Contacts of the helix formed by residues 167 - 179 (chain D) in PDB entry 5BOU
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 GLY 167 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28D THR* 3.4 17.0 + - - -
165D GLY 3.3 0.8 - - - -
166D SER* 1.3 80.5 + - - +
168D SER* 1.3 58.3 + - - +
169D GLU* 3.6 3.1 - - - -
170D GLY* 3.8 2.9 + - - -
171D ALA* 3.1 31.4 + - - +
199D VAL* 3.6 24.4 - - - +
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Residues in contact with SER 168 (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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24D LYS* 6.0 1.7 - - - +
163D ALA* 3.5 31.2 - - - +
164D ILE* 3.8 10.5 - - - -
165D GLY 3.1 19.6 + - - -
166D SER 3.4 2.5 + - - -
167D GLY* 1.3 75.4 - - - +
169D GLU* 1.3 61.1 + - - +
171D ALA* 3.1 1.4 + - - +
172D GLN* 2.6 38.8 + - - +
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Residues in contact with GLU 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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166D SER 4.1 14.7 - - - +
167D GLY* 4.4 1.6 - - - -
168D SER* 1.3 85.4 + - - +
170D GLY* 1.3 65.6 + - - +
172D GLN* 4.1 6.0 - - - +
173D ALA* 3.3 23.0 + - - +
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Residues in contact with GLY 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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167D GLY 3.8 3.4 + - - -
168D SER 3.3 0.2 - - - -
169D GLU* 1.3 87.3 + - - +
171D ALA* 1.3 62.5 + - - +
173D ALA* 3.7 5.5 + - - +
174D GLU* 3.3 22.0 + - - +
198D GLN* 5.4 2.0 + - - -
199D VAL* 4.7 8.5 - - - -
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Residues in contact with ALA 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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28D THR* 5.1 0.7 - - + -
30D ILE* 4.4 5.4 - - + -
163D ALA* 3.5 22.2 - - + -
167D GLY 3.1 21.7 + - - +
168D SER 3.6 0.2 - - - +
170D GLY* 1.3 75.4 - - - +
172D GLN* 1.3 58.8 + - - +
174D GLU* 3.1 4.0 + - - +
175D LEU* 2.8 33.0 + - + +
195D ILE* 3.5 27.4 - - + +
199D VAL* 4.3 6.4 - - + +
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Residues in contact with GLN 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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159D TYR* 4.0 1.6 - - - -
161D ALA 3.4 20.2 + - - -
162D LYS* 3.4 20.6 - - - +
163D ALA* 2.9 30.8 + - - +
168D SER 2.6 21.7 + - - +
169D GLU* 4.1 6.3 - - - +
170D GLY 3.4 0.2 - - - -
171D ALA* 1.3 70.4 - - - +
173D ALA* 1.3 60.9 + - - +
175D LEU* 3.3 7.9 + - - +
176D LEU* 2.9 34.8 + - + +
53E ASP* 3.0 29.3 + - - +
55E LEU* 3.8 11.5 - - - +
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Residues in contact with ALA 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 GLU 3.3 16.2 + - - +
170D GLY* 3.8 7.0 - - - +
172D GLN* 1.3 78.7 - - - +
174D GLU* 1.3 61.0 + - - +
176D LEU* 3.3 22.3 - - - +
177D ASN* 3.5 17.1 + - - -
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Residues in contact with GLU 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 GLY 3.3 11.9 + - - +
171D ALA* 3.1 11.1 + - - +
173D ALA* 1.3 77.6 - - - +
175D LEU* 1.3 63.9 + - - +
177D ASN* 3.3 12.2 + - - +
178D GLU* 3.1 48.1 + - + +
194D LYS* 3.9 8.7 + - - +
195D ILE* 3.8 24.7 - - + -
198D GLN* 3.4 30.7 + - - +
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Residues in contact with LEU 175 (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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30D ILE* 4.2 7.4 - - + -
32D ILE* 3.7 31.4 - - + -
161D ALA* 4.0 11.0 - - + -
162D LYS 3.8 28.0 - - - +
163D ALA* 3.9 8.3 - - + +
171D ALA* 2.8 22.0 + - + +
172D GLN* 3.6 24.0 - - - +
174D GLU* 1.3 73.1 - - - +
176D LEU* 1.3 64.8 + - - +
178D GLU* 4.5 2.7 - - - +
179D TRP* 3.2 29.6 + - + +
191D LEU* 5.1 3.4 - - + -
195D ILE* 3.5 24.2 - - + -
55E LEU* 4.2 8.5 - - + +
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Residues in contact with LEU 176 (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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172D GLN* 2.9 19.2 + - + +
173D ALA* 3.3 15.9 - - - +
174D GLU 3.2 0.2 - - - -
175D LEU* 1.3 78.7 - - - +
177D ASN* 1.3 63.2 + - - +
179D TRP 4.5 6.2 + - - +
53E ASP* 4.6 18.6 - - + +
54E GLU* 3.8 28.9 - - + +
55E LEU* 3.4 32.4 - - + +
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Residues in contact with ASN 177 (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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173D ALA* 3.5 15.7 + - - +
174D GLU* 3.3 15.6 + - - +
175D LEU 3.3 0.2 - - - -
176D LEU* 1.3 81.5 - - - +
178D GLU* 1.3 66.7 + - + +
179D TRP 3.6 2.8 - - - +
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Residues in contact with GLU 178 (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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174D GLU* 3.1 40.0 + - + +
175D LEU* 3.5 3.1 + - - +
177D ASN* 1.3 83.5 - - + +
179D TRP* 1.3 64.3 + - - +
180D HIS* 3.5 16.6 + - - -
183D LEU* 4.4 2.3 - - - +
191D LEU* 3.7 44.3 - - + +
194D LYS* 3.9 18.9 + - - +
195D ILE* 5.1 1.8 - - + -
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Residues in contact with TRP 179 (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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32D ILE* 4.1 8.5 - - + -
33D ALA 3.1 23.5 + - - -
34D THR* 5.4 0.8 - - - +
160D ASN* 3.5 55.3 + - + -
161D ALA* 4.3 7.2 - - + -
175D LEU* 3.2 20.0 + - + +
176D LEU 4.6 6.6 - - - +
177D ASN 4.6 2.4 - - - +
178D GLU* 1.3 78.9 - - - +
180D HIS* 1.3 74.8 + - - +
181D SER* 3.9 27.8 - - - -
183D LEU* 3.6 23.2 - - + +
191D LEU* 4.8 2.4 - - + +
55E LEU* 4.2 20.1 - - + +
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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