Contacts of the strand formed by residues 143 - 150 (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 SER 143 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146G MET* 5.6 0.4 - - - -
194G TYR* 4.8 5.2 - - - -
63H NRQ 2.9 19.1 + - - -
141H GLU 4.5 1.6 - - - -
142H ALA* 1.3 76.4 - - - +
144H THR* 1.3 62.5 + - - +
158H SER* 4.3 0.7 - - - -
159H ASP 4.1 7.9 - - - -
160H MET* 3.9 21.5 - - - -
196H ASP* 3.4 3.6 - - - +
197H ARG* 2.8 63.8 + - - +
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Residues in contact with THR 144 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144G THR* 3.8 35.6 - - - +
194G TYR* 4.8 6.8 - - - -
220G ARG* 3.7 12.0 + - - -
143H SER* 1.3 75.1 + - - +
145H GLU* 1.3 68.8 + - - +
146H MET* 5.0 0.4 - - + +
157H ARG 4.0 0.7 - - - +
158H SER* 3.1 19.7 + - - -
159H ASP 4.5 4.6 + - - +
194H TYR* 4.3 8.5 - - + -
195H VAL 3.3 5.4 - - - +
196H ASP* 2.7 26.6 + - - +
197H ARG* 3.4 3.6 - - - -
220H ARG* 3.8 5.8 - - - +
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Residues in contact with GLU 145 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63H NRQ 6.2 0.2 - - - -
67H LYS* 3.0 22.6 + - - -
92H ARG* 5.3 0.9 + - - -
144H THR* 1.3 76.3 - - - +
146H MET* 1.3 69.4 + - - +
147H LEU* 3.5 20.9 - - + +
156H GLY* 3.5 16.3 - - - -
157H ARG 3.4 15.7 - - - +
158H SER* 4.2 2.3 - - - -
176H THR* 4.5 4.2 + - - -
178H TYR* 2.8 22.8 + - - -
194H TYR* 3.1 6.2 - - - +
195H VAL* 2.8 41.5 + - + +
197H ARG* 3.1 26.6 + - - +
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Residues in contact with MET 146 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141G GLU* 5.1 0.2 - - - -
142G ALA 4.3 9.4 - - - +
143G SER* 5.4 0.7 - - - -
159G ASP* 3.8 41.5 - - + +
160G MET 4.0 10.8 - - - +
161G ALA* 4.1 22.4 - - + +
171G ILE* 4.6 8.5 - - + -
144H THR* 4.2 1.0 + - + -
145H GLU* 1.3 73.2 - - - +
147H LEU* 1.3 64.3 + - - +
148H TYR* 4.4 8.2 - - + -
155H GLU 3.8 0.7 - - - +
156H GLY* 3.4 4.3 - - - -
157H ARG* 3.0 42.8 + - + +
192H VAL* 4.0 14.1 - - + -
193H TYR 3.4 3.8 - - - -
194H TYR* 3.6 31.0 - - + -
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Residues in contact with LEU 147 (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* 5.5 0.4 - - - +
70H ILE* 6.4 0.2 - - + -
80H PHE* 4.3 15.5 - - + -
145H GLU* 3.5 39.3 - - - +
146H MET* 1.3 75.6 - - - +
148H TYR* 1.3 63.3 + - - +
154H LEU* 3.8 20.9 - - + -
155H GLU 3.3 7.6 - - - +
156H GLY* 4.6 0.4 - - - -
178H TYR* 4.3 12.3 - - + -
191H GLY 4.1 0.7 - - - +
192H VAL* 3.2 8.1 - - - +
193H TYR* 2.6 74.7 + - + +
195H VAL* 3.8 20.2 - - + -
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Residues in contact with TYR 148 (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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161G ALA* 5.5 1.6 - - + -
169G HIS* 4.3 20.0 - + + +
171G ILE* 3.1 43.2 - - + +
146H MET* 4.4 13.7 - - + -
147H LEU* 1.3 78.2 - - - +
149H PRO* 1.3 81.2 - - + +
150H ALA* 4.7 6.5 - - + -
154H LEU* 3.4 7.8 - - - +
155H GLU* 2.8 69.1 + - + +
157H ARG* 3.3 39.2 + - + -
192H VAL* 4.1 14.4 - - + +
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Residues in contact with PRO 149 (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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168G GLY* 5.7 3.5 - - - -
169G HIS* 4.5 16.2 + - + -
148H TYR* 1.3 94.6 - - + +
150H ALA* 1.3 64.1 + - - +
153H GLY 3.4 7.2 - - - +
154H LEU* 4.1 5.2 - - + -
189H MET* 3.9 17.3 - - + -
190H PRO 3.4 23.8 - - - +
191H GLY* 4.1 8.7 - - - +
192H VAL 4.3 10.1 - - - +
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Residues in contact with ALA 150 (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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148H TYR* 3.8 10.3 + - + +
149H PRO* 1.3 76.5 - - - +
151H ASP* 1.3 66.9 + - + +
152H GLY 3.4 2.2 - - - +
153H GLY* 2.8 29.7 + - - +
154H LEU 4.1 0.7 + - - -
155H GLU* 4.4 26.5 - - + +
189H MET* 5.0 0.4 - - - +
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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