Contacts of the helix formed by residues 161 - 173 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159A SER* 3.1 10.2 + - - +
160A GLN* 1.3 82.4 - - + +
162A GLU* 1.3 67.2 + - - +
163A GLU* 3.9 16.4 - - + +
164A SER* 3.0 24.4 + - - +
165A ARG* 3.1 13.1 + - - +
223A ALA* 5.9 1.1 - - + +
227A GLU* 3.8 27.4 - - + +
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Residues in contact with GLU 162 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160A GLN 3.9 1.6 + - - -
161A VAL* 1.3 72.5 - - - +
163A GLU* 1.3 58.6 + - - +
165A ARG* 3.1 33.5 + - - +
166A ILE* 2.9 53.8 + - + +
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Residues in contact with GLU 163 (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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161A VAL* 3.2 11.0 - - + +
162A GLU* 1.3 77.7 - - - +
164A SER* 1.3 57.8 + - - +
166A ILE* 3.3 19.9 + - - +
167A GLN* 2.9 42.3 + - + +
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Residues in contact with SER 164 (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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155A ILE* 4.0 5.1 - - - +
159A SER* 3.4 23.3 - - - -
161A VAL* 3.0 16.6 + - - +
163A GLU* 1.3 79.1 - - - +
165A ARG* 1.3 63.8 + - - +
167A GLN* 3.5 1.3 + - - -
168A ALA* 3.0 25.8 + - - +
220A LEU* 3.7 20.8 - - - +
223A ALA* 3.7 26.7 - - - +
224A VAL* 4.6 6.1 - - - +
227A GLU* 4.7 1.2 + - - -
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Residues in contact with ARG 165 (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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155A ILE 4.0 0.7 - - - +
156A ARG* 3.3 39.2 + - + +
157A ALA 5.0 3.8 - - - -
159A SER* 3.0 37.5 + - - +
160A GLN* 3.6 21.0 + - - +
161A VAL 3.1 6.7 + - - +
162A GLU* 3.1 39.6 + - + +
164A SER* 1.3 76.6 - - - +
166A ILE* 1.3 58.9 + - + +
168A ALA* 3.5 2.1 + - - +
169A GLY* 3.1 24.1 + - - -
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Residues in contact with ILE 166 (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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162A GLU* 2.9 47.6 + - + +
163A GLU* 3.6 20.9 - - - +
165A ARG* 1.3 75.2 - - + +
167A GLN* 1.3 60.7 + - - +
169A GLY* 3.2 3.3 + - - -
170A ARG* 2.8 43.7 + - + +
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Residues in contact with GLN 167 (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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163A GLU* 2.9 28.6 + - - +
164A SER* 3.9 4.3 - - - +
166A ILE* 1.3 73.3 - - - +
168A ALA* 1.3 66.9 + - - +
170A ARG* 3.7 9.0 - - + +
171A LEU* 3.0 32.4 + - + +
216A GLU* 3.2 42.7 + - - +
219A LEU* 4.0 12.7 - - - +
220A LEU* 3.7 33.0 + - + +
223A ALA* 5.6 2.3 - - - +
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Residues in contact with ALA 168 (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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152A LEU* 3.6 25.7 - - + +
155A ILE* 4.0 9.0 - - + -
156A ARG* 3.8 12.1 - - + +
164A SER 3.0 18.7 + - - +
165A ARG 3.8 4.0 - - - +
167A GLN* 1.3 76.0 - - - +
169A GLY* 1.3 58.3 + - - +
171A LEU* 3.2 5.4 + - - +
172A LEU* 3.0 35.2 + - - +
220A LEU* 4.1 14.1 - - + +
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Residues in contact with GLY 169 (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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156A ARG* 3.9 24.6 - - - +
165A ARG 3.1 15.2 + - - -
166A ILE* 3.2 3.6 + - - -
168A ALA* 1.3 77.4 - - - +
170A ARG* 1.3 61.4 + - - +
172A LEU* 3.4 4.5 + - - +
173A GLU* 3.1 29.2 + - - +
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Residues in contact with ARG 170 (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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166A ILE* 2.8 34.4 + - + +
167A GLN* 3.7 10.5 - - + +
168A ALA 3.3 0.4 - - - -
169A GLY* 1.3 76.5 - - - +
171A LEU* 1.3 63.3 + - + +
173A GLU* 3.3 21.9 + - - +
174A ARG* 3.1 21.0 + - - +
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Residues in contact with LEU 171 (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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152A LEU* 3.9 31.0 - - + -
167A GLN* 3.0 21.6 + - + +
168A ALA 3.2 7.4 + - - +
170A ARG* 1.3 76.2 - - - +
172A LEU* 1.3 63.4 + - - +
174A ARG* 3.0 26.8 + - - +
181A LEU* 3.3 15.4 - - + +
213A VAL* 4.3 23.6 - - + -
216A GLU* 3.7 34.8 - - + +
217A VAL* 4.1 20.6 - - + +
220A LEU* 4.3 10.1 - - + -
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Residues in contact with LEU 172 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A SER* 3.9 15.7 - - - +
152A LEU* 3.7 28.9 - - + +
153A ALA* 3.9 27.6 - - + +
156A ARG* 4.0 18.2 - - - -
168A ALA 3.0 21.0 + - - +
169A GLY* 3.7 4.9 - - - +
170A ARG 3.3 0.2 - - - -
171A LEU* 1.3 78.2 - - - +
173A GLU* 1.3 56.1 + - - +
180A ALA* 3.6 2.8 - - - +
181A LEU* 3.3 8.1 + - + -
182A GLN* 3.0 71.1 + - + +
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Residues in contact with GLU 173 (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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169A GLY 3.1 19.5 + - - +
170A ARG* 3.3 26.4 + - - +
172A LEU* 1.3 75.2 - - - +
174A ARG* 1.3 67.0 + - - +
175A SER* 3.3 4.3 + - - -
180A ALA* 4.2 11.3 - - - +
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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