Contacts of the helix formed by residues 159 - 174 (chain D) in PDB entry 6NR8
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 ASP 159 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156D GLU* 3.7 21.7 + - + +
157D LEU 4.6 0.2 - - - -
158D SER* 1.3 74.7 - - - +
160D ARG* 1.3 67.3 + - - +
161D GLU* 3.2 14.6 + - - +
162D THR* 2.4 33.1 + - - +
163D LEU* 3.2 25.4 + - - +
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Residues in contact with ARG 160 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158D SER 3.2 4.9 + - - -
159D ASP* 1.3 74.7 + - - +
161D GLU* 1.3 70.5 + - - +
163D LEU* 3.5 5.8 + - - -
164D LEU* 3.2 38.2 + - - +
185D PRO* 3.2 27.6 + - - +
188D VAL* 3.4 26.0 - - + +
189D ASN* 2.6 43.8 + - - +
192D MET* 4.0 32.3 - - + -
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Residues in contact with GLU 161 (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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159D ASP* 3.2 13.4 + - - +
160D ARG* 1.3 87.4 + - - +
162D THR* 1.3 64.2 + - - +
164D LEU* 3.1 35.2 + - - +
165D ASN* 2.9 40.5 + - - +
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Residues in contact with THR 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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155D VAL* 4.4 7.6 - - + -
156D GLU* 3.7 34.6 - - + +
159D ASP* 2.4 38.2 + - - +
160D ARG 3.4 0.4 - - - -
161D GLU* 1.3 77.2 - - - +
163D LEU* 1.3 60.9 + - - +
165D ASN* 3.5 8.0 + - + +
166D SER* 2.8 37.0 + - - +
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Residues in contact with LEU 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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156D GLU 3.3 22.4 - - - +
157D LEU* 3.4 37.9 - - + +
159D ASP 3.2 14.3 + - - +
160D ARG* 3.6 14.8 - - - +
161D GLU 3.2 0.4 - - - -
162D THR* 1.3 78.1 - - - +
164D LEU* 1.3 60.4 + - - +
166D SER* 4.1 3.3 - - - -
167D ALA* 3.1 27.0 + - - +
188D VAL* 4.3 16.4 - - + +
192D MET* 4.6 4.3 - - - -
195D ILE* 3.7 18.4 - - + -
412D ILE* 5.2 13.7 - - + +
415D LEU* 4.4 12.0 - - + +
416D VAL* 4.7 7.2 - - + -
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Residues in contact with LEU 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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160D ARG* 3.2 31.5 + - - +
161D GLU* 3.1 30.1 + - - +
163D LEU* 1.3 75.8 - - - +
165D ASN* 1.3 66.7 + - - +
167D ALA* 4.2 0.9 - - - +
168D THR* 3.3 30.1 + - + +
184D SER* 3.7 19.3 - - - +
185D PRO* 3.8 30.7 - - + -
188D VAL* 3.9 11.4 - - + +
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Residues in contact with ASN 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* 2.9 40.1 + - - +
162D THR* 3.5 6.7 + - - +
163D LEU 3.4 0.2 - - - -
164D LEU* 1.3 79.3 - - - +
166D SER* 1.3 62.2 + - - +
167D ALA 3.5 0.3 + - - -
168D THR* 4.0 6.8 - - - +
169D THR* 2.8 29.9 + - - +
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Residues in contact with SER 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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155D VAL* 4.3 8.0 - - - +
162D THR* 2.8 30.5 + - - +
163D LEU 4.1 2.9 - - - -
164D LEU 3.3 0.2 - - - -
165D ASN* 1.3 79.7 - - - +
167D ALA* 1.3 62.2 + - - +
169D THR* 5.0 1.1 - - - -
170D SER* 3.7 17.8 + - - -
415D LEU* 3.8 21.0 - - - +
421D LEU* 3.8 27.8 - - - +
509D VAL* 4.0 8.1 - - - +
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Residues in contact with ALA 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 LEU 3.1 18.5 + - - +
