Contacts of the helix formed by residues 145 - 158 (chain B) in PDB entry 4HH3
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 ARG 145 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137A MET* 3.6 32.7 - - - +
140A ASP* 2.7 31.3 + - - +
144A GLN* 3.3 35.5 + - - +
243A ALA 4.8 4.3 - - - +
244A ALA* 4.9 0.8 - - - +
138B GLU 4.9 1.0 + - - -
141B TYR* 3.7 18.0 - - - +
142B GLU* 3.6 42.5 + - - +
143B THR 3.7 1.4 - - - -
144B GLN* 1.3 78.6 - - - +
146B GLU* 1.3 60.9 + - - +
147B MET 3.4 2.5 - - - -
148B GLU* 4.0 4.4 + - + +
149B THR* 3.9 12.3 + - - -
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Residues in contact with GLU 146 (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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243A ALA* 3.8 20.9 - - + +
244A ALA* 3.7 32.2 - - + +
248A LEU* 4.7 0.3 - - - +
144B GLN* 3.1 8.4 + - - +
145B ARG* 1.3 78.1 - - - +
147B MET* 1.3 76.9 + - + +
149B THR* 3.2 5.4 + - - -
150B ARG* 3.0 64.5 + - - +
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Residues in contact with MET 147 (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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144A GLN* 3.6 22.9 + - - +
145A ARG* 3.9 13.9 - - - +
147A MET* 4.1 3.4 - - - +
148A GLU* 3.6 39.9 - - + +
151A TYR* 3.8 30.5 - - + -
144B GLN 4.8 1.0 + - - +
145B ARG 3.4 1.0 - - - -
146B GLU* 1.3 87.7 - - + +
148B GLU* 1.3 65.7 + - - +
150B ARG* 3.8 37.9 - - - +
151B TYR* 3.0 26.3 + - - +
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Residues in contact with GLU 148 (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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140A ASP* 5.5 0.5 - - - +
143A THR* 4.6 8.7 - - - +
144A GLN* 3.1 31.4 + - - +
147A MET* 3.8 25.5 - - + +
145B ARG* 4.5 3.1 - - + +
146B GLU 3.4 0.4 - - - -
147B MET* 1.3 76.6 - - - +
149B THR* 1.3 58.7 + - - +
151B TYR* 3.5 2.1 + - - +
152B ARG* 2.9 73.5 + - + +
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Residues in contact with THR 149 (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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241A PHE* 3.9 16.2 - - + -
242A ARG 3.5 25.0 + - - +
243A ALA* 4.8 5.0 + - - -
145B ARG 3.9 9.5 + - - -
146B GLU* 3.2 12.3 + - - -
148B GLU* 1.3 76.9 - - - +
150B ARG* 1.3 65.2 + - - +
152B ARG* 3.3 6.6 + - + +
153B VAL* 3.0 29.6 + - + +
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Residues in contact with ARG 150 (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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151A TYR* 3.1 45.2 + - + -
164A LEU* 3.5 20.1 - - - +
173A VAL* 4.4 15.2 + - - +
174A ASP* 4.2 8.3 + - - +
241A PHE* 4.3 23.3 - - + -
243A ALA* 5.1 0.4 - - + -
248A LEU* 3.7 14.9 - - + +
146B GLU* 3.0 50.3 + - - +
147B MET* 3.8 24.8 - - - +
149B THR* 1.3 75.9 - - - +
151B TYR* 1.3 58.5 + - - +
153B VAL* 3.9 0.5 - - - +
154B VAL* 2.9 36.2 + - + +
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Residues in contact with TYR 151 (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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147A MET* 3.8 29.4 - - + +
150A ARG* 3.0 55.0 + - + -
151A TYR* 3.8 18.1 - - + +
154A VAL* 4.2 10.7 - - + +
147B MET 3.0 19.7 + - - +
148B GLU* 3.7 3.4 - - - +
150B ARG* 1.3 77.7 - - - +
152B ARG* 1.3 83.4 + - - +
154B VAL* 4.1 1.2 - - - +
155B LEU* 3.0 39.6 + - + +
164B LEU* 3.4 12.7 - - + +
174B ASP* 2.6 38.1 + - - +
