Contacts of the helix formed by residues 72 - 87 (chain A) in PDB entry 1EZW
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 HIS 72 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A ARG* 1.3 72.5 - - - +
73A PRO* 1.3 82.5 - - + +
74A LEU* 3.0 52.6 + - + +
75A ILE* 2.9 29.9 + - + +
76A THR* 3.1 9.7 + - - -
117A TRP* 3.3 54.3 + + + +
154A VAL* 4.1 10.9 - - + +
155A LYS 5.4 2.6 + - - -
156A THR* 4.8 4.1 - - + +
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Residues in contact with PRO 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A PRO* 6.2 0.4 - - + -
71A ARG 3.9 0.9 - - - +
72A HIS* 1.3 92.2 - - + +
74A LEU* 1.3 57.4 + - - +
76A THR* 3.3 10.6 + - - +
77A ALA* 2.9 27.9 + - - +
117A TRP* 3.3 14.1 - - + +
134A VAL* 3.8 26.2 - - + -
137A VAL* 4.0 20.2 - - + +
138A ILE* 4.2 3.5 - - - +
153A TYR* 3.3 24.9 - - + +
154A VAL* 3.8 24.0 - - + -
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Residues in contact with LEU 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A HIS* 3.0 30.7 + - + +
73A PRO* 1.3 75.2 - - - +
75A ILE* 1.3 62.6 + - + +
77A ALA* 3.5 4.0 + - - +
78A SER* 3.0 26.7 + - - -
137A VAL* 3.6 21.8 - - + -
141A TYR* 4.1 20.1 - - + -
147A VAL* 3.9 26.7 - - + -
156A THR* 4.3 11.0 - - + -
159A ALA* 4.0 22.7 - - + -
161A VAL* 5.8 0.4 - - + -
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Residues in contact with ILE 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ARG* 4.3 22.0 - - + -
72A HIS* 2.9 27.2 + - + +
74A LEU* 1.3 79.7 - - + +
76A THR* 1.3 66.3 + - - +
78A SER* 3.3 9.4 + - - -
79A ASN* 2.9 31.6 + - - +
362A CL 4.6 6.3 - - + -
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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
----------------------------------------------------------
45A TYR* 4.4 10.9 + - - +
66A THR* 4.4 9.2 + - + -
67A ASN 4.5 9.0 + - - -
71A ARG* 4.0 20.4 + - - +
72A HIS 3.1 11.2 + - - -
73A PRO* 3.6 11.0 - - - +
75A ILE* 1.3 77.8 - - - +
77A ALA* 1.4 63.6 + - - +
79A ASN* 3.1 11.5 + - - +
80A ILE* 2.9 29.7 + - + +
93A ILE* 5.8 0.4 - - + -
95A MET* 4.2 15.9 - - + -
134A VAL* 5.3 1.1 - - - +
138A ILE* 4.0 21.8 - - + -
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Residues in contact with ALA 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A PRO 2.9 17.9 + - - +
74A LEU* 3.6 7.0 - - - +
75A ILE 3.2 0.2 - - - -
76A THR* 1.4 75.9 - - - +
78A SER* 1.3 57.9 + - - +
80A ILE* 3.2 4.3 + - - +
81A ALA* 2.9 29.6 + - - +
137A VAL 4.7 1.1 - - - +
138A ILE* 4.0 26.7 - - - +
141A TYR* 3.4 37.1 - - + -
142A LEU* 4.8 2.0 - - + +
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Residues in contact with SER 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A LEU 3.0 14.4 + - - -
75A ILE* 3.3 15.9 + - - -
77A ALA* 1.3 76.7 - - - +
79A ASN* 1.3 57.1 + - - +
81A ALA* 3.3 1.7 + - - +
82A THR* 2.7 42.9 + - - -
141A TYR* 3.4 27.0 + - - -
163A ALA* 5.3 2.3 - - - +
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Residues in contact with ASN 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A TYR* 3.0 27.9 + - + +
46A MET* 3.4 35.2 - - - +
71A ARG* 3.9 9.3 - - - +
75A ILE* 2.9 23.6 + - - +
76A THR* 3.4 7.5 - - - +
78A SER* 1.3 75.0 + - - +
80A ILE* 1.3 59.3 + - - +
82A THR* 3.2 3.5 + - - -
83A LEU* 2.9 30.7 + - - +
362A CL 3.4 27.5 - - - +
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Residues in contact with ILE 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A TYR* 4.8 7.4 - - + +
