Contacts of the helix formed by residues 161 - 176 (chain A) in PDB entry 2H5X
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 ALA 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 GLY 4.0 0.8 + - - -
160A PHE* 1.3 73.8 - - - +
162A ALA* 1.3 54.4 + - - +
163A LYS 4.9 1.6 - - - +
164A GLN* 3.2 25.1 + - + +
165A ALA* 2.7 34.4 + - - +
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Residues in contact with ALA 162 (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 VAL* 5.7 0.4 - - - +
156A VAL* 4.1 16.3 - - + +
160A PHE 3.6 2.8 + - - -
161A ALA* 1.3 66.1 - - - +
163A LYS* 1.3 55.3 + - - +
164A GLN 2.6 16.2 + - - -
165A ALA* 2.8 17.1 + - - +
166A GLU* 2.8 23.3 + - - +
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Residues in contact with LYS 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 ALA* 3.6 2.0 - - - +
162A ALA* 1.3 74.8 - - - +
164A GLN* 1.3 57.1 + - - +
166A GLU* 2.9 30.5 - - + +
167A GLU* 2.8 35.7 - - + +
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Residues in contact with GLN 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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160A PHE* 4.8 10.8 - - - -
161A ALA* 3.6 27.3 - - + +
162A ALA 2.6 1.6 + - - -
163A LYS* 1.3 76.1 - - - +
165A ALA* 1.3 68.4 + - - +
166A GLU 3.2 1.1 - - - -
167A GLU* 3.1 22.8 + - + +
168A ALA* 3.2 14.6 + - - +
192A LEU* 3.8 24.1 - - + +
194A LYS* 5.5 7.8 + - - -
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Residues in contact with ALA 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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152A VAL* 4.3 7.2 - - + +
155A LEU* 3.8 31.7 - - + +
156A VAL* 4.4 9.0 - - + -
160A PHE* 4.3 8.7 - - + -
161A ALA 2.7 19.1 + - - +
162A ALA* 3.4 9.2 - - - +
164A GLN* 1.3 78.8 - - - +
166A GLU* 1.3 55.0 + - - +
167A GLU 3.3 0.2 + - - -
168A ALA* 3.3 5.7 + - - +
169A THR* 2.7 32.0 + - - -
192A LEU* 5.1 2.9 - - - -
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Residues in contact with GLU 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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148A ARG* 4.6 20.2 + - - +
152A VAL* 3.7 23.0 - - + +
162A ALA* 2.8 21.8 + - - +
163A LYS* 2.9 46.5 - - + +
165A ALA* 1.3 75.5 - - - +
167A GLU* 1.3 65.3 + - + +
168A ALA 3.3 0.2 - - - -
169A THR* 3.8 2.0 - - - -
170A ASP* 2.7 37.6 + - - +
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Residues in contact with GLU 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 LYS* 2.8 42.2 - - + +
164A GLN* 3.1 16.3 + - + +
166A GLU* 1.3 80.8 - - + +
168A ALA* 1.3 58.4 + - - +
170A ASP* 3.7 7.4 + - - +
171A THR* 2.8 26.5 + - - -
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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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164A GLN 3.2 10.4 + - - +
165A ALA 3.7 7.6 - - - +
167A GLU* 1.3 75.4 - - - +
169A THR* 1.3 58.8 + - - +
171A THR* 3.2 7.4 + - - -
172A VAL* 2.9 36.4 + - + +
188A ALA* 4.0 21.8 - - + +
191A LEU* 5.1 7.9 - - + -
192A LEU* 4.1 23.8 - - + -
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Residues in contact with THR 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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148A ARG* 3.9 12.6 - - + +
151A VAL* 3.6 37.0 - - + +
152A VAL* 3.4 15.8 - - + +
155A LEU* 4.0 4.0 - - - +
165A ALA 2.7 21.7 + - - -
166A GLU 3.9 4.9 - - - -
167A GLU 3.4 0.4 - - - -
168A ALA* 1.3 77.8 - - - +
170A ASP* 1.3 58.6 + - - +
172A VAL* 3.8 5.3 - - - +
173A LEU* 2.9 53.9 + - + +
184A ALA* 5.6 2.0 - - + +
188A ALA* 4.6 3.3 - - - +
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Residues in contact with ASP 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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148A ARG* 2.6 45.4 + - - +
166A GLU* 2.7 21.9 + - - +
167A GLU* 4.1 7.2 - - - +
169A THR* 1.3 75.0 - - - +
171A THR* 1.3 58.5 + - - +
173A LEU* 4.1 4.4 - - - +
174A ALA* 2.7 39.0 + - + +
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Residues in contact with THR 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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167A GLU 2.8 19.4 + - - -
168A ALA* 3.2 8.9 + - - -
170A ASP* 1.3 77.4 - - - +
172A VAL* 1.3 54.4 + - - +
174A ALA* 3.7 3.2 - - - +
175A ALA* 2.7 43.9 + - + +
191A LEU* 4.3 20.0 - - + -
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Residues in contact with VAL 172 (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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168A ALA 2.9 17.5 + - - +
169A THR* 3.8 5.2 - - - +
171A THR* 1.3 75.9 - - - +
173A LEU* 1.3 57.8 + - + +
175A ALA* 3.7 4.0 - - - +
176A ASN* 2.8 37.3 + - + +
179A ALA* 5.3 3.6 - - + -
184A ALA* 3.6 23.3 - - + +
187A SER* 3.3 27.8 - - - +
188A ALA* 3.6 28.5 - - + +
191A LEU* 3.8 15.9 - - + -
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Residues in contact with LEU 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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147A VAL* 3.4 26.9 - - + -
148A ARG* 3.7 44.9 - - + +
151A VAL* 5.8 0.2 - - + -
169A THR* 2.9 32.5 + - + +
170A ASP* 4.1 3.8 - - - +
172A VAL* 1.3 73.2 - - - +
174A ALA* 1.3 60.0 + - - +
176A ASN 2.7 28.1 - - - +
177A HIS* 3.2 21.1 + - - +
179A ALA* 4.4 6.3 - - + -
184A ALA* 4.4 14.8 - - + -
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Residues in contact with ALA 174 (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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170A ASP* 2.7 25.2 + - + +
171A THR* 3.9 3.4 - - - +
173A LEU* 1.3 72.4 - - - +
175A ALA* 1.3 62.5 + - - +
176A ASN 3.1 0.2 - - - -
177A HIS* 3.1 30.8 + - - +
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Residues in contact with ALA 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A THR* 2.7 29.5 + - + +
172A VAL* 3.8 4.5 - - - +
174A ALA* 1.3 74.0 - - - +
176A ASN* 1.3 60.4 + - + +
177A HIS* 5.0 1.5 + - - -
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Residues in contact with ASN 176 (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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172A VAL* 2.8 17.6 + - + +
173A LEU* 2.7 16.3 - - - +
174A ALA 3.1 0.2 - - - -
175A ALA* 1.3 80.2 - - + +
177A HIS* 1.3 61.9 + - - +
178A ASP* 3.3 9.1 + - - +
179A ALA* 3.0 36.2 + - + +
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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