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Residues in contact with ARG 152 (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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147A MET* 4.8 10.3 - - - +
150A ARG* 5.2 3.0 - - - +
148B GLU* 2.9 64.3 + - + +
149B THR* 3.7 7.2 - - + +
151B TYR* 1.3 92.1 - - - +
153B VAL* 1.3 61.2 + - + +
155B LEU* 4.0 3.6 - - - +
156B ASP* 3.0 31.2 + - - +
174B ASP* 3.6 21.4 + - - -
187B ARG* 4.5 11.3 - - - +
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Residues in contact with VAL 153 (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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239A ARG* 4.1 23.6 - - - +
241A PHE* 3.9 42.8 - - + -
250A LEU* 3.9 21.3 - - + -
149B THR* 3.0 22.8 + - + +
150B ARG 4.0 2.5 - - - +
152B ARG* 1.3 75.4 - - + +
154B VAL* 1.3 61.6 + - + +
156B ASP* 3.3 4.2 + - - +
157B VAL* 2.9 37.9 + - + +
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Residues in contact with VAL 154 (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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151A TYR* 3.8 24.0 - - + -
154A VAL* 4.0 17.3 - - + -
155A LEU* 4.2 19.7 - - + +
162A MET* 3.9 24.1 - - + +
164A LEU* 5.6 5.4 - - + -
241A PHE* 5.9 1.6 - - + -
250A LEU* 4.7 22.9 - - + -
150B ARG* 2.9 21.7 + - + +
151B TYR* 4.1 2.2 - - - +
153B VAL* 1.3 77.9 - - + +
155B LEU* 1.3 63.9 + - - +
157B VAL* 4.2 0.2 - - - +
158B SER* 3.0 24.6 + - - -
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Residues in contact with LEU 155 (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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154A VAL* 4.0 27.5 - - + +
151B TYR* 3.0 36.3 + - + +
152B ARG* 4.0 3.6 - - - +
154B VAL* 1.3 78.5 - - - +
156B ASP* 1.3 62.0 + - - +
158B SER* 3.6 3.2 + - - -
162B MET* 4.3 16.4 - - + +
164B LEU* 5.3 4.0 - - + -
174B ASP* 3.4 38.1 - - + +
175B LEU* 4.1 9.6 - - - +
176B ASN* 3.2 51.8 + - + +
250B LEU* 6.1 0.4 - - + -
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Residues in contact with ASP 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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239A ARG* 3.4 22.9 + - - -
152B ARG 3.0 19.7 + - - +
153B VAL* 3.8 4.5 - - - +
155B LEU* 1.3 80.6 - - - +
157B VAL* 1.3 59.7 + - - +
158B SER 4.1 3.3 - - - +
176B ASN* 4.5 9.6 - - - +
177B SER* 4.8 17.7 + - - -
187B ARG* 6.1 1.2 - - - -
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Residues in contact with VAL 157 (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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162A MET* 4.8 3.1 - - - -
239A ARG* 3.3 41.5 - - + +
250A LEU* 3.9 23.1 - - + -
252A GLN* 3.0 51.6 + - + +
153B VAL* 2.9 21.5 + - + +
154B VAL 4.2 1.3 - - - +
156B ASP* 1.3 76.5 - - - +
158B SER* 1.3 67.1 + - - +
159B ARG* 3.3 5.0 + - - +
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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
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154A VAL* 5.1 3.8 - - - -
158A SER* 2.6 32.0 + - - -
160A ASP* 3.5 8.1 - - - -
162A MET* 3.9 11.4 - - - -
154B VAL* 3.0 20.4 + - - -
155B LEU* 3.8 8.2 - - - +
156B ASP 3.4 3.5 - - - +
157B VAL* 1.3 78.4 - - - +
159B ARG* 1.3 59.1 + - - +
160B ASP* 3.2 11.6 + - - +
162B MET* 5.4 1.7 - - - -
176B ASN* 3.1 23.2 + - - -
178B ALA* 4.6 1.9 - - - +
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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