Contacts of the helix formed by residues 179 - 188 (chain D) in PDB entry 4CEV
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 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 LEU 3.9 0.9 + - - +
178D ASP* 1.3 72.5 - - - +
180D GLY* 1.3 63.9 - - - +
182D LYS* 3.2 37.2 + - - +
183D LYS* 3.1 22.9 + - - +
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Residues in contact with GLY 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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127D VAL 5.6 0.4 - - - -
128D ASN* 5.0 0.4 - - - -
132D THR* 4.0 32.3 + - - +
178D ASP* 3.2 3.0 - - - +
179D GLU* 1.3 79.6 - - - +
181D GLU* 1.3 56.2 + - - +
183D LYS* 3.4 11.5 + - - +
184D PHE* 2.9 27.6 + - - +
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Residues in contact with GLU 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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404A ORN 3.3 10.8 + - - -
125D GLY* 3.7 2.7 + - - -
126D ASP* 3.1 13.7 + - - -
127D VAL* 3.0 44.6 + - + +
128D ASN* 3.2 30.2 + - - +
140D GLY 4.4 0.3 - - - +
176D SER 4.5 0.7 - - - +
177D LEU* 3.8 13.9 - - + -
178D ASP* 2.9 42.0 + - + +
180D GLY* 1.3 76.5 - - - +
182D LYS* 1.3 59.5 + - - +
184D PHE* 3.5 2.8 - - - +
185D ILE* 2.9 35.5 + - - +
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Residues in contact with LYS 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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177D LEU* 3.8 30.6 + - + +
178D ASP 2.9 13.5 + - - +
179D GLU* 3.2 39.0 + - - +
181D GLU* 1.3 75.5 - - - +
183D LYS* 1.3 57.9 + - - +
186D ARG* 3.0 34.6 + - - +
297F LYS 3.3 18.8 + - - +
298F LEU 3.5 21.8 - - - -
299F MET* 3.3 37.4 + - - +
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Residues in contact with LYS 183 (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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179D GLU 3.1 9.2 + - - +
180D GLY* 3.4 12.8 - - - +
182D LYS* 1.3 77.3 - - - +
184D PHE* 1.3 58.9 + - - +
186D ARG* 3.2 35.6 + - - +
187D GLU* 2.9 67.3 + - - +
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Residues in contact with PHE 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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127D VAL* 3.7 28.5 - - + +
129D THR* 5.4 4.9 - - + -
144D ALA* 4.0 14.8 - - + -
147D LEU* 3.6 20.4 - - + -
149D PHE* 3.8 32.5 - + + -
180D GLY 2.9 17.2 + - - +
181D GLU* 3.5 9.2 - - - +
183D LYS* 1.3 76.3 - - - +
185D ILE* 1.3 56.2 + - - +
187D GLU* 4.9 2.7 - - - -
188D LYS* 2.8 75.3 + - + +
190D ILE* 3.6 22.0 - - + -
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Residues in contact with ILE 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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127D VAL* 4.1 15.0 - - + -
171D LEU* 3.8 22.9 - - + -
177D LEU* 3.5 42.4 - - + -
181D GLU 2.9 18.1 + - - +
184D PHE* 1.3 76.7 - - - +
186D ARG* 1.3 63.5 + - - +
189D GLY* 3.1 3.5 + - - -
190D ILE* 3.1 58.7 + - + +
192D ILE* 3.8 14.6 - - + -
299F MET* 3.3 20.9 - - + -
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Residues in contact with ARG 186 (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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182D LYS* 3.0 21.0 + - - +
183D LYS* 3.2 46.8 - - - +
185D ILE* 1.3 80.3 - - - +
187D GLU* 1.3 89.7 + - - +
189D GLY* 3.3 9.7 + - - -
299F MET* 3.4 15.0 - - + +
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Residues in contact with GLU 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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183D LYS* 2.9 58.2 + - - +
184D PHE* 4.1 3.3 - - - +
186D ARG* 1.3 90.0 + - - +
188D LYS* 1.3 68.6 + - + +
189D GLY* 3.0 5.9 + - - -
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Residues in contact with LYS 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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149D PHE* 3.4 35.4 - - + -
166D PRO* 3.2 28.6 - - + +
167D GLU* 5.1 0.3 + - - -
184D PHE* 2.8 67.3 + - + +
187D GLU* 1.3 80.3 + - + +
189D GLY* 1.3 63.5 + - - +
190D ILE* 4.0 15.7 - - + -
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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