Contacts of the strand formed by residues 88 - 96 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67C LYS* 4.3 12.8 - - + -
68C THR* 3.7 23.1 - - - -
79C PHE* 4.8 3.1 - + + -
80C PHE* 3.8 46.9 - + + -
83C SER* 3.9 20.2 - - - +
84C PHE* 3.9 4.5 - + - -
87C GLY* 1.3 75.6 - - - +
89C THR* 1.3 76.8 + - - +
90C TRP* 4.3 17.0 - + + -
108C THR* 3.0 56.9 + - + +
117C TYR* 6.1 0.2 - + - -
179C ARG 3.3 16.4 - - - +
180C SER* 3.8 8.1 - - - -
181C LYS* 3.5 10.0 - - - +
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Residues in contact with THR 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ASN* 3.5 37.6 + - - +
88C PHE* 1.3 91.0 - - - +
90C TRP* 1.3 66.9 + - - +
106C GLN* 3.3 14.6 - - - +
107C ASP* 3.5 21.3 - - + +
178C TYR* 3.8 2.1 - - - +
179C ARG* 2.8 43.6 + - - +
181C LYS* 3.8 9.9 - - + -
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Residues in contact with TRP 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C SER* 3.6 33.0 - - - -
63C NRQ 3.2 35.0 + - - -
67C LYS* 4.5 10.3 - - + -
88C PHE* 4.3 15.3 - + - -
89C THR* 1.3 78.6 - - - +
91C GLU* 1.3 70.7 + - - +
92C ARG* 3.4 43.5 - - + -
104C ALA* 3.8 24.7 - - + -
105C THR* 3.5 1.9 - - - -
106C GLN* 2.9 66.4 + - + +
119C VAL* 4.4 2.2 - - + -
176C THR* 4.2 0.9 - - + -
177C THR 3.3 6.3 - - - +
178C TYR* 3.5 25.6 - + + -
179C ARG* 6.1 0.4 - - - -
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Residues in contact with GLU 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ASN* 3.2 24.2 - - - +
21A ASN* 3.5 4.2 + - - +
124A VAL* 3.9 19.1 - - + -
125A ASN* 3.1 26.2 + - - +
90C TRP* 1.3 75.2 - - - +
92C ARG* 1.3 60.9 + - - +
104C ALA 3.4 7.0 - - - +
105C THR* 4.3 7.6 - - + -
175C LYS 3.9 0.5 - - - +
176C THR* 3.1 5.5 - - - +
177C THR* 2.9 48.6 + - - +
179C ARG* 2.4 44.1 + - - +
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Residues in contact with ARG 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A VAL* 3.8 7.7 - - - +
60C THR* 2.9 34.4 + - - -
61C SER* 4.5 1.2 + - - +
63C NRQ 2.8 30.7 + - - +
67C LYS* 4.8 0.2 - - - +
90C TRP* 3.4 36.2 - - + -
91C GLU* 1.3 77.1 - - - +
93C VAL* 1.3 66.6 + - - +
94C THR* 3.7 21.5 - - - +
102C LEU 4.6 0.4 - - - +
103C THR* 3.2 6.8 - - - -
104C ALA* 2.9 34.4 + - + +
145C GLU* 5.2 0.4 + - - -
174C LEU* 4.1 19.6 - - - +
175C LYS 3.5 9.2 - - - +
176C THR* 2.9 22.0 + - - +
178C TYR* 3.3 23.8 + - - -
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Residues in contact with VAL 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A VAL* 4.0 28.7 - - + -
124A VAL* 3.8 20.4 - - + +
125A ASN* 4.8 6.5 - - + +
92C ARG* 1.3 74.6 - - - +
94C THR* 1.3 64.0 + - - +
95C THR* 4.1 12.3 + - - +
101C VAL* 3.7 25.8 - - + -
102C LEU 3.8 2.2 - - - -
103C THR* 4.2 3.1 - - + +
173C ASN 3.6 2.8 - - - +
174C LEU* 3.7 0.2 - - - -
175C LYS* 3.1 56.5 + - + +
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Residues in contact with THR 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C THR* 5.0 4.1 + - - +
92C ARG* 3.7 20.8 - - - +
93C VAL* 1.3 75.5 - - - +
95C THR* 1.3 62.8 + - - +
96C TYR* 3.7 29.1 + - + +
100C GLY 3.8 0.7 - - - +
101C VAL* 3.3 6.9 - - - +
102C LEU* 2.9 43.6 + - - +
172C CYS* 3.8 20.0 - - + -
173C ASN 3.2 10.3 - - - +
174C LEU* 3.8 10.8 - - + +
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Residues in contact with THR 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C VAL* 4.3 14.0 + - - +
94C THR* 1.3 74.9 + - - +
96C TYR* 1.3 70.0 + - - +
97C GLU* 4.9 2.3 - - - +
99C GLY 5.6 0.7 - - - +
100C GLY 3.7 2.0 - - - +
101C VAL* 4.3 16.9 - - + +
172C CYS* 3.2 5.7 - - - -
173C ASN* 2.9 42.6 + - - +
175C LYS* 5.3 7.0 + - - +
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Residues in contact with TYR 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C ILE* 3.4 32.9 + - + +
94C THR* 3.7 25.8 - - + +
95C THR* 1.3 85.0 - - - +
97C GLU* 1.3 65.0 + - - +
98C ASP* 3.2 19.1 - - - +
99C GLY* 3.2 14.4 + - - -
100C GLY* 2.8 23.4 + - - +
102C LEU* 4.8 4.3 - - + -
126C PHE* 3.7 22.9 - + - -
132C VAL* 4.6 2.7 - - + -
140C TRP* 3.3 35.8 - + - -
162C LEU* 4.2 13.0 - - + -
170C LEU* 3.7 23.3 - - + -
171C ILE 3.9 2.0 - - - -
172C CYS* 3.7 13.5 - - + -
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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