Contacts of the helix formed by residues 162 - 174 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B LEU* 3.7 22.4 - - + -
159B GLY* 3.5 18.4 - - - +
160B PRO 3.0 0.6 - - - -
161B GLU* 1.3 111.6 - - + +
163B LYS* 1.3 61.3 + - - +
164B GLN 3.3 2.0 - - - -
165B ALA* 3.0 13.5 + - + +
166B ILE* 2.8 46.0 + - + +
178B VAL* 4.5 8.7 - - + -
182B MET* 3.9 15.5 - - + -
455C TYR* 4.0 22.7 - + + -
456C VAL* 3.2 36.3 - - + -
657C VAL* 5.0 9.6 - - + -
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Residues in contact with LYS 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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159B GLY* 4.5 1.5 - - - -
160B PRO* 3.0 31.8 + - + +
161B GLU 3.2 0.4 - - - -
162B PHE* 1.3 77.6 - - - +
164B GLN* 1.3 78.9 + - - +
166B ILE* 3.5 8.6 + - - +
167B GLN* 3.2 50.5 + - - +
454D ILE* 3.6 27.9 + - - +
457D GLY* 4.6 15.2 - - - -
565D MET* 6.3 2.7 - - + -
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Residues in contact with GLN 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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160B PRO 4.7 0.2 + - - -
161B GLU 4.7 4.5 + - - +
162B PHE 3.3 0.4 - - - -
163B LYS* 1.3 94.8 - - - +
165B ALA* 1.3 62.6 + - - +
167B GLN* 3.6 17.7 + - - +
168B ALA* 3.3 21.1 + - - +
455C TYR* 5.6 6.5 - - + +
451D PRO 5.8 1.4 + - - -
453D PRO* 3.5 43.8 - - + +
454D ILE 4.9 1.0 + - - +
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Residues in contact with ALA 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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161B GLU 5.3 0.4 + - - -
162B PHE* 3.0 18.0 + - + +
164B GLN* 1.3 80.9 - - - +
166B ILE* 1.3 61.2 - - + +
168B ALA* 3.4 7.5 + - - +
169B SER* 3.3 17.3 + - - -
178B VAL* 3.5 19.1 - - + +
455C TYR* 5.1 17.7 - - + -
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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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158B LEU* 3.9 24.7 - - + -
159B GLY* 5.1 2.2 - - - +
162B PHE* 2.8 38.8 + - + +
163B LYS* 3.8 7.0 - - - +
164B GLN 3.3 0.2 - - - -
165B ALA* 1.3 74.1 - - - +
167B GLN* 1.3 67.6 + - + +
169B SER* 3.2 4.3 + - - -
170B ILE* 3.0 35.6 + - + +
176B ASN* 3.0 37.7 - - + +
178B VAL* 3.5 19.7 - - + -
336B ASN* 4.6 2.9 - - - +
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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 LYS* 3.2 43.1 + - - +
164B GLN* 4.0 19.3 + - - +
166B ILE* 1.3 79.6 - - + +
168B ALA* 1.3 62.3 + - - +
170B ILE* 3.4 13.8 + - + +
171B LYS* 3.1 24.6 + - - +
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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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164B GLN 3.3 12.0 + - - +
165B ALA* 3.5 11.7 - - - +
166B ILE 3.2 0.4 - - - -
167B GLN* 1.3 76.8 - - - +
169B SER* 1.3 59.2 + - - +
171B LYS* 2.8 28.0 + - - +
172B GLU* 3.0 11.1 + - - +
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Residues in contact with SER 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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165B ALA 3.3 8.3 + - - -
166B ILE 3.2 10.1 + - - -
168B ALA* 1.3 78.2 - - - +
170B ILE* 1.3 59.1 + - - +
172B GLU* 3.1 8.4 + - - +
173B PHE* 2.8 32.6 + - - -
175B PHE 3.4 6.1 + - - +
176B ASN 3.8 0.3 - - - -
177B MET* 2.9 41.8 + - - +
178B VAL* 3.6 11.7 + - - +
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Residues in contact with ILE 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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166B ILE* 3.0 31.5 + - + +
167B GLN* 3.6 14.4 - - + +
168B ALA 3.1 0.2 - - - -
169B SER* 1.3 77.5 - - - +
171B LYS* 1.3 59.0 + - - +
174B GLY* 2.7 35.5 + - - +
175B PHE 3.5 17.3 - - - +
176B ASN* 4.0 3.8 - - + -
336B ASN* 5.1 2.2 - - - +
444B LEU* 3.7 29.2 - - + -
445B GLU 3.7 23.3 - - - +
446B GLY* 4.3 4.7 - - - -
447B TRP* 3.8 4.3 - - - -
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Residues in contact with LYS 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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167B GLN 3.1 13.0 + - - +
168B ALA* 2.8 16.4 + - - +
170B ILE* 1.3 77.2 - - - +
172B GLU* 1.3 59.5 + - - +
446B GLY 3.7 11.0 + - - +
447B TRP* 3.3 14.7 + - - -
448B GLN* 3.1 47.9 + - + +
448D GLN* 5.5 7.9 + - - +
450D ASN* 3.7 23.4 + - - +
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Residues in contact with GLU 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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168B ALA 3.0 10.9 + - - +
169B SER* 3.1 6.1 + - - +
171B LYS* 1.3 76.9 - - - +
173B PHE* 1.3 92.2 + - + +
251B LYS* 3.2 42.4 + - - +
253B HIS* 5.4 1.2 + - - -
447B TRP* 3.4 10.9 + - - -
448B GLN 5.6 0.2 - - - +
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Residues in contact with PHE 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B SER* 2.8 15.5 + - - +
172B GLU* 1.3 119.5 - - + +
174B GLY* 1.3 62.3 + - - +
175B PHE* 3.0 16.3 + - + +
177B MET* 3.4 35.9 - - + -
217B ASN 3.6 18.2 - - - -
218B GLU* 4.2 0.4 - - - -
219B GLY* 3.6 33.7 - - - -
251B LYS* 3.8 11.4 - - - -
253B HIS* 4.4 10.3 - + - -
443B ARG* 3.5 18.5 + - - -
447B TRP* 3.5 13.0 - - - +
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Residues in contact with GLY 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 ILE* 2.7 33.7 + - - -
173B PHE* 1.3 71.3 - - - +
175B PHE* 1.3 67.0 + - - +
443B ARG* 3.9 5.0 - - - -
444B LEU* 3.0 30.9 + - - +
447B TRP* 3.5 22.3 - - - -
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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