Contacts of the strand formed by residues 90 - 94 (chain A) in PDB entry 5BZR
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 90 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83A TYR* 3.8 26.9 - - + -
84A GLY 3.4 9.0 - - - +
85A PHE* 3.8 26.7 - - + -
89A ASN* 1.3 75.7 - - - +
91A VAL* 1.3 66.4 + - - +
110A ILE* 3.8 2.1 - - - +
111A LEU* 2.9 51.0 + - + +
119A TYR* 3.8 26.7 - - + -
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Residues in contact with VAL 91 (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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67A MET* 4.3 0.4 - - + -
70A MET* 4.1 7.6 - - + -
82A ARG 3.5 0.2 - - - +
83A TYR* 3.5 2.2 - - - -
84A GLY 2.9 32.3 + - - +
86A ILE* 3.8 45.3 - - + -
89A ASN* 4.0 10.5 - - + -
90A VAL* 1.3 81.0 - - - +
92A ILE* 1.3 69.7 + - - +
93A PRO* 4.7 0.9 - - + -
108A VAL* 3.8 24.0 - - + -
109A TYR 3.1 13.0 - - - +
110A ILE* 4.2 9.2 - - + -
111A LEU 4.6 0.4 - - - +
122A TYR* 3.4 12.5 - - + -
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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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80A THR* 3.2 36.1 - - - +
81A CYS* 4.2 1.3 - - - -
82A ARG 3.5 11.9 - - - +
83A TYR* 3.6 37.5 - - + +
91A VAL* 1.3 81.2 - - - +
93A PRO* 1.3 66.2 - - - +
94A ARG* 3.5 14.4 + - - +
102A ALA* 4.1 16.4 - - + +
107A GLY 3.5 0.7 - - - +
108A VAL* 4.6 0.2 - - - -
109A TYR* 2.9 36.7 + - + +
122A TYR* 4.0 0.4 - - - -
203A GOL 3.6 30.1 - - - +
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Residues in contact with PRO 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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70A MET* 4.0 21.3 - - + -
74A LEU* 4.0 10.1 - - + -
78A PHE* 3.7 40.8 - - + +
79A GLU* 3.2 3.4 - - - +
80A THR* 3.0 42.0 + - - +
91A VAL* 4.5 0.9 - - + -
92A ILE* 1.3 83.1 - - - +
94A ARG* 1.3 60.4 + - - +
107A GLY 3.7 4.9 - - - +
108A VAL* 4.3 5.2 - - + -
122A TYR* 3.2 24.2 - - + +
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Residues in contact with ARG 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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74A LEU* 3.4 11.6 - - - +
79A GLU* 3.5 27.2 + - - +
80A THR 2.8 42.6 + - - +
81A CYS* 4.1 0.8 - - - +
92A ILE* 3.7 11.7 - - - +
93A PRO* 1.3 74.8 - - - +
95A ILE* 1.3 60.8 + - - +
96A HIS* 2.8 27.8 + - - +
98A ASN* 3.4 21.6 - - - +
101A CYS* 3.6 29.8 + - - +
102A ALA* 3.8 18.6 - - + -
105A HIS 3.2 25.3 + - - +
106A THR* 3.6 1.9 - - - -
107A GLY* 2.8 40.3 + - - +
109A TYR* 5.0 0.7 - - + -
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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