63A PRO* 3.8 35.4 - - + -
76A THR* 2.9 27.7 + - + +
77A ALA* 3.7 6.1 - - - +
79A ASN* 1.3 77.3 - - + +
81A ALA* 1.3 57.6 + - - +
83A LEU* 3.8 8.3 - - + +
84A ASP* 2.9 28.9 + - - +
91A ALA* 4.0 5.2 - - + +
92A ILE 4.1 2.9 - - - +
93A ILE* 3.8 37.5 - - + -
138A ILE* 5.2 2.9 - - + -
142A LEU* 4.8 4.5 - - + -
171A ILE* 3.7 25.8 - - + -
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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
----------------------------------------------------------
77A ALA 2.9 21.1 + - - +
78A SER* 3.8 3.8 - - - +
80A ILE* 1.3 73.1 - - - +
82A THR* 1.3 57.6 + - - +
84A ASP* 3.4 1.7 + - - +
85A TRP* 3.0 29.6 + - - +
141A TYR* 3.8 19.5 - - + -
142A LEU* 4.0 13.7 - - + +
163A ALA* 4.8 8.3 - - + +
164A ARG 4.2 3.3 - - - +
165A SER* 3.8 26.0 - - - +
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Residues in contact with THR 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A MET* 4.1 14.6 - - + -
78A SER* 2.7 29.4 + - - -
79A ASN* 3.5 4.5 - - - -
81A ALA* 1.3 74.4 - - - +
83A LEU* 1.3 66.0 + - - +
85A TRP* 3.2 5.4 + - - +
86A ILE* 2.9 49.6 + - + +
163A ALA* 5.3 6.5 - - - +
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Residues in contact with LEU 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A TYR* 5.7 0.4 - - + -
46A MET* 4.2 14.5 - - - +
49A LEU* 3.6 55.9 - - + +
50A THR* 4.2 7.6 - - - +
53A ALA* 4.2 11.9 - - + -
61A LEU* 3.6 29.8 - - + +
62A GLY* 4.1 3.8 - - - -
63A PRO* 4.7 5.2 - - + -
79A ASN 2.9 16.5 + - - +
80A ILE* 3.8 8.1 - - + +
82A THR* 1.3 75.9 - - - +
84A ASP* 1.3 62.9 + - - +
86A ILE* 3.5 4.4 + - + -
87A SER* 2.9 30.8 + - - +
91A ALA* 4.3 9.6 - - + -
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Residues in contact with ASP 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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80A ILE 2.9 18.9 + - - +
81A ALA 3.6 4.5 - - - +
83A LEU* 1.3 77.5 - - - +
85A TRP* 1.3 61.0 + - - +
87A SER* 3.2 2.7 + - - -
88A GLY 3.2 3.5 + - - -
89A GLY* 2.8 35.4 + - - -
91A ALA* 3.0 18.4 + - + +
165A SER* 3.4 5.8 - - - -
166A ILE* 2.7 27.7 + - - +
167A GLN* 2.8 39.6 + - - +
171A ILE* 3.8 15.3 - - + -
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Residues in contact with TRP 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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81A ALA 3.0 17.4 + - - +
82A THR* 3.2 5.8 + - - +
84A ASP* 1.3 77.4 - - - +
86A ILE* 1.3 82.9 + - + +
88A GLY* 3.1 10.2 + - - -
164A ARG* 3.3 24.9 - - + +
165A SER* 4.6 1.3 - - - +
166A ILE* 3.6 30.2 - - + +
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Residues in contact with ILE 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A THR* 4.1 33.0 - - + +
53A ALA* 4.4 15.3 - - + +
54A VAL* 4.7 12.6 - - + -
82A THR* 2.9 40.1 + - + +
83A LEU* 4.1 4.3 - - + +
85A TRP* 1.3 95.8 - - + +
87A SER* 1.3 60.8 + - - +
88A GLY 3.4 0.9 + - - -
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Residues in contact with SER 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ALA* 3.9 14.4 - - - -
61A LEU* 4.2 6.3 - - - -
83A LEU* 2.9 22.8 + - - -
84A ASP* 3.2 4.9 + - - -
86A ILE* 1.3 76.0 - - - +
88A GLY* 1.3 59.4 + - - +
90A ARG* 2.8 75.4 + - - +
91A ALA* 3.7 2.3 + - - -
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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
------------------------------------------------------------
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