Contacts of the helix formed by residues 162 - 174 (chain F) in PDB entry 6IWQ
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 PHE 162 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158F LEU* 3.7 22.7 - - + -
159F GLY* 3.6 23.1 - - - +
160F PRO 2.9 0.4 - - - -
161F GLU* 1.3 107.3 - - + +
163F LYS* 1.3 64.1 + - - +
164F GLN 3.3 0.9 - - - -
165F ALA* 3.0 15.9 + - + +
166F ILE* 2.9 40.1 + - + +
178F VAL* 4.6 11.4 - - + -
182F MET* 4.1 22.7 - - + -
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Residues in contact with LYS 163 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159F GLY* 4.9 0.6 - - - -
160F PRO* 3.1 23.6 + - + +
161F GLU 3.2 0.8 + - - -
162F PHE* 1.3 76.3 - - - +
164F GLN* 1.3 81.7 + - + +
166F ILE* 4.0 7.5 - - - +
167F GLN* 2.7 54.0 + - - +
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Residues in contact with GLN 164 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161F GLU 4.4 5.2 + - - +
162F PHE 3.3 0.6 - - - -
163F LYS* 1.3 106.3 + - + +
165F ALA* 1.3 58.3 + - - +
167F GLN* 3.6 10.4 - - - +
168F ALA* 2.8 28.6 + - - +
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Residues in contact with ALA 165 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162F PHE* 3.0 18.2 + - + +
164F GLN* 1.3 77.8 - - - +
166F ILE* 1.3 57.9 + - - +
168F ALA* 3.1 8.0 + - - +
169F SER* 2.5 33.7 + - - -
178F VAL* 3.7 13.8 - - + +
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Residues in contact with ILE 166 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158F LEU* 3.9 14.8 - - + -
159F GLY* 5.2 1.8 - - - +
162F PHE* 2.9 34.5 + - + +
163F LYS* 4.0 5.6 - - - +
165F ALA* 1.3 74.0 - - - +
167F GLN* 1.3 58.2 + - - +
169F SER* 3.1 6.7 + - - -
170F ILE* 2.8 44.5 + - + +
176F ASN* 2.4 60.3 - - + +
178F VAL* 3.6 18.2 - - + -
336F ASN* 4.6 2.9 - - - +
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Residues in contact with GLN 167 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163F LYS* 2.7 40.3 + - + +
164F GLN* 3.6 12.7 - - - +
166F ILE* 1.3 77.5 - - - +
168F ALA* 1.3 64.1 + - - +
170F ILE* 3.4 13.6 + - - +
171F LYS* 3.3 30.5 + - - +
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Residues in contact with ALA 168 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164F GLN 2.8 15.5 + - - +
165F ALA* 3.1 11.6 + - - +
167F GLN* 1.3 76.7 - - - +
169F SER* 1.3 63.9 + - - +
171F LYS* 3.0 20.7 + - - +
172F GLU* 3.1 11.1 + - - +
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Residues in contact with SER 169 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165F ALA 2.5 25.2 + - - -
166F ILE* 3.1 5.2 + - - -
168F ALA* 1.3 74.9 - - - +
170F ILE* 1.3 57.6 + - - +
172F GLU* 3.2 7.2 + - - +
173F PHE* 2.8 31.8 + - - -
175F PHE 3.5 5.7 - - - +
177F MET* 3.6 32.8 - - - -
178F VAL* 3.0 17.6 - - - +
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Residues in contact with ILE 170 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166F ILE* 2.8 44.6 + - + +
167F GLN* 3.8 13.2 - - - +
169F SER* 1.3 76.2 - - - +
171F LYS* 1.3 60.0 + - - +
174F GLY* 2.4 36.8 + - - +
175F PHE 3.4 16.6 - - - +
176F ASN* 4.7 0.7 - - + -
336F ASN* 5.1 2.0 - - - +
444F LEU* 3.4 37.5 - - + -
445F GLU 3.7 23.8 - - - +
446F GLY 4.9 0.7 - - - -
447F TRP* 3.6 5.0 - - - +
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Residues in contact with LYS 171 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167F GLN* 3.3 19.2 + - - +
168F ALA* 3.0 13.8 + - - +
170F ILE* 1.3 81.4 - - - +
172F GLU* 1.3 62.6 + - - +
446F GLY 3.8 18.6 - - - +
447F TRP* 3.5 1.0 - - - -
448F GLN* 3.4 34.7 + - + +
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Residues in contact with GLU 172 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168F ALA 3.1 8.7 + - - +
169F SER* 3.2 5.1 + - - +
171F LYS* 1.3 81.2 - - - +
173F PHE* 1.3 109.9 + - + +
251F LYS* 4.2 27.1 + - - +
253F HIS* 5.2 1.6 + - - -
447F TRP* 3.5 11.3 + - - -
448F GLN 5.1 0.7 - - - +
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Residues in contact with PHE 173 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169F SER* 2.8 19.0 + - - +
172F GLU* 1.3 123.5 - - + +
174F GLY* 1.3 58.7 + - - +
175F PHE* 3.0 19.8 + - + +
177F MET* 3.5 33.7 - - + -
217F ASN 3.4 26.0 - - - -
218F GLU* 4.3 2.0 - - - +
219F GLY* 3.7 24.2 - - - +
251F LYS* 4.6 5.2 - - - -
253F HIS* 4.3 16.4 - + - -
443F ARG* 3.8 18.5 + - - -
447F TRP* 3.5 10.6 + - - +
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Residues in contact with GLY 174 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170F ILE* 2.4 37.3 + - - -
173F PHE* 1.3 68.3 - - - +
175F PHE* 1.3 65.8 + - - +
443F ARG* 3.4 6.4 - - - +
444F LEU* 3.1 29.9 + - - +
447F TRP* 3.3 23.3 - - - -
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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