Contacts of the strand formed by residues 78 - 83 (chain X) 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 GLN 78 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21X THR* 3.9 8.6 + - - +
22X CYS 3.1 20.0 - - - +
23X SER* 2.7 31.7 + - - -
29X ILE* 4.3 4.8 - - - +
72X ARG* 3.4 2.6 - - - +
73X ASP* 2.9 31.4 + - + +
76X LYS* 3.7 39.8 + - + +
77X ASN* 1.3 75.3 - - - +
79X PHE* 1.3 61.4 + - - +
80X PHE* 3.8 26.7 - - + -
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Residues in contact with PHE 79 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4X LEU* 4.5 3.6 - - + -
22X CYS* 2.8 64.5 + - + +
24X VAL* 3.8 10.5 - - + -
29X ILE* 4.3 9.4 - - + -
35X TRP* 3.7 51.8 - + + -
36X ASN 3.6 21.5 - - - -
37X TRP* 3.6 25.6 - + - -
52X ILE* 4.1 16.2 - - + -
70X ILE* 4.6 1.6 - - + -
71X THR 3.3 13.2 - - - +
72X ARG* 4.0 5.2 - - + +
78X GLN* 1.3 74.4 - - - +
80X PHE* 1.3 63.4 + - - +
96X CYS* 3.7 8.5 - - + -
97X ALA 4.6 0.7 - - - -
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Residues in contact with PHE 80 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20X LEU 3.2 7.9 - - - +
21X THR* 3.5 31.9 - - + -
37X TRP* 3.4 6.5 - - - +
69X SER 3.8 0.6 - - - +
70X ILE* 3.2 29.8 - - - +
71X THR* 2.8 39.0 + - - +
72X ARG 3.9 21.5 - - - -
73X ASP* 4.0 9.6 - - + -
78X GLN* 3.8 37.0 - - + -
79X PHE* 1.3 76.4 - - - +
81X LEU* 1.3 63.5 + - - +
82X LYS* 6.1 1.1 - - + -
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Residues in contact with LEU 81 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18X LEU* 4.1 3.4 - - + +
19X SER* 3.4 5.7 - - - -
20X LEU* 2.9 42.8 + - + +
37X TRP* 3.3 35.4 - - + +
49X VAL* 4.1 10.3 - - + -
68X LEU* 3.9 34.1 - - + -
69X SER 4.3 0.4 - - - -
70X ILE* 4.2 10.1 - - + -
80X PHE* 1.3 76.2 - - - +
82X LYS* 1.3 69.0 + - - +
83X LEU* 4.4 11.0 - - + +
94X TYR* 3.5 37.9 - - + -
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Residues in contact with LYS 82 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17X SER* 4.2 15.9 - - - -
18X LEU 3.2 5.8 - - - +
19X SER* 3.9 17.3 - - - +
67X ARG 3.7 2.4 - - - +
68X LEU* 3.0 25.9 - - - -
69X SER* 3.2 26.9 + - - +
71X THR* 5.8 1.6 - - - +
80X PHE* 6.1 1.1 - - + -
81X LEU* 1.3 75.8 - - - +
83X LEU* 1.3 58.8 + - - +
84X ASN* 3.6 23.0 + - - +
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Residues in contact with LEU 83 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17X SER* 3.5 0.2 - - - -
18X LEU* 2.9 49.0 + - + -
39X ARG* 3.4 31.4 - - - +
49X VAL* 5.8 1.8 - - + -
64X LEU* 4.7 11.0 - - + -
67X ARG* 3.8 33.0 - - + +
68X LEU* 4.1 21.1 - - + +
81X LEU* 4.1 9.7 - - + +
82X LYS* 1.3 70.4 - - - +
84X ASN* 1.3 64.4 + - - +
86X VAL* 3.4 6.5 - - + +
90X ASP* 3.8 14.8 - - + +
94X TYR* 3.5 19.1 - - + +
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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