Contacts of the strand formed by residues 88 - 96 (chain H) in PDB entry 3BXB
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 PHE 88 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67H LYS* 3.8 23.3 - - + -
68H THR* 3.7 18.8 - - - -
79H PHE* 5.1 3.4 - + + -
80H PHE* 3.4 62.1 - + + -
83H SER* 3.9 13.9 - - - +
84H PHE* 4.0 9.2 - + - -
87H GLY* 1.3 75.0 - - - +
89H THR* 1.3 67.8 + - - +
90H TRP* 4.5 7.9 - + - -
108H THR* 2.7 58.9 + - + +
117H TYR* 6.2 0.2 - + - -
178H TYR* 5.4 0.9 - + + -
179H ARG 3.1 22.0 - - - +
180H SER* 4.1 0.4 - - - -
181H LYS* 3.8 7.7 + - - +
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Residues in contact with THR 89 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E ASN* 4.2 25.8 + - + +
88H PHE* 1.3 81.5 - - - +
90H TRP* 1.3 65.1 + - - +
106H GLN* 3.3 16.4 - - - +
107H ASP* 3.4 26.7 - - + +
178H TYR* 3.5 2.1 - - - -
179H ARG* 2.9 53.3 + - - +
181H LYS* 4.0 10.0 - - + +
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Residues in contact with TRP 90 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61H SER* 3.8 24.7 - - - -
63H NRQ 3.1 44.6 + - - -
67H LYS* 4.2 17.7 - - + -
88H PHE* 4.5 6.5 - + - -
89H THR* 1.3 75.8 - - - +
91H GLU* 1.3 69.4 + - - +
92H ARG* 3.6 34.5 - - + -
104H ALA* 3.5 29.8 - - + -
105H THR* 3.6 0.9 - - - -
106H GLN* 2.9 64.1 + - + +
119H VAL* 4.5 2.2 - - + -
176H THR* 4.1 1.6 - - + -
177H THR 3.2 6.5 - - - +
178H TYR* 3.4 27.6 - + + -
179H ARG* 5.5 1.3 - - - +
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Residues in contact with GLU 91 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E ASN* 3.2 8.2 + - - +
21E ASN* 3.1 25.3 + - + +
123E GLY 4.4 2.4 - - - +
124E VAL* 3.9 20.3 - - + +
125E ASN* 3.1 25.9 + - + +
90H TRP* 1.3 76.1 - - - +
92H ARG* 1.3 61.7 + - - +
104H ALA 3.4 7.6 - - - +
105H THR* 4.1 9.2 - - + +
175H LYS 3.9 0.7 - - - +
176H THR* 3.3 2.3 - - - +
177H THR* 2.8 43.3 + - - +
179H ARG* 2.7 43.4 + - - +
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Residues in contact with ARG 92 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124E VAL* 3.9 7.5 - - - +
60H THR* 3.1 33.6 + - - -
61H SER* 4.7 1.6 + - - +
63H NRQ 2.6 31.2 + - - +
67H LYS* 4.9 0.2 - - - +
90H TRP* 3.6 33.1 - - + -
91H GLU* 1.3 76.9 - - - +
93H VAL* 1.3 66.6 - - - +
94H THR* 3.5 24.2 - - - +
102H LEU 4.6 0.7 - - - +
103H THR* 3.4 5.9 - - - -
104H ALA* 3.0 32.7 + - + +
145H GLU* 5.3 0.8 + - - -
174H LEU* 3.7 22.4 - - - +
175H LYS 3.1 9.6 - - - +
176H THR* 2.8 29.2 + - - +
178H TYR* 3.8 13.7 + - - -
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Residues in contact with VAL 93 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101E VAL* 4.3 22.4 - - + -
124E VAL* 3.8 21.3 - - + -
125E ASN* 4.6 6.3 - - + +
92H ARG* 1.3 75.2 - - - +
94H THR* 1.3 63.5 + - - +
95H THR* 4.0 13.7 + - - +
101H VAL* 3.8 26.7 - - + -
102H LEU 3.7 3.4 - - - -
103H THR* 4.0 5.8 - - + -
173H ASN 3.7 1.4 - - - +
174H LEU* 3.7 1.4 - - - -
175H LYS* 2.9 56.4 + - + +
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Residues in contact with THR 94 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60H THR* 4.8 4.7 + - - +
92H ARG* 3.5 23.6 - - - +
93H VAL* 1.3 72.5 - - - +
95H THR* 1.3 61.4 + - - +
96H TYR* 3.7 20.8 + - + +
101H VAL* 3.5 5.2 - - - +
102H LEU* 2.9 49.1 + - - +
172H CYS* 3.7 30.1 - - + -
173H ASN 3.4 6.3 - - - +
174H LEU* 3.8 9.3 - - + +
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Residues in contact with THR 95 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93H VAL* 4.0 15.3 + - - +
94H THR* 1.3 75.2 + - - +
96H TYR* 1.3 70.3 + - - +
97H GLU* 3.9 2.9 + - + +
99H GLY 6.0 0.2 - - - +
100H GLY 4.0 3.8 - - - +
101H VAL* 4.7 11.0 - - + +
172H CYS* 3.0 7.0 - - - -
173H ASN* 2.8 45.3 + - + +
175H LYS* 5.8 4.4 - - - -
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Residues in contact with TYR 96 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57H ILE* 3.4 34.4 + - + +
94H THR* 3.7 27.9 - - + +
95H THR* 1.3 83.4 - - - +
97H GLU* 1.3 66.1 + - - +
98H ASP* 3.2 9.6 + - - +
99H GLY* 3.3 10.7 + - - -
100H GLY* 2.9 28.6 + - - +
102H LEU* 4.8 3.6 - - + -
126H PHE* 3.7 31.6 - + + -
132H VAL* 4.8 2.5 - - + -
140H TRP* 3.4 32.6 - + - -
162H LEU* 4.5 5.2 - - + -
170H LEU* 3.9 28.5 - - + -
171H ILE 3.8 2.0 - - - -
172H CYS* 3.7 15.0 - - + -
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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