Contacts of the helix formed by residues 141 - 150 (chain A) in PDB entry 2HRB
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 LEU 141 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A SER* 1.3 69.1 + - - +
142A GLN* 1.3 64.9 + - - +
143A CYS 3.0 2.0 - - - -
144A LEU* 3.0 38.0 + - + +
145A ARG* 3.7 3.3 + - - +
227A CYS* 3.5 26.0 - - + +
229A GLY* 5.2 1.1 - - - -
230A PRO* 4.6 10.8 - - + -
270A HIS* 3.7 33.9 - - + +
275A GLN* 3.8 28.5 - - + +
1001A NAP 5.4 1.2 - - - -
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Residues in contact with GLN 142 (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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140A SER* 3.2 18.2 - - - +
141A LEU* 1.3 74.9 - - + +
143A CYS* 1.3 64.1 + - - +
144A LEU 3.1 0.2 - - - -
145A ARG* 3.3 18.8 + - - +
146A ALA* 3.0 23.4 + - - +
192A SER* 5.1 4.3 + - - -
194A TYR* 4.2 25.2 - - + -
195A GLY* 4.2 8.3 - - - -
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Residues in contact with CYS 143 (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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140A SER* 3.0 23.2 + - - +
142A GLN* 1.3 78.1 - - - +
144A LEU* 1.3 64.5 + - - +
146A ALA* 3.4 2.6 + - - +
147A PHE* 2.9 27.7 + - - +
195A GLY 3.8 11.2 + - - -
198A LYS* 3.5 8.7 - - + +
199A LEU* 3.4 35.6 - - - +
202A THR* 3.3 26.7 - - - -
268A LEU* 3.8 20.4 - - - -
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Residues in contact with LEU 144 (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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141A LEU* 3.0 33.1 + - + +
143A CYS* 1.3 78.7 - - - +
145A ARG* 1.3 60.4 + - - +
147A PHE* 3.1 8.9 + - + +
148A GLU* 2.9 45.0 + - - +
199A LEU* 6.2 0.4 - - + -
268A LEU* 3.9 17.5 - - + -
275A GLN* 4.7 15.3 - - + +
276A ASN 5.5 3.1 - - - +
277A TRP* 3.7 45.5 - - + +
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Residues in contact with ARG 145 (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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141A LEU 3.7 2.5 + - - +
142A GLN* 3.3 25.9 + - - +
144A LEU* 1.3 78.3 - - - +
146A ALA* 1.3 56.4 + - - +
148A GLU* 3.3 25.8 + - - +
149A ASN* 2.9 61.5 + - - +
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Residues in contact with ALA 146 (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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142A GLN 3.0 10.6 + - - +
143A CYS 3.4 9.6 - - - +
145A ARG* 1.3 72.5 - - - +
147A PHE* 1.3 64.1 - - - +
149A ASN* 3.1 15.0 + - - +
150A CYS* 3.1 18.1 + - - -
190A PRO* 3.6 19.1 - - + +
192A SER* 5.2 2.9 - - - +
195A GLY* 3.5 34.8 - - - +
196A VAL* 4.0 4.7 - - + +
199A LEU* 4.8 3.4 - - + -
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Residues in contact with PHE 147 (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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143A CYS 2.9 15.1 + - - +
144A LEU* 3.1 12.8 + - + +
146A ALA* 1.3 75.9 - - - +
148A GLU* 1.3 70.7 + - + +
150A CYS* 3.2 8.7 + - + +
155A GLN* 3.2 83.3 + - + +
158A PHE* 4.4 10.3 - + + -
159A HIS* 3.8 17.7 - + + -
199A LEU* 4.2 17.9 - - + +
277A TRP* 3.6 51.1 - + + -
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Residues in contact with GLU 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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144A LEU* 2.9 33.1 + - - +
145A ARG* 3.7 31.4 + - - +
147A PHE* 1.3 85.0 - - + +
149A ASN* 1.3 60.5 + - - +
150A CYS 3.7 1.4 - - - +
155A GLN* 3.3 17.9 + - - +
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Residues in contact with ASN 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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145A ARG* 2.9 63.7 + - - +
146A ALA* 3.1 2.1 + - - +
148A GLU* 1.3 75.6 - - - +
150A CYS* 1.3 61.1 + - - +
151A SER 3.9 0.7 + - - -
188A GLY 4.0 2.1 - - - +
189A TRP 4.2 1.9 - - - +
190A PRO* 3.5 36.1 - - + +
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Residues in contact with CYS 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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146A ALA 3.1 18.9 + - - -
147A PHE* 3.2 16.9 + - - +
148A GLU 3.7 1.7 - - - +
149A ASN* 1.3 78.7 - - - +
151A SER* 1.3 66.3 + - - +
152A GLU 3.7 0.5 + - - -
154A LEU* 3.8 20.6 - - + -
155A GLN* 2.9 29.3 + - + +
158A PHE* 4.3 18.2 - - - -
188A GLY 3.3 5.2 - - - -
189A TRP* 4.8 1.8 - - - -
190A PRO* 3.7 17.5 - - - -
196A VAL* 5.7 0.7 - - - -
199A LEU* 4.5 5.6 - - - -
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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