Contacts of the helix formed by residues 147 - 155 (chain A) in PDB entry 1B4V
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 TYR 147 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142A GLU* 3.2 41.2 + - + -
143A MET* 3.9 13.5 - - - +
146A ARG* 1.3 90.6 - - + +
148A PHE* 1.3 60.3 + - - +
150A ARG* 3.3 16.8 + - - +
151A ALA* 3.0 29.1 + - - +
492A ALA* 3.5 22.2 - - - +
495A GLU* 3.8 11.3 - - + +
496A ARG* 3.6 50.9 + - + +
499A GLU* 2.9 33.1 + - - +
500A ARG* 5.9 1.4 + - - -
503A LYS* 5.8 0.2 + - - -
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Residues in contact with PHE 148 (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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125A GLU* 3.5 25.0 - - + +
126A PRO* 3.6 33.7 - - + -
131A PHE* 4.5 6.1 - + - -
143A MET* 2.8 51.4 + - + +
144A TYR* 3.6 42.8 - + - +
147A TYR* 1.3 70.8 - - - +
149A PRO* 1.3 69.7 - - + +
151A ALA* 3.2 3.5 + - - +
152A ASN* 2.9 23.9 + - - +
488A VAL* 3.8 20.0 - - + +
489A THR* 3.9 15.0 - - - -
492A ALA* 3.4 20.2 - - + -
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Residues in contact with PRO 149 (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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125A GLU* 5.2 2.2 - - - +
144A TYR 3.4 22.4 - - - +
145A ASP 3.8 11.7 - - - +
146A ARG 3.5 14.1 - - - +
148A PHE* 1.3 95.7 - - + +
150A ARG* 1.3 60.7 + - - +
152A ASN* 3.4 8.3 + - + +
153A SER* 3.1 24.4 + - - -
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Residues in contact with ARG 150 (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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28A ARG* 3.8 17.0 - - - +
146A ARG* 3.2 46.3 + - - +
147A TYR* 3.5 21.4 - - - +
149A PRO* 1.3 81.2 - - - +
151A ALA* 1.3 61.5 + - - +
153A SER* 3.4 4.3 + - - -
154A MET* 3.1 26.3 + - + +
232A TYR* 4.6 0.2 - - - -
495A GLU* 3.5 39.9 + - - +
499A GLU* 3.1 30.7 + - - +
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Residues in contact with ALA 151 (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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147A TYR 3.0 16.6 + - - +
148A PHE* 3.6 4.9 - - - +
150A ARG* 1.3 75.1 - - - +
152A ASN* 1.3 65.2 + - - +
155A LEU* 2.9 36.4 + - + +
232A TYR* 3.8 11.2 - - - -
488A VAL* 4.4 6.7 - - + +
491A THR* 3.6 24.9 - - + +
492A ALA* 3.9 16.8 - - + +
495A GLU* 4.9 1.7 - - + +
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Residues in contact with ASN 152 (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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125A GLU* 5.2 7.8 + - + +
148A PHE 2.9 16.6 + - - +
149A PRO* 3.6 9.0 - - + +
151A ALA* 1.3 78.3 - - - +
153A SER* 1.3 65.6 + - - +
155A LEU* 5.0 0.9 - - - -
156A ARG 3.4 1.4 + - - -
157A VAL* 3.2 68.0 + - - +
159A HIS* 5.2 7.0 + - - -
488A VAL* 5.7 4.2 - - + +
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Residues in contact with SER 153 (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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149A PRO 3.1 14.7 + - - -
150A ARG* 3.8 5.4 - - - -
152A ASN* 1.3 83.4 + - - +
154A MET* 1.3 64.9 + - - +
156A ARG* 3.2 17.0 + - - +
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Residues in contact with MET 154 (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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27A LEU* 4.2 20.4 - - + -
28A ARG* 3.7 24.7 - - - +
150A ARG* 3.1 17.9 + - + +
153A SER* 1.3 78.5 - - - +
155A LEU* 1.3 60.0 + - - +
156A ARG* 3.1 5.5 + - - +
231A THR* 3.5 22.5 - - - +
232A TYR* 3.2 42.8 - - + +
235A ALA* 4.6 12.3 - - + -
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Residues in contact with LEU 155 (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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20A TYR* 3.9 25.1 - - + -
151A ALA* 2.9 29.7 + - + +
154A MET* 1.3 74.0 - - - +
156A ARG* 1.3 68.4 + - - +
157A VAL* 4.0 13.0 - - + -
194A VAL* 3.4 21.4 - - + +
226A GLN 4.3 2.4 - - - +
228A LEU* 4.1 5.2 - - + -
231A THR* 3.8 13.8 - - - +
232A TYR* 3.8 26.0 - - + -
487A PHE* 3.9 21.8 - - + -
488A VAL* 4.1 16.8 - - + -
491A THR* 4.0 18.8 - - + +
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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