Contacts of the strand formed by residues 169 - 180 (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 HIS 169 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148G TYR* 4.1 21.5 - + + +
149G PRO* 4.9 11.0 + - + +
192G VAL* 3.6 17.5 - - + +
141H GLU* 2.6 34.7 + - + +
161H ALA* 3.7 23.6 - - + -
162H LEU 3.3 17.0 - - - -
163H LYS* 4.0 4.9 - - + +
164H LEU* 3.8 11.7 - - - +
167H GLY 4.9 4.5 - - - -
168H GLY* 1.3 82.0 - - - -
170H LEU* 1.3 61.2 + - - +
171H ILE* 4.0 20.3 + - + +
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Residues in contact with LEU 170 (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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96H TYR* 3.9 25.9 - - + -
97H GLU* 4.6 3.6 - - + +
98H ASP* 4.0 36.8 - - + +
131H PRO* 3.9 23.3 - - + -
132H VAL* 4.1 10.5 - - + -
140H TRP* 4.8 0.5 - - - -
160H MET 3.8 0.7 - - - +
161H ALA* 3.8 0.9 - - - -
162H LEU* 2.8 53.3 + - + +
164H LEU* 3.7 16.8 - - + +
169H HIS* 1.3 74.1 - - - +
171H ILE* 1.3 70.9 + - - +
172H CYS 4.1 0.2 + - - -
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Residues in contact with ILE 171 (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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146G MET* 4.7 2.5 - - + -
148G TYR* 3.3 48.7 - - + +
157G ARG* 4.0 19.1 - - + -
96H TYR* 3.8 0.9 - - - -
97H GLU* 3.0 54.5 + - + +
159H ASP* 4.9 2.5 - - + +
160H MET 3.5 11.7 - - - +
161H ALA* 3.8 23.8 - - + -
169H HIS* 4.0 9.2 + - + +
170H LEU* 1.3 87.6 - - - +
172H CYS* 1.3 72.6 + - - +
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Residues in contact with CYS 172 (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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94H THR* 3.7 21.1 - - + -
95H THR 3.0 18.8 - - - +
96H TYR* 3.7 18.2 - - + -
97H GLU* 5.4 1.3 - - - -
140H TRP* 3.8 32.8 - - - -
159H ASP* 3.5 3.2 - - - -
160H MET* 2.9 34.1 + - - -
171H ILE* 1.3 83.1 - - - +
173H ASN* 1.3 57.5 + - - +
174H LEU* 3.8 11.9 - - - +
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Residues in contact with ASN 173 (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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159G ASP* 3.1 19.5 + - - +
173G ASN* 3.2 14.6 + - - +
175G LYS* 6.1 2.5 - - - +
93H VAL 3.7 1.2 - - - +
94H THR* 3.4 5.0 - - - +
95H THR* 2.8 40.2 + - + +
97H GLU* 6.2 0.2 - - - +
157H ARG* 4.7 2.4 - - - -
158H SER 3.0 15.1 + - - +
159H ASP* 2.6 28.3 + - - +
172H CYS* 1.3 74.5 - - - +
174H LEU* 1.3 64.9 + - - +
175H LYS* 3.4 31.2 + - - +
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Residues in contact with LEU 174 (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* 4.6 7.0 - - + +
63H NRQ 4.4 10.3 - - + -
92H ARG* 3.7 31.9 - - - +
93H VAL 3.7 3.4 - - - -
94H THR* 3.8 15.7 - - + +
156H GLY 3.6 0.6 - - - +
157H ARG* 3.5 9.7 - - - -
158H SER* 2.7 44.4 + - - +
160H MET* 3.8 35.7 - - + -
172H CYS* 3.8 24.5 - - - +
173H ASN* 1.3 80.9 - - - +
175H LYS* 1.3 64.2 + - - +
176H THR* 4.0 2.5 - - - +
197H ARG* 5.3 0.2 - - - +
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Residues in contact with LYS 175 (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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99E GLY* 5.7 2.9 - - - -
125E ASN* 4.1 23.6 - - - +
97G GLU* 3.2 29.7 + - - +
173G ASN* 5.6 3.8 - - - +
91H GLU 3.9 0.5 - - - +
92H ARG* 3.1 2.9 - - - -
93H VAL* 2.9 54.5 + - + +
95H THR* 5.8 4.0 - - - -
156H GLY 3.7 3.4 - - - -
157H ARG* 3.8 22.7 - - - +
173H ASN* 3.4 19.6 + - - +
174H LEU* 1.3 77.3 - - - +
176H THR* 1.3 60.3 + - - +
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Residues in contact with THR 176 (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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90H TRP* 4.1 6.3 - - + -
91H GLU 3.3 12.8 - - - +
92H ARG* 2.8 36.3 + - + +
145H GLU* 4.5 3.6 + - - -
155H GLU* 3.2 9.7 - - - +
156H GLY 2.8 38.1 + - - +
157H ARG* 4.0 0.6 - - - +
174H LEU* 4.6 3.3 - - - +
175H LYS* 1.3 74.3 + - - +
177H THR* 1.3 68.3 + - - +
178H TYR* 3.3 43.1 + - + +
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Residues in contact with THR 177 (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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125E ASN* 3.6 12.3 + - - +
90H TRP* 3.2 4.3 - - - +
91H GLU* 2.8 49.4 + - - +
154H LEU 3.7 7.2 - - - +
155H GLU* 2.9 29.9 + - + -
176H THR* 1.3 73.4 - - - +
178H TYR* 1.3 64.4 + - - +
179H ARG* 3.6 37.9 + - + +
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Residues in contact with TYR 178 (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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67H LYS* 2.9 38.3 + - + -
79H PHE* 4.1 11.9 - - + -
80H PHE* 3.6 25.1 - + + -
88H PHE* 5.4 1.6 - + + -
89H THR 3.5 5.4 - - - +
90H TRP* 3.4 23.3 - + + -
92H ARG* 3.8 7.2 + - - -
145H GLU* 2.8 28.8 + - - -
147H LEU* 4.3 10.5 - - + -
153H GLY* 3.8 4.9 - - - -
154H LEU* 2.8 52.1 + - + +
156H GLY* 4.1 8.7 - - - -
176H THR* 3.3 30.3 - - + +
177H THR* 1.3 75.9 - - - +
179H ARG* 1.3 66.1 + - - +
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Residues in contact with ARG 179 (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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20E ASN* 3.8 27.5 + - - +
21E ASN* 4.1 23.9 - - - +
125E ASN* 5.6 0.8 - - - +
126E PHE 5.4 0.6 + - - -
79H PHE* 4.2 2.7 - - - -
88H PHE* 3.1 7.7 - - - +
89H THR* 2.9 47.8 + - - +
90H TRP* 5.5 0.8 - - - +
91H GLU* 2.7 53.7 + - - +
153H GLY* 5.2 3.6 - - - -
177H THR* 3.6 22.2 + - + +
178H TYR* 1.3 79.5 - - - +
180H SER* 1.3 64.8 + - - +
181H LYS* 5.1 0.3 - - - +
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Residues in contact with SER 180 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79H PHE* 3.7 12.4 - - - -
83H SER* 2.7 26.2 + - - -
88H PHE* 4.1 6.7 - - - -
152H GLY 5.4 3.4 + - - -
179H ARG* 1.3 79.6 - - - +
181H LYS* 1.3 62.0 + - - +
182H LYS* 3.7 16.6 + - - +
187H LEU* 3.5 31.4 - - - +
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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