A ALA* 4.2 11.2 - - + +
110A GLY 5.3 1.6 - - - +
111A VAL* 3.1 16.9 - - - +
112A ASP* 2.6 58.2 + - + +
115A SER* 3.4 17.6 + - - -
116A LEU* 4.4 4.6 - - - +
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Residues in contact with ALA 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 ALA 2.7 22.1 + - - +
84A ASN* 3.1 11.6 + - - +
86A GLN* 1.3 70.1 - - - +
88A ALA* 1.3 57.4 + - - +
89A GLY 3.5 0.4 - - - -
110A GLY 5.5 4.2 + - - +
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Residues in contact with ALA 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 ASN 3.2 12.0 + - - +
85A ALA* 3.9 5.5 - - - +
86A GLN 2.6 6.7 + - - -
87A ALA* 1.3 75.4 - - - +
89A GLY* 1.3 63.4 + - - +
90A GLY 3.6 0.9 - - - -
141A ASP* 5.4 0.7 - - - +
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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