Contacts of the helix formed by residues 165 - 174 (chain D) in PDB entry 5A0Q
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 ALA 165 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31D THR* 3.2 28.3 - - + -
160D ALA* 3.4 18.4 - - + +
161D ILE 3.4 2.7 - - - -
162D GLY 3.2 32.0 + - - +
163D ARG 3.1 3.4 + - - -
164D GLY* 1.3 75.4 - - - +
166D LYS* 1.3 59.8 + - + +
168D VAL* 3.2 4.7 + - - +
169D ARG* 2.8 29.8 + - - +
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Residues in contact with LYS 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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27D LYS* 4.1 37.0 - - + +
160D ALA 5.3 1.3 - - - +
161D ILE* 6.3 0.4 - - - -
162D GLY 4.5 10.8 - - - +
164D GLY* 3.2 2.2 - - - +
165D ALA* 1.3 79.1 - - + +
167D SER* 1.3 57.8 + - - +
169D ARG* 3.1 44.9 + - - +
170D GLU* 3.1 30.2 + - - +
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Residues in contact with SER 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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164D GLY* 3.5 17.3 + - - -
165D ALA 3.3 0.2 - - - -
166D LYS* 1.3 77.9 - - - +
168D VAL* 1.4 57.0 + - - +
170D GLU* 3.5 10.9 + - - +
171D PHE* 3.0 26.0 + - - +
198D VAL* 4.5 14.7 - - - +
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Residues in contact with VAL 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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31D THR* 4.5 5.2 - - + -
33D VAL* 4.1 10.5 - - + -
160D ALA* 3.8 21.8 - - + -
164D GLY 3.4 9.7 + - - +
165D ALA* 3.2 12.1 + - - +
167D SER* 1.4 74.0 - - - +
169D ARG* 1.4 59.6 + - - +
170D GLU 3.3 0.2 - - - -
171D PHE* 3.2 6.6 + - - +
172D LEU* 2.8 29.8 + - + +
194D ALA* 3.3 45.1 - - + +
195D LEU* 4.2 9.2 - - + -
198D VAL* 4.0 15.3 - - + -
199D VAL* 4.3 4.5 - - + -
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Residues in contact with ARG 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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156D TRP* 4.8 18.2 - - - -
159D ASN* 3.2 29.2 - - - +
160D ALA* 3.5 31.8 + - + +
165D ALA 2.8 10.2 + - - +
166D LYS* 3.1 54.9 + - - +
168D VAL* 1.4 75.1 - - - +
170D GLU* 1.4 57.8 + - - +
172D LEU* 3.2 12.5 + - - +
173D GLU* 2.8 54.1 + - - +
56E SER* 4.9 6.3 + - - -
58E LEU* 4.5 2.7 - - + +
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Residues in contact with GLU 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 LYS 3.1 13.6 + - - +
167D SER* 3.7 11.3 - - - +
168D VAL 3.3 0.2 - - - -
169D ARG* 1.4 82.0 - - - +
171D PHE* 1.4 59.7 + - - +
173D GLU* 3.2 31.3 + - - +
174D LYS* 3.3 18.7 + - - +
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Residues in contact with PHE 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 SER 3.0 15.9 + - - +
168D VAL* 3.3 12.6 - - - +
170D GLU* 1.4 71.5 - - - +
172D LEU* 1.3 67.0 + - + +
174D LYS* 3.4 29.6 - - - +
175D ASN* 3.0 46.6 + - - +
193D LYS* 3.8 31.0 - - + -
194D ALA* 3.6 36.3 - - + -
197D GLU* 3.1 40.4 - - + -
198D VAL* 4.0 15.9 - - + -
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Residues in contact with LEU 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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33D VAL* 4.1 22.0 - - + -
34D GLY 4.5 1.6 - - - +
35D VAL* 4.2 15.9 - - + -
158D ALA* 4.2 11.0 - - + -
159D ASN* 4.8 6.1 - - - +
160D ALA* 5.0 0.9 - - + -
168D VAL* 2.8 22.1 + - + +
169D ARG* 3.3 13.0 - - - +
171D PHE* 1.3 80.3 - - + +
173D GLU* 1.3 55.7 - - - +
175D ASN* 2.9 5.1 + - + -
176D TYR* 2.7 39.5 + - + +
190D LEU* 3.0 39.3 - - + +
193D LYS* 6.1 0.9 - - - -
194D ALA* 4.4 13.5 - - + -
58E LEU* 4.1 10.3 - - + -
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Residues in contact with GLU 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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156D TRP* 6.0 0.7 - - - -
169D ARG* 2.8 46.9 + - - +
170D GLU* 3.2 26.7 + - + +
172D LEU* 1.3 75.5 - - - +
174D LYS* 1.4 58.6 + - - +
176D TYR* 4.0 10.5 + - - +
57E PRO* 3.9 32.7 - - + +
58E LEU* 3.8 23.9 - - + +
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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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170D GLU 3.3 10.0 + - - +
171D PHE* 3.4 49.4 - - - +
173D GLU* 1.4 76.6 - - - +
175D ASN* 1.3 69.4 + - - +
176D TYR 3.7 0.7 - - - -
197D GLU* 5.5 2.2 + - - -
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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