Contacts of the strand formed by residues 85 - 90 (chain Y) 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 THR 85 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44X ASN* 3.9 17.8 + - - +
37Y GLN* 3.7 1.6 - - - -
38Y GLN* 2.8 56.2 + - - +
84Y ALA* 1.3 74.5 - - - +
86Y TYR* 1.3 64.1 + - - +
87Y PHE* 3.7 25.1 - - + -
101Y GLY* 4.5 2.0 - - - -
102Y THR 3.5 25.4 - - - +
103Y LYS* 4.0 21.9 + - + +
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Residues in contact with TYR 86 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6Y GLN* 2.8 22.7 + - - +
21Y ILE* 4.1 21.8 - - + -
35Y TRP* 4.8 9.0 - + + -
36Y TYR 3.4 6.1 - - - +
37Y GLN* 3.9 17.1 + - + -
47Y LEU* 3.6 33.2 - - + -
62Y PHE* 3.9 17.3 - + - -
73Y LEU* 4.6 14.8 - - + -
75Y ILE* 4.3 7.6 - - + +
82Y ASP* 2.7 39.5 + - - +
84Y ALA* 3.4 25.4 - - + -
85Y THR* 1.3 73.0 - - - +
87Y PHE* 1.3 61.6 + - - +
101Y GLY* 3.8 0.7 - - - -
102Y THR 3.1 22.4 + - - +
104Y LEU* 4.3 11.4 - - + -
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Residues in contact with PHE 87 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40X LEU* 4.2 15.0 - - + -
44X ASN* 4.0 26.0 - - - -
46X LEU* 3.5 45.5 - - + -
6Y GLN* 3.2 7.9 - - - -
35Y TRP* 3.2 20.0 - - - -
36Y TYR* 3.0 35.5 + - + -
38Y GLN* 4.0 18.8 - - + -
44Y ILE* 5.5 0.9 - - + -
85Y THR* 3.7 37.7 - - + -
86Y TYR* 1.3 76.8 - - - +
88Y CYS* 1.3 62.3 + - - +
98Y PHE* 4.3 8.5 - - + -
99Y GLY 4.1 15.3 - - - -
101Y GLY* 4.0 10.1 - - - -
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Residues in contact with CYS 88 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4Y LEU* 3.1 19.1 - - + +
6Y GLN* 3.6 9.6 + - - -
23Y CYS* 2.0 51.8 - - + -
33Y LEU* 4.5 3.8 - - + -
34Y ASN 3.1 13.2 - - - +
35Y TRP* 4.1 10.3 - - + +
36Y TYR* 5.0 0.9 - - - +
87Y PHE* 1.3 78.9 - - - +
89Y GLN* 1.3 59.8 + - - +
97Y THR 3.8 0.3 - - - +
98Y PHE* 3.2 6.3 - - - -
99Y GLY 2.8 27.7 + - - +
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Residues in contact with GLN 89 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107X TYR* 5.8 1.0 - - - +
108X ALA* 5.3 1.0 - - - +
109X MET* 3.1 26.4 - - - +
4Y LEU* 4.7 1.3 - - - -
33Y LEU* 3.2 12.3 - - - +
34Y ASN* 3.0 46.5 + - + +
36Y TYR* 2.6 38.7 + - + -
88Y CYS* 1.3 73.7 - - - +
90Y HIS* 1.3 79.6 + - - +
91Y HIS* 3.9 5.1 + - - +
96Y TRP* 3.5 22.1 - - - +
97Y THR 3.2 13.0 - - - +
98Y PHE* 3.9 18.6 - - + -
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Residues in contact with HIS 90 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2Y ILE* 3.6 28.6 - - + +
4Y LEU* 3.9 12.3 - - + +
29Y ILE* 3.7 29.4 - - + -
32Y PHE 3.2 9.2 - - - +
33Y LEU* 4.7 0.2 - - - +
89Y GLN* 1.3 88.3 - - - +
91Y HIS* 1.3 64.6 + - - +
92Y ILE* 3.4 29.2 - - + -
93Y LYS 3.4 18.2 + - - -
95Y PRO 3.4 9.7 + - - -
96Y TRP* 3.6 10.9 - - - +
97Y THR* 3.3 45.2 + - - -
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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