164D LEU 4.2 2.2 - - - +
165D ASN 3.3 0.2 - - - -
166D SER* 1.3 77.9 - - - +
168D THR* 1.3 60.1 + - - +
170D SER* 3.1 9.1 + - - -
171D LEU* 2.9 30.3 + - + +
184D SER* 4.3 10.1 - - - +
188D VAL* 4.9 1.3 - - + -
411D VAL* 4.2 16.8 - - + +
412D ILE* 4.1 27.6 - - + +
415D LEU* 6.2 0.9 - - + -
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Residues in contact with THR 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 LEU* 3.3 20.3 + - + +
165D ASN* 4.0 10.5 - - - +
167D ALA* 1.3 78.3 - - - +
169D THR* 1.3 58.3 + - - +
171D LEU* 3.4 12.8 - - - +
172D ASN* 2.5 55.0 + - - +
180D SER 4.8 3.1 + - - -
181D SER* 5.2 5.5 + - - -
184D SER* 3.8 20.4 - - - -
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Residues in contact with THR 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 ASN 2.8 20.3 + - - -
166D SER 4.4 0.2 - - - -
167D ALA 3.2 0.6 - - - -
168D THR* 1.3 83.0 - - - +
170D SER* 1.3 50.9 + - - +
172D ASN* 3.9 6.3 - - - +
173D SER* 2.5 36.5 + - - -
507D LEU* 3.5 39.2 - - + +
509D VAL* 3.7 23.1 - - + +
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Residues in contact with SER 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 SER 3.7 6.3 + - - -
167D ALA 3.1 9.1 + - - -
169D THR* 1.3 79.0 - - - +
171D LEU* 1.3 58.3 + - - +
173D SER* 3.0 9.3 + - - -
174D LYS* 2.9 37.9 + - - +
411D VAL* 4.5 19.5 - - - -
509D VAL* 3.2 29.7 + - - +
510D GLN* 3.3 13.2 - - - -
511D PRO* 3.9 6.3 - - - +
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Residues in contact with LEU 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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167D ALA* 2.9 21.0 + - + +
168D THR* 3.0 10.7 + - - +
170D SER* 1.3 77.2 - - - +
172D ASN* 1.3 62.3 + - - +
174D LYS* 3.5 14.5 + - + +
176D VAL* 3.3 21.8 - - + +
177D SER* 3.5 6.4 - - - -
180D SER* 4.1 24.7 - - - +
184D SER* 3.7 33.2 - - - +
407D ASP* 4.0 10.1 - - + +
408D ALA* 3.8 40.2 - - + +
411D VAL* 4.0 16.2 - - + -
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Residues in contact with ASN 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 THR* 2.5 41.1 + - - +
169D THR* 4.1 6.0 - - + +
171D LEU* 1.3 71.8 - - - +
173D SER* 1.3 63.2 + - - +
174D LYS 3.4 6.5 - - - +
177D SER* 3.4 26.8 + - - -
181D SER* 4.7 9.5 + - - +
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Residues in contact with SER 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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54D PRO* 4.6 15.8 - - - +
169D THR 2.5 24.6 + - - -
170D SER* 3.0 11.9 + - - -
172D ASN* 1.3 79.5 - - - +
174D LYS* 1.3 62.7 + - - +
495D VAL* 5.1 6.3 - - - +
507D LEU 4.2 1.7 + - - -
508D VAL* 3.7 39.5 - - - +
509D VAL 3.8 6.2 + - - -
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Residues in contact with LYS 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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54D PRO* 5.2 3.6 - - - -
104D ASP* 4.7 28.3 - - - +
105D GLY* 4.7 7.7 - - - +
170D SER* 2.9 22.9 + - - +
171D LEU* 3.5 18.9 + - + +
172D ASN 3.3 10.0 - - - +
173D SER* 1.3 85.6 - - - +
175D VAL* 1.3 69.8 + - + +
176D VAL* 4.5 9.1 - - + +
177D SER* 4.9 1.6 + - - -
407D ASP* 6.2 4.7 - - + -
411D VAL* 5.6 7.4 - - + -
510D GLN* 6.3 2.2 - - - +
514D VAL* 6.1 2.8 - - - +
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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