Contacts of the helix formed by residues 78 - 88 (chain A) in PDB entry 1EZV
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 78 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A ASN 3.3 6.9 + - - -
75A ILE* 2.8 27.1 + - - -
76A PHE 3.5 0.4 - - - -
77A LEU* 1.3 78.7 - - - +
79A LYS* 1.3 59.0 + - - +
80A GLU* 3.0 6.1 + - - -
81A ASN 3.1 4.5 + - - -
82A SER* 2.8 33.7 + - - -
135A ASN* 2.9 31.2 + - - -
139A THR* 4.1 8.9 + - - -
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Residues in contact with LYS 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 LEU 3.8 0.8 + - - -
78A SER* 1.3 75.8 + - - +
80A GLU* 1.3 62.1 + - + +
82A SER* 4.3 0.7 - - - -
83A ALA* 3.1 25.3 + - + +
263B ALA* 3.5 26.8 - - + +
265B SER 4.5 4.5 - - - +
266B GLU* 3.3 27.8 + - - +
268B SER* 3.9 19.8 + - - -
269B GLY* 4.3 9.8 - - - +
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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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78A SER* 3.0 2.3 + - - +
79A LYS* 1.3 81.2 - - + +
81A ASN* 1.3 61.9 + - - +
82A SER 3.4 0.2 + - - -
83A ALA* 3.6 3.1 + - - +
84A VAL* 3.3 25.1 + - - +
126A GLN* 5.4 3.8 - - - +
129A ASN 4.9 4.7 - - - +
130A LEU* 5.7 3.4 - - + -
132A SER* 3.9 7.8 + - - -
135A ASN* 3.5 37.8 + - - +
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Residues in contact with ASN 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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75A ILE 4.0 3.6 - - - +
76A PHE* 2.9 38.6 + - - +
78A SER* 3.1 6.1 + - - +
80A GLU* 1.3 79.1 - - - +
82A SER* 1.3 61.8 + - - +
84A VAL* 3.6 4.6 + - - +
85A ALA* 3.4 5.7 + - - +
92A LEU* 4.1 1.2 - - - +
118A PHE* 3.1 49.8 - - - -
122A SER* 3.4 14.1 + - - -
126A GLN* 3.4 28.2 + - - +
130A LEU* 3.6 23.3 - - + +
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Residues in contact with SER 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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77A LEU* 3.8 14.3 + - - +
78A SER 2.8 17.9 + - - -
79A LYS* 4.3 0.4 - - - -
81A ASN* 1.3 77.9 - - - +
83A ALA* 1.3 58.8 + - - +
84A VAL 3.4 0.2 - - - -
85A ALA* 3.6 2.8 + - - +
86A ALA* 3.2 26.2 + - - +
90A LEU 5.3 0.3 - - - +
92A LEU* 3.7 24.2 - - - +
263B ALA* 3.5 18.1 + - - +
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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 LYS* 3.1 19.0 + - + +
80A GLU* 4.0 4.0 - - - +
81A ASN 3.4 0.2 - - - -
82A SER* 1.3 75.7 - - - +
84A VAL* 1.3 59.1 + - + +
85A ALA 3.1 1.3 - - - -
86A ALA* 4.3 0.2 - - - -
87A LYS* 3.1 38.5 + - + +
263B ALA* 3.3 26.2 - - - +
264B LEU* 3.6 10.8 - - + +
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Residues in contact with VAL 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 GLU 3.3 17.0 + - - +
81A ASN* 3.8 10.5 - - - +
82A SER 3.4 0.4 - - - -
83A ALA* 1.3 76.6 - - + +
85A ALA* 1.3 59.9 + - - +
87A LYS* 4.0 7.8 - - - +
88A GLU* 3.9 16.3 + - - +
118A PHE* 3.6 18.2 - - + -
121A GLN* 4.0 17.7 - - - +
126A GLN* 5.0 9.0 - - - +
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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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81A ASN 3.4 6.4 + - - +
82A SER 3.6 5.6 + - - +
83A ALA 3.1 0.4 - - - -
84A VAL* 1.3 79.0 - - - +
86A ALA* 1.3 54.2 + - - +
87A LYS 3.3 0.7 - - - -
88A GLU* 3.3 3.2 + - - +
89A GLY 3.2 7.1 + - - -
90A LEU* 2.7 53.5 + - + +
92A LEU* 4.0 14.6 - - + -
118A PHE* 3.5 32.7 - - + -
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Residues in contact with ALA 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 SER 3.2 18.5 + - - +
83A ALA* 3.2 1.3 + - - -
85A ALA* 1.3 73.6 - - - +
87A LYS* 1.3 66.0 + - - +
89A GLY* 3.3 8.2 + - - +
90A LEU 3.8 8.7 + - - +
262B SER* 5.0 2.7 - - - -
263B ALA 5.1 1.1 - - - +
264B LEU* 3.6 36.6 - - + +
316B PRO 4.0 3.6 - - - +
320B TYR* 3.6 34.8 - - + +
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Residues in contact with LYS 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* 3.1 23.9 + - - +
84A VAL* 4.0 9.0 - - - +
86A ALA* 1.3 78.2 - - - +
88A GLU* 1.3 57.5 + - - +
89A GLY* 3.1 4.5 + - - -
264B LEU* 3.7 17.7 - - + +
316B PRO* 4.0 32.2 - - + +
319B ASN* 5.1 7.3 + - - +
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Residues in contact with GLU 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 VAL 3.9 9.4 + - - +
85A ALA* 3.3 11.5 + - - +
86A ALA 3.3 0.4 - - - -
87A LYS* 1.3 79.0 - - - +
89A GLY* 1.3 61.0 + - - +
90A LEU* 3.4 21.3 - - + +
111A SER* 5.5 2.6 + - - -
114A LYS* 4.1 38.8 + - + +
118A PHE* 6.0 1.6 - - + -
319B ASN* 4.9 6.1 + - - +
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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