Contacts of the helix formed by residues 161 - 174 (chain B) in PDB entry 1HE1
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 VAL 161 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159B SER* 3.1 8.6 + - - +
160B GLN* 1.3 81.5 - - + +
162B GLU* 1.3 65.5 + - - +
163B GLU* 3.9 14.8 - - + +
164B SER* 3.0 25.3 + - - +
165B ARG* 3.1 13.3 + - - +
223B ALA* 5.8 2.2 - - + +
227B GLU* 3.5 29.8 - - + +
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Residues in contact with GLU 162 (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 GLN 3.9 1.8 + - - -
161B VAL* 1.3 71.7 - - - +
163B GLU* 1.3 58.4 + - - +
165B ARG* 3.2 30.8 + - + +
166B ILE* 2.9 50.2 + - + +
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Residues in contact with GLU 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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161B VAL* 3.2 11.7 - - + +
162B GLU* 1.3 79.1 - - - +
164B SER* 1.3 57.0 + - - +
166B ILE* 3.3 11.7 + - - +
167B GLN* 2.9 64.5 + - - +
170B ARG* 4.4 9.2 + - - -
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Residues in contact with SER 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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155B ILE* 4.0 5.7 - - - +
159B SER* 3.3 25.1 + - - -
161B VAL* 3.0 16.7 + - - +
163B GLU* 1.3 76.9 - - - +
165B ARG* 1.3 66.2 + - - +
167B GLN* 4.6 0.7 - - - -
168B ALA* 2.9 26.5 + - - +
220B LEU* 3.8 20.3 - - - +
223B ALA* 3.9 24.6 - - - +
224B VAL* 4.4 5.6 - - - +
227B GLU* 4.6 1.7 + - - -
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Residues in contact with ARG 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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155B ILE 3.9 6.3 - - - +
156B ARG* 3.2 41.6 - - + +
157B ALA 5.1 2.9 - - - -
159B SER* 2.8 32.2 + - - +
160B GLN* 3.3 24.2 + - - +
161B VAL 3.1 6.3 + - - +
162B GLU* 3.2 35.0 + - - +
164B SER* 1.3 75.6 - - - +
166B ILE* 1.3 61.1 + - + +
168B ALA* 3.8 1.7 - - - +
169B GLY* 3.0 25.1 + - - -
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Residues in contact with ILE 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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162B GLU* 2.9 44.9 + - + +
163B GLU* 3.5 14.4 - - - +
165B ARG* 1.3 77.1 - - + +
167B GLN* 1.3 60.9 + - - +
169B GLY 3.4 1.2 + - - -
170B ARG* 2.8 49.2 + - + +
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Residues in contact with GLN 167 (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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163B GLU* 2.9 50.4 + - - +
164B SER 3.9 3.1 - - - +
166B ILE* 1.3 76.7 - - - +
168B ALA* 1.3 63.9 + - - +
170B ARG* 3.3 26.5 + - - +
171B LEU* 3.0 35.4 + - + +
216B GLU* 4.6 4.3 - - - +
219B LEU* 4.7 6.0 - - - +
220B LEU* 3.9 35.0 + - + +
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Residues in contact with ALA 168 (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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152B LEU* 3.5 30.8 - - + +
155B ILE* 3.9 9.2 - - + -
156B ARG* 3.9 11.0 - - + +
164B SER 2.9 19.2 + - - +
165B ARG 3.8 3.6 - - - +
167B GLN* 1.3 76.7 - - - +
169B GLY* 1.3 63.6 + - - +
171B LEU* 3.2 3.8 + - - +
172B LEU* 3.0 28.3 + - - +
220B LEU* 3.9 13.6 - - + +
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Residues in contact with GLY 169 (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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156B ARG* 3.9 28.4 - - - +
165B ARG 3.0 17.1 + - - -
166B ILE* 3.8 1.1 - - - -
168B ALA* 1.3 76.0 - - - +
170B ARG* 1.3 62.6 + - - +
172B LEU* 3.3 2.8 + - - +
173B GLU* 3.1 36.0 + - - +
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Residues in contact with ARG 170 (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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163B GLU* 4.4 11.7 + - - -
166B ILE* 2.8 35.3 + - + +
167B GLN* 3.5 24.1 - - - +
169B GLY* 1.3 75.7 - - - +
171B LEU* 1.3 64.5 + - - +
173B GLU* 3.3 13.8 + - - +
174B ARG* 3.0 41.1 + - - +
216B GLU* 4.7 9.2 + - - -
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Residues in contact with LEU 171 (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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152B LEU* 4.0 28.9 - - + -
167B GLN* 3.0 24.8 + - + +
168B ALA 3.7 3.6 - - - +
170B ARG* 1.3 79.6 - - + +
172B LEU* 1.3 62.1 + - - +
174B ARG* 3.0 37.6 + - - +
181B LEU* 3.2 17.4 - - + +
213B VAL* 4.7 11.2 - - + +
216B GLU* 3.7 36.1 - - + +
217B VAL* 4.2 24.0 - - + +
220B LEU* 4.2 12.1 - - + -
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Residues in contact with LEU 172 (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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149B SER* 3.7 29.4 - - - +
152B LEU* 3.6 20.0 - - + +
153B ALA* 3.8 20.2 - - + +
156B ARG* 3.5 37.7 - - - +
168B ALA 3.0 20.8 + - - +
169B GLY 3.7 4.5 - - - +
171B LEU* 1.3 75.6 - - - +
173B GLU* 1.3 58.3 + - + +
180B ALA* 3.6 3.5 - - - +
181B LEU* 3.4 7.7 + - + -
182B GLN* 3.0 60.7 + - + +
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Residues in contact with GLU 173 (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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156B ARG* 4.5 12.1 + - - +
169B GLY* 3.1 25.9 + - - +
170B ARG* 3.7 9.8 - - - +
171B LEU 3.1 0.2 - - - -
172B LEU* 1.3 77.6 - - + +
174B ARG* 1.3 67.3 + - - +
175B SER* 3.3 4.0 + - - -
180B ALA* 4.0 13.4 - - - +
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Residues in contact with ARG 174 (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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170B ARG* 3.0 27.2 + - - +
171B LEU* 3.0 31.4 + - - +
173B GLU* 1.3 76.1 - - - +
175B SER* 1.3 67.6 + - - +
176B ILE* 3.4 21.3 + - + +
180B ALA* 3.3 0.3 - - - -
181B LEU* 2.8 32.1 + - + -
209B GLN* 5.2 2.4 + - - +
212B GLN* 4.4 10.1 - - - +
213B VAL* 4.0 18.9 - - + +
216B GLU* 2.7 43.0 + - - -
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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