Contacts of the strand formed by residues 95 - 101 (chain A) in PDB entry 3BZH
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 95 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A THR* 3.7 25.4 - - + -
83A ILE 3.8 2.7 - - - -
84A LEU* 3.8 15.3 - - + -
93A GLY 4.4 6.3 - - - +
94A GLY* 1.3 78.1 - - - +
96A PHE* 1.3 60.0 + - - +
97A PHE* 4.0 23.9 - - + -
117A THR* 4.1 5.0 + - - +
192A ALA* 2.9 27.1 + - - +
193A THR* 6.2 0.2 - - - -
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Residues in contact with PHE 96 (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 SER 3.8 0.2 - - - +
82A THR* 3.3 5.4 - - - +
83A ILE* 2.8 46.4 + - + +
85A GLY* 4.0 8.7 - - - -
91A TYR* 3.9 34.5 - + + -
94A GLY* 3.8 21.3 - - - -
95A VAL* 1.3 74.6 - - - +
97A PHE* 1.3 63.0 + - - +
98A LEU* 3.8 4.0 - - + +
115A PHE* 3.8 26.5 - + + -
117A THR* 3.7 18.6 - - + -
118A ARG 4.1 4.5 - - - -
119A ILE* 3.7 33.9 - - + -
156A LEU* 5.0 5.4 - - + -
188A THR* 4.2 7.2 - - - -
192A ALA* 3.5 21.8 - - + -
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Residues in contact with PHE 97 (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 ARG* 3.2 42.8 - - - +
81A SER 3.4 3.6 - - - +
82A THR* 3.8 24.9 - - + -
95A VAL* 4.0 29.6 - - + -
96A PHE* 1.3 72.5 - - - +
98A LEU* 1.3 61.6 + - - +
115A PHE* 3.7 1.0 - - - +
116A ARG* 2.7 33.8 + - + -
117A THR* 2.9 28.4 + - - +
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Residues in contact with LEU 98 (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 ARG* 3.5 7.6 - - - -
81A SER* 2.8 41.8 + - - +
83A ILE* 3.7 36.8 - - + -
96A PHE 3.8 12.6 - - - +
97A PHE* 1.3 82.1 - - - +
99A ASP* 1.3 67.7 + - - +
100A ILE* 5.0 0.4 - - + -
113A VAL* 3.8 24.7 - - + -
114A THR 3.2 11.2 - - - +
115A PHE* 3.9 37.7 - - + -
116A ARG* 4.0 1.1 - - - +
149A LEU* 4.5 6.5 - - + -
152A ILE* 4.1 6.7 - - + -
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Residues in contact with ASP 99 (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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72A LYS* 3.0 35.9 + - - +
79A TRP 3.7 2.5 - - - -
80A ARG* 4.1 5.7 + - - -
98A LEU* 1.3 76.3 - - - +
100A ILE* 1.3 62.1 + - - +
101A THR* 4.2 8.5 - - - +
112A LYS 3.5 1.3 - - - +
113A VAL* 3.3 4.5 - - - +
114A THR* 2.9 38.2 + - - +
116A ARG* 3.2 41.3 + - - +
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Residues in contact with ILE 100 (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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69A ALA* 4.3 11.2 - - + -
77A TYR 3.8 0.9 - - - +
78A GLU* 3.7 1.4 - - - +
79A TRP* 2.8 49.8 + - + +
80A ARG 4.6 0.2 - - - +
81A SER* 3.8 28.5 - - - -
98A LEU* 4.9 0.4 - - + +
99A ASP* 1.3 77.0 - - - +
101A THR* 1.3 65.8 + - - +
102A PHE* 3.8 23.3 - - + -
111A PRO* 4.3 9.4 - - + -
112A LYS 3.4 3.6 - - - -
113A VAL* 4.2 17.0 - - + -
145A ILE* 3.6 39.5 - - + -
149A LEU* 4.4 8.1 - - + -
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Residues in contact with THR 101 (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 TYR* 3.4 2.0 - - + -
78A GLU* 2.7 38.1 + - - +
99A ASP* 5.0 5.9 - - - +
100A ILE* 1.3 76.0 + - - +
102A PHE* 1.3 75.5 + - - +
103A THR* 4.1 6.5 + - + +
111A PRO* 3.5 3.0 - - - +
112A LYS* 2.8 57.5 + - + +
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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