Contacts of the helix formed by residues 160 - 171 (chain A) in PDB entry 2Q5H
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 160 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147A PHE* 2.8 41.2 + - + +
148A MET 4.2 1.6 - - - +
149A VAL* 4.5 8.3 - - - +
158A PHE 3.4 4.2 + - - -
159A ARG* 1.3 69.8 - - - +
161A ASP* 1.3 66.6 + - - +
163A LEU* 3.0 5.8 + - - +
164A LEU* 2.8 26.4 + - - +
200A LEU* 4.1 19.3 - - + -
204A PHE* 4.1 12.8 - - + -
221A PRO* 4.6 2.5 - - + -
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Residues in contact with ASP 161 (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 ASP* 5.5 0.2 - - - +
147A PHE* 5.3 4.0 - - + +
159A ARG* 2.7 52.3 + - - +
160A ALA* 1.3 76.8 - - - +
162A HIS* 1.3 68.2 + - - -
164A LEU* 3.5 5.0 + - - +
165A LYS* 2.9 27.1 + - - +
192A LEU* 3.6 33.3 - - + +
193A ASP* 4.1 15.3 - - - +
200A LEU* 5.4 5.2 - - + -
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Residues in contact with HIS 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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158A PHE* 6.0 0.7 - - + -
159A ARG* 3.4 56.5 + - + +
160A ALA 3.3 0.4 - - - -
161A ASP* 1.3 82.8 + - - +
163A LEU* 1.3 66.2 + - + +
165A LYS* 3.7 18.1 - - + +
166A ALA* 3.1 24.3 + - - +
281A SER* 5.2 8.5 + - - -
283A ARG* 3.5 33.0 + - - +
288A ARG* 5.7 6.9 - - - -
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Residues in contact with LEU 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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149A VAL* 4.4 3.1 - - + -
158A PHE* 4.3 18.2 - - + -
159A ARG 3.2 17.7 + - - +
160A ALA* 3.0 2.8 + - - +
162A HIS* 1.3 83.5 + - + +
164A LEU* 1.3 65.3 + - - +
166A ALA* 3.2 20.7 - - + +
167A HIS* 3.3 7.2 + - + +
204A PHE* 4.0 8.1 - - + -
209A VAL* 3.6 28.7 - - + -
210A LYS 4.3 3.1 - - - +
212A PRO* 3.6 37.5 - - + -
218A LEU* 3.7 17.7 - - + -
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Residues in contact with LEU 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 ALA 2.8 16.0 + - - +
161A ASP* 3.6 4.3 - - - +
163A LEU* 1.3 78.8 - - - +
165A LYS* 1.3 61.2 - - - +
167A HIS* 2.8 27.2 + - - +
168A LEU* 3.1 43.8 + - + -
188A VAL* 5.0 5.4 - - + -
189A LEU* 4.6 0.7 - - + -
192A LEU* 3.8 26.2 - - + -
200A LEU* 5.0 6.3 - - + -
203A LEU* 4.5 17.5 - - + +
204A PHE* 3.8 20.4 - - + -
207A TYR* 5.1 2.0 - - + -
209A VAL* 3.8 25.1 - - + -
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Residues in contact with LYS 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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161A ASP 2.9 18.3 + - - +
162A HIS* 3.7 17.9 - - + +
164A LEU* 1.3 76.1 - - - +
166A ALA* 1.3 56.4 + - - +
168A LEU* 3.4 3.1 + - - +
169A GLN* 2.7 65.0 + - - +
189A LEU* 4.0 29.3 - - + +
192A LEU* 3.9 15.3 - - + -
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Residues in contact with ALA 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 HIS 3.1 15.0 + - - +
163A LEU* 3.2 19.7 - - + +
164A LEU 3.0 0.6 + - - -
165A LYS* 1.3 72.7 - - - +
167A HIS* 1.3 64.3 + - - +
169A GLN* 3.3 20.6 + - - +
170A LYS* 3.5 17.1 + - - +
212A PRO* 6.4 0.7 - - + -
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Residues in contact with HIS 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 LEU 3.3 7.4 + - - +
164A LEU* 2.8 17.9 + - - +
166A ALA* 1.3 73.9 - - - +
168A LEU* 1.3 58.4 + - + +
169A GLN 3.1 5.4 + - - -
170A LYS* 3.2 10.6 + - + +
171A LEU* 3.2 59.0 + - + +
207A TYR* 3.1 31.2 + - - +
208A ASN 3.7 10.9 + - - -
209A VAL* 4.3 25.0 - - + +
210A LYS* 4.5 10.9 + - + +
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Residues in contact with LEU 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 LEU* 3.1 43.5 + - + +
165A LYS 3.4 2.9 + - - +
166A ALA 3.4 0.2 - - - -
167A HIS* 1.3 73.9 - - - +
169A GLN* 1.3 58.2 + - - +
171A LEU* 4.3 9.0 - - + -
172A MET* 3.1 33.0 - - - +
185A MET* 4.0 17.4 - - + +
188A VAL* 3.9 26.0 - - + -
189A LEU* 3.8 22.2 - - + +
207A TYR* 3.4 46.9 - - + -
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Residues in contact with GLN 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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165A LYS* 2.7 61.5 + - - +
166A ALA* 3.6 11.7 - - - +
167A HIS 3.1 1.2 + - - -
168A LEU* 1.3 81.3 - - - +
170A LYS* 1.3 63.0 + - - +
172A MET* 3.8 9.2 - - + -
173A SER* 3.1 30.5 + - - +
189A LEU* 4.3 12.1 - - + +
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Residues in contact with LYS 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 ALA 3.5 14.1 + - - +
167A HIS* 3.2 9.8 + - + +
169A GLN* 1.3 76.9 - - - +
171A LEU* 1.3 65.9 + - + +
173A SER* 2.8 26.9 - - - +
174A ASP* 3.7 4.9 - - - +
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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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167A HIS* 3.2 45.8 + - + +
168A LEU* 4.3 3.6 - - + -
170A LYS* 1.3 80.8 - - + +
172A MET* 1.3 66.3 + - - +
173A SER 3.5 0.3 + - - -
174A ASP* 3.7 9.0 - - - +
177A CYS* 3.6 26.2 - - - +
181A LYS* 6.0 1.6 - - - -
185A MET* 3.6 16.6 - - + -
207A TYR* 4.2 25.1 - - + +
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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