Contacts of the strand formed by residues 88 - 96 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A NRQ 5.7 0.2 - - - -
67A LYS* 4.0 28.5 - - + -
68A THR* 3.5 25.1 - - - -
79A PHE* 5.0 4.0 - + + -
80A PHE* 3.7 46.7 - + + -
83A SER* 4.1 13.5 - - - +
84A PHE* 3.7 11.9 - + - -
87A GLY* 1.3 77.5 - - - +
89A THR* 1.3 77.6 + - - +
90A TRP* 4.5 7.4 - + + -
108A THR* 3.0 56.1 + - + +
117A TYR* 5.8 0.9 - + - -
179A ARG 3.3 15.3 - - - +
180A SER* 4.2 2.0 - - - -
181A LYS* 3.4 5.0 - - - +
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Residues in contact with THR 89 (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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88A PHE* 1.3 86.4 - - - +
90A TRP* 1.3 64.3 + - - +
106A GLN* 3.3 15.7 - - - +
107A ASP* 3.5 25.4 - - + +
178A TYR* 3.6 2.8 - - - -
179A ARG* 2.8 41.6 + - - +
181A LYS* 4.2 12.1 - - + +
21C ASN* 2.8 39.5 + - - +
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Residues in contact with TRP 90 (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 SER* 3.6 28.5 - - - -
63A NRQ 3.1 36.6 + - - -
67A LYS* 4.4 16.2 - - + -
88A PHE* 4.5 7.4 - + - -
89A THR* 1.3 77.6 - - - +
91A GLU* 1.3 70.0 + - - +
92A ARG* 3.5 34.1 - - + -
104A ALA* 3.5 37.2 - - + -
105A THR* 3.5 1.6 - - - -
106A GLN* 2.7 73.4 + - + +
119A VAL* 4.5 1.3 - - + -
176A THR* 4.3 1.3 - - + -
177A THR 3.3 6.3 - - - +
178A TYR* 3.6 25.6 - + + -
21C ASN* 5.1 3.1 + - - +
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Residues in contact with GLU 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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90A TRP* 1.3 76.3 - - - +
92A ARG* 1.3 62.7 + - - +
104A ALA 3.1 6.3 - - - -
105A THR* 3.8 19.2 - - + +
175A LYS 4.0 0.2 - - - +
176A THR* 3.2 4.9 - - - +
177A THR* 3.0 44.2 + - - +
179A ARG* 2.7 34.3 + - - +
20C ASN* 3.3 22.2 + - - +
21C ASN* 3.5 9.2 + - - +
123C GLY 4.7 0.2 - - - +
124C VAL* 3.6 20.5 - - + +
125C ASN* 2.9 25.9 + - + +
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Residues in contact with ARG 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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60A THR* 3.1 37.1 + - - -
61A SER* 4.7 1.0 + - - +
63A NRQ 2.6 27.7 + - - +
67A LYS* 4.9 0.6 - - - +
90A TRP* 3.5 35.6 - - + -
91A GLU* 1.3 77.9 - - - +
93A VAL* 1.3 71.6 + - - +
94A THR* 3.6 18.4 - - - +
102A LEU 4.4 0.4 - - - +
103A THR* 3.1 7.5 - - - +
104A ALA* 2.8 33.0 + - + +
145A GLU* 5.2 0.8 + - - -
174A LEU* 3.8 20.6 - - - +
175A LYS 3.3 14.6 - - - +
176A THR* 3.2 19.0 + - + +
178A TYR* 3.8 20.0 + - - -
124C VAL* 3.9 7.1 - - - +
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Residues in contact with VAL 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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92A ARG* 1.3 73.0 - - - +
94A THR* 1.3 64.3 + - - +
95A THR* 4.1 13.4 + - - +
101A VAL* 3.7 27.6 - - + -
102A LEU 3.3 3.8 - - - -
103A THR* 4.0 7.2 - - + -
173A ASN 3.8 1.4 - - - +
174A LEU* 3.7 1.2 - - - -
175A LYS* 3.0 51.9 + - + +
101C VAL* 4.2 23.1 - - + -
124C VAL* 3.7 21.1 - - + -
125C ASN* 4.9 5.4 - - + +
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Residues in contact with THR 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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60A THR* 5.0 3.5 + - - -
92A ARG* 3.6 12.0 - - - +
93A VAL* 1.3 72.1 - - - +
95A THR* 1.3 63.2 + - - +
96A TYR* 3.7 28.1 - - + +
100A GLY 3.8 0.9 - - - +
101A VAL* 3.4 5.2 - - - +
102A LEU* 2.7 44.8 + - - +
172A CYS* 3.7 12.8 - - + -
173A ASN 3.3 3.8 - - - -
174A LEU* 3.4 36.6 - - + +
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Residues in contact with THR 95 (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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93A VAL* 4.1 15.4 - - - +
94A THR* 1.3 73.0 - - - +
96A TYR* 1.3 71.0 + - - +
97A GLU* 4.0 1.6 + - - +
99A GLY 6.0 0.4 - - - +
100A GLY 3.7 2.5 - - - +
101A VAL* 4.5 16.3 - - + +
172A CYS* 3.3 2.7 - - - -
173A ASN* 2.8 44.1 + - - +
175A LYS* 5.7 4.3 + - - -
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Residues in contact with TYR 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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57A ILE* 3.4 34.5 + - + +
94A THR* 3.7 26.3 - - + +
95A THR* 1.3 83.9 - - - +
97A GLU* 1.3 65.1 + - - +
98A ASP* 3.1 15.9 - - - +
99A GLY* 3.0 16.1 + - - -
100A GLY* 2.7 27.3 + - - +
102A LEU* 4.9 3.8 - - + -
126A PHE* 3.7 27.1 - + - -
132A VAL* 4.6 2.0 - - + -
140A TRP* 3.4 33.1 - + - -
162A LEU* 4.3 12.6 - - + -
170A LEU* 3.9 22.4 - - + -
171A ILE 5.1 0.2 - - - -
172A CYS* 3.7 12.6 - - + -
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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