Contacts of the helix formed by residues 150 - 166 (chain B) in PDB entry 2BAP
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 MET 150 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135A SER* 4.2 30.3 - - - +
138A MET* 3.3 38.6 - - + -
148B ARG 3.5 0.4 + - - -
149B ASP* 1.3 88.5 + - - +
151B HIS* 1.3 67.5 + - + +
152B LEU 3.0 3.1 - - - -
153B LEU* 2.9 20.1 + - + +
154B SER* 2.8 30.0 + - - -
201B ASP* 4.6 0.6 + - - -
204B ASN* 3.8 9.9 + - - -
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Residues in contact with HIS 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A MET* 3.7 39.4 - - + +
142A GLU* 5.0 6.5 - - - -
147B LEU* 3.3 21.7 - - + +
148B ARG* 4.1 8.4 + - + +
149B ASP 3.0 14.3 + - - -
150B MET* 1.3 88.0 - - - +
152B LEU* 1.3 58.6 + - - +
154B SER* 3.8 3.7 - - - -
155B CYS* 3.5 13.2 + - - +
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Residues in contact with LEU 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B LEU* 4.8 3.8 - - + -
147B LEU* 3.7 28.7 - - + +
148B ARG* 2.8 23.0 + - - +
149B ASP* 5.0 1.1 - - - +
150B MET 3.0 0.2 - - - -
151B HIS* 1.3 74.0 - - - +
153B LEU* 1.3 65.6 + - - +
154B SER 3.1 1.6 - - - -
155B CYS* 2.8 14.9 + - + +
156B LEU* 2.9 37.8 + - + +
185B ILE* 4.1 36.6 - - + -
188B ARG* 5.3 6.5 - - - +
189B LEU* 5.3 5.8 - - + -
204B ASN* 3.3 32.3 - - + +
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Residues in contact with LEU 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B MET* 2.9 24.5 + - + +
152B LEU* 1.3 77.6 - - - +
154B SER* 1.3 64.3 + - - +
156B LEU* 3.3 6.8 + - - +
157B GLU* 3.0 52.5 + - + +
201B ASP* 4.9 2.9 - - - +
203B ARG* 3.9 55.4 - - + +
204B ASN* 3.8 18.5 + - - +
207B GLU* 4.3 5.2 - - + -
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Residues in contact with SER 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A MET* 4.3 14.8 - - - +
139A TYR* 3.1 31.4 + - - -
155A CYS* 5.0 6.6 + - - -
158A SER* 3.1 30.1 + - - -
150B MET 2.8 14.3 + - - -
151B HIS 3.8 7.6 - - - -
153B LEU* 1.3 76.0 - - - +
155B CYS* 1.3 61.1 - - - +
157B GLU* 3.3 2.9 + - - -
158B SER* 3.1 15.1 + - - -
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Residues in contact with CYS 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A SER* 5.1 5.8 - - - -
138B MET* 5.7 0.2 - - - -
139B TYR* 3.8 18.1 - - - -
142B GLU* 3.7 30.3 - - + -
143B LEU* 4.4 17.0 - - - -
147B LEU* 4.4 10.1 - - + -
151B HIS 3.5 11.6 + - - +
152B LEU* 2.8 18.3 + - + +
154B SER* 1.3 75.2 + - - +
156B LEU* 1.3 56.7 + - + +
158B SER* 3.5 7.6 + - - -
159B LEU* 3.1 23.1 + - - +
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Residues in contact with LEU 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B LEU* 3.8 28.7 - - + -
152B LEU* 2.9 40.7 + - + +
153B LEU* 3.8 3.8 - - - +
155B CYS* 1.3 74.1 - - - +
157B GLU* 1.3 57.0 + - - +
158B SER 3.1 1.6 - - - -
159B LEU* 2.8 35.3 + - + +
160B ARG* 3.0 16.6 + - - +
182B LEU* 3.9 15.0 - - + -
185B ILE* 5.3 1.6 - - + -
204B ASN* 3.5 27.4 - - - +
207B GLU* 3.6 17.3 - - + +
208B ILE* 3.8 14.8 - - + -
211B CYS* 4.1 5.5 - - - -
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Residues in contact with GLU 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A TYR* 4.4 1.4 + - - -
158A SER* 3.7 7.6 + - - +
161A VAL* 4.0 19.2 - - + +
162A SER* 3.0 27.3 + - - -
153B LEU* 3.0 38.6 + - + +
154B SER* 3.3 5.9 + - - +
156B LEU* 1.3 75.8 - - - +
158B SER* 1.3 57.5 + - - +
160B ARG* 3.4 7.3 - - - +
161B VAL* 3.3 25.6 - - - +
207B GLU* 3.6 29.9 - - - +
210B ARG* 5.7 0.5 + - - -
