Contacts of the strand formed by residues 89 - 94 (chain A) in PDB entry 2ZA5
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 VAL 89 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A LEU* 3.5 33.2 + - + +
71A LEU* 4.2 24.9 + - + +
72A ARG* 4.8 0.7 - - - -
73A VAL* 3.7 30.3 - - + +
87A LEU 4.1 3.1 - - - +
88A PRO* 1.3 78.9 - - + +
90A SER* 1.3 60.9 + - - +
91A ARG 3.5 19.7 - - - +
92A ILE* 4.4 4.9 - - + -
110A LEU* 4.0 14.4 - - + -
111A GLU 3.2 16.4 - - - +
112A LEU* 4.2 6.1 - - + +
113A GLU* 4.1 6.6 - - - +
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Residues in contact with SER 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A LEU* 3.2 15.2 - - - +
89A VAL* 1.3 73.7 - - - +
91A ARG* 1.3 60.2 + - - +
111A GLU* 2.7 43.5 + - - +
112A LEU 3.2 10.9 + - - -
113A GLU* 3.8 24.5 + - - +
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Residues in contact with ARG 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A TRP* 3.9 13.7 - - - -
68A LEU* 4.0 8.3 - - + -
89A VAL* 3.5 5.4 - - - +
90A SER* 1.3 82.2 + - - +
92A ILE* 1.3 64.4 + - - +
93A ILE* 4.1 29.3 - - + +
109A LEU 4.0 0.5 - - - +
110A LEU* 3.7 1.0 - - - -
111A GLU* 3.0 65.4 + - + +
255A TYR* 4.6 13.9 + - - +
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Residues in contact with ILE 92 (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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61A VAL* 3.9 28.3 - - + +
66A LYS* 4.7 10.5 - - + +
67A ASP 5.4 1.1 - - - +
68A LEU* 3.6 34.6 - - + +
71A LEU* 3.9 19.5 - - + -
89A VAL* 4.4 0.9 - - + -
91A ARG* 1.3 75.5 - - - +
93A ILE* 1.3 66.2 + - - +
94A VAL* 4.0 7.0 - - + -
109A LEU 3.7 2.9 - - - -
110A LEU* 3.9 24.0 - - + -
182C TYR* 3.6 36.4 - - - +
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Residues in contact with ILE 93 (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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53A TRP* 3.7 29.8 - - + -
91A ARG* 4.1 22.7 - - + +
92A ILE* 1.3 76.1 - - - +
94A VAL* 1.3 63.5 + - - +
108A ALA* 3.2 2.7 - - - -
109A LEU* 2.7 45.4 + - + +
251A TRP* 3.4 27.1 - - + -
255A TYR* 3.4 48.7 - - + +
182C TYR* 5.6 0.2 - - - -
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Residues in contact with VAL 94 (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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58A ALA* 3.5 27.6 - - + +
61A VAL* 3.8 24.5 - - + +
62A GLY* 5.3 0.7 - - - -
92A ILE* 4.0 2.8 + - + -
93A ILE* 1.3 77.6 - - - +
95A HIS* 1.3 76.1 + - - +
96A PRO* 3.2 8.0 - - - +
98A PHE* 4.1 10.8 - - + +
108A ALA* 4.1 4.0 - - + -
251A TRP* 3.8 3.2 - - - -
182C TYR* 3.4 61.0 - - + +
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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