Contacts of the strand formed by residues 88 - 96 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63G NRQ 5.3 0.2 - - - -
67G LYS* 3.6 22.9 - - + -
68G THR* 3.6 18.8 - - - -
79G PHE* 5.1 3.4 - - + -
80G PHE* 3.5 60.8 - + + -
83G SER* 4.3 6.7 - - - +
84G PHE* 4.2 3.6 - + - -
87G GLY* 1.3 76.2 - - - +
89G THR* 1.3 72.8 + - - +
90G TRP* 4.0 14.6 - + + -
108G THR* 2.7 67.6 + - + +
117G TYR* 5.8 0.4 - + - -
178G TYR* 5.7 0.2 - - + -
179G ARG 3.3 17.3 - - - +
180G SER* 4.4 3.8 - - - -
181G LYS* 4.1 2.2 - - - +
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Residues in contact with THR 89 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F ASN* 3.2 31.0 + - + +
88G PHE* 1.3 82.1 - - - +
90G TRP* 1.3 63.9 + - - +
106G GLN 3.4 15.5 - - - +
107G ASP* 3.6 20.9 - - + +
178G TYR* 3.6 2.1 - - - -
179G ARG* 2.9 43.8 + - + +
181G LYS* 4.3 12.6 - - + -
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Residues in contact with TRP 90 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F ASN* 4.1 4.4 + - - -
60G THR 4.2 0.2 - - - -
61G SER* 3.8 19.7 - - - -
63G NRQ 3.1 43.0 + - - -
67G LYS* 4.4 8.7 - - + +
88G PHE* 4.0 19.5 - + - -
89G THR* 1.3 75.9 - - - +
91G GLU* 1.3 66.1 + - - +
92G ARG* 3.6 44.0 - - + -
104G ALA* 4.0 20.9 - - + -
105G THR* 3.4 1.7 - - - -
106G GLN* 2.7 72.8 + - + +
119G VAL* 4.4 2.5 - - + -
176G THR* 4.1 4.7 - - + -
177G THR 3.1 12.1 - - - +
178G TYR* 3.6 19.7 - + + -
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Residues in contact with GLU 91 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20F ASN* 3.2 25.0 - - - +
21F ASN* 3.3 9.5 + - - +
124F VAL* 3.9 21.8 - - + -
125F ASN* 3.3 21.7 + - + +
90G TRP* 1.3 75.0 - - - +
92G ARG* 1.3 60.4 + - - +
104G ALA 3.4 4.5 - - - -
105G THR* 3.9 10.1 - - + -
175G LYS 3.8 0.9 - - - +
176G THR* 3.3 4.4 - - - +
177G THR* 2.8 48.9 + - - +
179G ARG* 2.5 44.2 + - - +
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Residues in contact with ARG 92 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124F VAL* 3.6 8.1 - - - +
60G THR* 2.9 38.7 + - - -
61G SER* 4.7 1.2 + - - +
63G NRQ 2.9 26.4 + - - +
67G LYS* 4.8 0.6 - - - +
90G TRP* 3.6 33.5 - - + -
91G GLU* 1.3 75.8 - - - +
93G VAL* 1.3 73.6 + - - +
94G THR* 3.8 9.9 - - - +
102G LEU 5.3 0.7 - - - +
103G THR* 3.2 6.6 - - - -
104G ALA* 2.9 35.8 + - + +
145G GLU* 5.1 1.2 + - - -
174G LEU* 3.7 27.7 - - - +
175G LYS 3.2 13.5 - - - +
176G THR* 3.2 25.8 + - + +
178G TYR* 3.8 13.1 + - - -
197G ARG* 6.0 0.4 - - - +
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Residues in contact with VAL 93 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101F VAL* 4.2 22.7 - - + -
124F VAL* 3.5 22.7 - - + -
125F ASN* 4.7 5.4 - - + -
92G ARG* 1.3 72.4 - - - +
94G THR* 1.3 65.0 + - - +
95G THR* 4.2 10.6 + - - +
101G VAL* 3.8 26.9 - - + -
102G LEU 3.6 2.5 - - - -
103G THR* 3.8 9.2 - - + +
173G ASN 3.6 1.9 - - - +
174G LEU* 3.8 0.3 - - - -
175G LYS* 3.0 57.1 + - + +
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Residues in contact with THR 94 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60G THR* 4.9 4.7 + - - -
92G ARG* 3.8 19.6 - - - -
93G VAL* 1.3 74.9 - - - +
95G THR* 1.3 62.6 + - - +
96G TYR* 3.4 31.0 + - + +
100G GLY 4.1 0.2 - - - +
101G VAL* 3.4 9.7 - - - +
102G LEU* 2.8 45.7 + - - +
172G CYS* 3.7 23.1 - - - -
173G ASN 3.2 7.0 - - - +
174G LEU* 3.8 9.0 - - + +
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Residues in contact with THR 95 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93G VAL* 4.2 14.2 + - - +
94G THR* 1.3 75.6 + - - +
96G TYR* 1.3 70.1 + - - +
97G GLU* 3.9 3.4 + - + +
100G GLY 3.9 4.9 - - - +
101G VAL* 4.9 10.3 - - + +
172G CYS* 3.1 5.2 - - - -
173G ASN* 2.8 51.1 + - + +
175G LYS* 5.5 3.7 + - - +
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Residues in contact with TYR 96 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57G ILE* 3.4 36.6 + - + +
94G THR* 3.4 30.5 - - + +
95G THR* 1.3 81.1 - - - +
97G GLU* 1.3 63.2 + - - +
98G ASP* 3.1 18.4 - - - +
99G GLY* 3.1 13.7 + - - -
100G GLY* 2.9 23.7 + - - +
102G LEU* 4.9 3.1 - - + -
126G PHE* 3.9 29.2 - + + -
132G VAL* 4.6 1.8 - - + -
140G TRP* 3.3 35.6 - + - -
162G LEU* 4.3 10.3 - - + -
170G LEU* 4.0 23.6 - - + -
171G ILE 3.8 2.2 - - - -
172G CYS* 3.8 9.9 - - + -
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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