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Residues in contact with SER 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A SER* 3.2 29.6 + - - -
157A GLU* 2.7 16.6 + - - +
158A SER* 3.9 11.4 - - - +
139B TYR* 2.6 24.7 + - - -
154B SER 3.1 12.4 + - - -
155B CYS 3.7 8.5 - - - -
156B LEU 3.1 0.6 - - - -
157B GLU* 1.3 76.1 - - - +
159B LEU* 1.3 55.9 + - - +
160B ARG 3.5 0.2 - - - -
161B VAL* 3.8 2.0 + - - +
162B SER* 2.4 38.8 + - - -
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Residues in contact with LEU 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B TYR* 3.6 42.0 - - + -
143B LEU* 4.4 9.0 - - + -
155B CYS 3.1 13.3 + - - +
156B LEU* 2.8 33.1 + - + +
158B SER* 1.3 76.0 - - - +
160B ARG* 1.3 55.5 + - - +
162B SER* 3.3 2.9 + - - -
163B LEU* 2.7 53.3 + - + +
170B TRP* 5.1 2.0 - - + -
174B PHE* 3.9 19.1 - - + -
182B LEU* 4.2 19.7 - - + -
211B CYS* 4.1 11.4 - - + -
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Residues in contact with ARG 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A VAL* 6.5 0.2 - - - -
165A ASN* 5.9 2.8 - - - +
156B LEU 3.0 15.8 + - - +
157B GLU* 3.4 13.0 - - - +
159B LEU* 1.3 78.1 - - - +
161B VAL* 1.3 62.2 + - + +
163B LEU* 2.8 13.7 + - - +
164B ASN* 2.7 55.0 + - - +
207B GLU* 3.0 34.4 + - - +
210B ARG* 3.5 35.6 + - - +
211B CYS* 4.2 20.6 - - - +
214B ALA* 5.0 1.6 - - + -
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Residues in contact with VAL 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A GLU* 4.8 13.9 - - + +
160A ARG* 3.1 26.7 - - - +
161A VAL* 3.6 22.7 - - + -
157B GLU 3.3 21.3 - - - +
158B SER* 3.8 5.4 - - - +
160B ARG* 1.3 85.9 - - + +
162B SER* 1.3 63.5 + - - +
164B ASN* 3.3 7.7 + - - +
165B ASN* 3.1 42.7 + - - +
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Residues in contact with SER 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A GLU* 2.8 23.4 + - - -
139B TYR* 2.9 12.2 + - - -
158B SER 2.4 26.2 + - - -
159B LEU 3.5 5.2 - - - -
161B VAL* 1.3 79.0 - - - +
163B LEU* 1.3 61.3 + - - +
164B ASN 3.4 0.2 + - - -
165B ASN* 4.2 1.6 - - - +
166B ASN* 2.4 36.3 + - - +
170B TRP* 3.8 21.5 - - - -
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Residues in contact with LEU 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B LEU* 2.7 42.2 + - + +
160B ARG* 2.8 10.0 + - - +
162B SER* 1.3 76.0 - - - +
164B ASN* 1.3 61.1 + - - +
166B ASN* 3.9 10.2 + - - +
170B TRP* 3.9 25.1 - - + -
171B VAL* 4.2 37.7 - - + +
174B PHE* 4.6 21.3 - - + -
182B LEU* 5.5 0.9 - - + -
211B CYS* 4.0 27.1 - - + +
214B ALA* 4.3 11.1 - - + +
215B PHE* 4.7 6.3 - - + -
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Residues in contact with ASN 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B ARG* 2.7 45.2 + - - +
161B VAL* 3.7 8.9 + - - +
163B LEU* 1.3 75.6 - - - +
165B ASN* 1.3 68.1 + - - +
166B ASN 3.3 6.7 + - - +
213B LYS* 6.3 0.4 - - - +
214B ALA* 3.3 25.9 - - - +
217B ASN* 6.1 1.4 - - - +
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Residues in contact with ASN 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A ARG* 5.0 4.0 - - - +
210A ARG* 5.9 2.0 - - - +
161B VAL* 3.1 37.1 + - - +
162B SER* 4.2 1.1 - - - +
164B ASN* 1.3 81.4 - - - +
166B ASN* 1.3 65.2 + - - +
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Residues in contact with ASN 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A ARG* 5.5 5.2 + - - -
162B SER* 2.4 31.6 + - - +
163B LEU 4.1 6.3 - - - +
164B ASN 3.3 8.2 - - - +
165B ASN* 1.3 83.8 - - - +
167B PRO* 1.4 79.6 - - + +
170B TRP* 3.2 53.2 + - + -
171B VAL* 5.4 0.2 - - + -
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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