Contacts of the helix formed by residues 179 - 188 (chain D) in PDB entry 3E5X
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 SER 179 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177D PRO 4.0 1.8 - - - -
178D LEU* 1.3 77.3 - - - +
180D GLN* 1.3 64.7 + - - +
181D LYS* 3.5 14.4 - - - +
182D SER* 2.8 35.5 + - - -
183D ILE* 3.1 22.9 + - - +
209D LYS* 5.1 0.2 - - - -
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Residues in contact with GLN 180 (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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178D LEU 3.9 0.2 + - - -
179D SER* 1.3 74.6 - - - +
181D LYS* 1.3 63.0 + - - +
183D ILE* 3.5 5.9 + - - +
184D GLY* 2.9 19.2 + - - -
191D HIS* 4.4 5.7 - - + +
194D VAL* 3.8 14.7 - - + +
195D SER* 2.8 39.8 + - - +
198D LEU* 3.4 34.7 - - + +
209D LYS* 4.7 5.9 - - + +
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Residues in contact with LYS 181 (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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62D LYS* 5.8 2.4 - - - +
77D TYR* 5.3 2.9 + - - +
179D SER* 3.2 14.5 + - - +
180D GLN* 1.3 79.0 - - - +
182D SER* 1.3 61.7 + - - +
184D GLY* 3.1 4.9 + - - +
185D GLU* 2.9 57.2 + - + +
191D HIS* 6.3 3.1 - - - -
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Residues in contact with SER 182 (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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77D TYR* 5.3 4.8 + - - -
178D LEU* 4.7 6.5 - - - -
179D SER* 2.8 30.4 + - - -
180D GLN 3.3 0.2 - - - -
181D LYS* 1.3 75.9 - - - +
183D ILE* 1.3 56.2 + - - +
185D GLU* 3.0 19.1 + - - +
186D ILE* 2.8 51.6 + - - +
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Residues in contact with ILE 183 (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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153D ILE* 4.2 22.2 - - + -
156D LEU* 4.6 7.4 - - + -
157D PHE* 3.9 15.3 - - + -
178D LEU* 3.6 32.3 - - + +
179D SER 3.1 17.6 + - - +
180D GLN* 3.6 6.3 - - - +
182D SER* 1.3 74.1 - - - +
184D GLY* 1.3 52.4 + - - +
186D ILE* 4.5 6.9 - - - +
187D THR* 2.4 52.9 + - + +
194D VAL* 4.0 18.2 - - + -
198D LEU* 4.1 9.6 - - + -
209D LYS* 3.8 23.8 - - + -
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Residues in contact with GLY 184 (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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180D GLN 2.9 14.8 + - - -
181D LYS* 3.1 7.2 + - - -
183D ILE* 1.3 75.0 - - - +
185D GLU* 1.3 51.7 + - - +
187D THR* 4.2 0.2 - - - -
188D GLY* 2.6 38.1 + - - -
189D VAL 3.3 20.2 + - - -
190D HIS 5.7 0.2 - - - -
191D HIS* 5.8 1.3 - - - -
194D VAL* 4.1 6.2 - - - +
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Residues in contact with GLU 185 (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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145C ASN* 4.7 5.7 + - - -
62D LYS* 3.9 14.6 + - - -
74D LEU* 3.8 37.7 - - + +
77D TYR* 3.2 28.1 + - - -
181D LYS* 2.9 44.2 + - + +
182D SER* 3.0 18.3 + - - +
184D GLY* 1.3 72.9 - - - +
186D ILE* 1.3 63.2 + - + +
188D GLY* 3.5 7.6 + - - -
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Residues in contact with ILE 186 (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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141C VAL* 5.8 1.6 - - - +
145C ASN* 5.5 1.4 + - - -
14D ILE 4.7 7.9 - - - +
15D ILE* 4.0 18.4 - - + -
16D PRO* 3.7 24.9 - - + -
74D LEU* 5.2 4.0 - - + -
136D TYR* 3.9 18.7 + - - +
140D GLN* 3.4 20.4 + - - +
156D LEU* 4.3 16.8 - - + -
178D LEU* 4.0 26.0 - - + -
182D SER* 2.8 28.4 + - - +
183D ILE* 4.1 3.8 - - - +
185D GLU* 1.3 75.2 - - + +
187D THR* 1.3 67.0 + - + +
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Residues in contact with THR 187 (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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145C ASN* 4.4 3.3 + - - +
140D GLN* 4.0 8.7 + - - +
143D GLU* 5.8 1.3 - - - +
144D MET* 4.9 0.9 - - - +
152D ARG* 2.3 54.8 + - + +
153D ILE* 4.1 14.7 - - + +
156D LEU* 3.9 26.7 - - + -
183D ILE* 2.4 34.5 + - + +
186D ILE* 1.3 77.6 - - + +
188D GLY* 1.3 57.7 + - - +
189D VAL* 3.2 27.4 + - - +
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Residues in contact with GLY 188 (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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145C ASN* 3.5 34.8 - - - +
152D ARG* 5.0 2.2 - - - -
184D GLY 2.6 20.0 + - - -
185D GLU* 3.5 3.9 + - - -
186D ILE 3.2 3.6 + - - -
187D THR* 1.3 73.0 - - - +
189D VAL* 1.3 60.6 + - - +
190D HIS* 3.7 12.1 + - - -
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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