Contacts of the helix formed by residues 161 - 174 (chain D) 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 GLU 161 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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455B TYR* 5.5 14.4 - - + -
159D GLY* 3.2 17.8 - - - +
160D PRO* 1.3 88.6 - - - +
162D PHE* 1.3 90.4 + - + +
163D LYS* 3.1 1.6 + - - +
164D GLN* 3.7 13.5 + - - +
165D ALA* 4.5 0.9 + - - +
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Residues in contact with PHE 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158D LEU* 3.9 20.6 - - + -
159D GLY* 3.4 25.1 - - - -
161D GLU* 1.3 99.3 - - + +
163D LYS* 1.3 50.5 + - - +
164D GLN 3.1 0.4 - - - -
165D ALA* 2.7 18.3 + - + +
166D ILE* 2.6 54.0 + - + +
178D VAL* 4.8 11.2 - - + -
182D MET* 4.4 23.3 - - + -
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Residues in contact with LYS 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453B PRO* 6.1 0.4 - - - -
454B ILE* 5.5 11.7 + - - +
159D GLY* 4.6 1.1 - - - -
160D PRO* 3.0 29.1 + - + +
161D GLU 4.8 0.2 - - - +
162D PHE* 1.3 77.6 - - - +
164D GLN* 1.3 75.8 - - + +
166D ILE* 4.0 12.1 - - + +
167D GLN* 2.7 69.5 + - - +
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Residues in contact with GLN 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453B PRO* 2.6 48.1 - - + +
454B ILE 4.7 0.3 + - - -
161D GLU 3.7 9.3 + - - +
162D PHE 3.1 0.4 - - - -
163D LYS* 1.3 105.1 - - + +
165D ALA* 1.3 62.1 + - - +
167D GLN* 3.8 10.7 + - - +
168D ALA* 3.3 19.9 + - - +
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Residues in contact with ALA 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161D GLU 4.5 0.4 + - - +
162D PHE* 2.7 24.1 + - + +
164D GLN* 1.3 74.9 - - - +
166D ILE* 1.3 63.8 + - - +
168D ALA* 3.4 6.8 + - - +
169D SER* 3.3 17.3 + - - -
178D VAL* 3.3 18.0 - - + +
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Residues in contact with ILE 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158D LEU* 4.1 20.2 - - + +
159D GLY* 5.1 0.4 - - - -
162D PHE* 2.6 39.4 + - + +
163D LYS* 3.7 7.6 - - - +
165D ALA* 1.3 68.9 - - - +
167D GLN* 1.3 67.7 + - + +
169D SER* 3.2 4.3 + - - -
170D ILE* 3.0 36.5 + - + +
176D ASN* 3.0 36.1 - - + +
178D VAL* 3.2 30.5 - - + -
336D ASN* 4.6 4.3 - - - +
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Residues in contact with GLN 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163D LYS* 2.7 64.6 + - - +
164D GLN* 3.8 11.9 + - - +
166D ILE* 1.3 73.9 - - + +
168D ALA* 1.3 62.1 + - - +
170D ILE* 3.4 13.9 + - + +
171D LYS* 3.1 23.6 + - - +
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Residues in contact with ALA 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164D GLN 3.3 13.1 + - - +
165D ALA* 3.6 11.0 - - - +
166D ILE 3.2 0.2 - - - -
167D GLN* 1.3 77.9 - - - +
169D SER* 1.3 57.8 + - - +
171D LYS* 2.9 23.7 + - - +
172D GLU* 3.2 11.5 + - - +
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Residues in contact with SER 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165D ALA 3.3 7.8 + - - -
166D ILE 3.2 10.3 + - - -
168D ALA* 1.3 78.8 - - - +
170D ILE* 1.3 59.6 + - - +
172D GLU* 4.6 8.1 - - - +
173D PHE* 2.9 33.3 + - - +
175D PHE 3.5 6.7 + - - +
176D ASN 3.9 0.9 - - - -
177D MET* 3.0 42.6 + - - +
178D VAL* 3.5 11.5 - - - +
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Residues in contact with ILE 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D ILE* 3.0 31.2 + - + +
167D GLN* 3.6 15.3 - - + +
169D SER* 1.3 75.0 - - - +
171D LYS* 1.3 67.2 + - - +
174D GLY* 2.9 34.0 + - - +
175D PHE 3.6 14.8 - - - +
176D ASN* 4.1 7.9 - - + -
336D ASN* 5.1 3.4 - - - +
444D LEU* 4.5 23.1 - - + +
445D GLU 4.2 19.3 - - - +
446D GLY 5.0 4.0 - - - +
447D TRP* 4.0 2.8 - - - -
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Residues in contact with LYS 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448B GLN* 5.3 10.3 - - - +
450B ASN* 4.3 19.2 + - - +
167D GLN 3.1 12.3 + - - +
168D ALA* 2.9 12.4 + - - +
170D ILE* 1.3 77.2 - - - +
172D GLU* 1.3 59.9 + - - +
446D GLY 3.8 12.3 - - - +
447D TRP* 3.4 0.5 - - - -
448D GLN* 2.8 81.1 + - - +
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Residues in contact with GLU 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168D ALA 3.2 7.8 + - - +
169D SER* 3.9 9.0 - - - +
170D ILE 3.2 0.4 - - - -
171D LYS* 1.3 82.3 - - - +
173D PHE* 1.3 89.7 + - + +
251D LYS* 2.6 45.3 + - - +
447D TRP* 3.4 12.1 + - - -
448D GLN* 5.7 0.4 - - - -
449D GLY 5.3 0.2 + - - -
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Residues in contact with PHE 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169D SER* 2.9 19.7 + - - +
172D GLU* 1.3 113.0 - - - +
174D GLY* 1.3 62.0 + - - +
175D PHE* 3.1 15.5 + - + +
177D MET* 2.9 42.2 - - + -
217D ASN 3.8 24.5 - - - -
219D GLY* 4.0 20.6 - - - +
251D LYS* 3.8 11.0 - - + -
253D HIS* 4.5 10.3 - + - -
443D ARG* 3.5 16.8 + - - -
447D TRP* 3.6 11.0 - - - +
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Residues in contact with GLY 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170D ILE* 2.9 25.1 + - - -
173D PHE* 1.3 77.4 - - - +
175D PHE* 1.3 71.1 + - - +
443D ARG* 3.8 3.1 - - - -
444D LEU* 3.1 26.2 + - - +
447D TRP* 3.5 28.0 - - - -
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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