Contacts of the helix formed by residues 172 - 184 (chain A) in PDB entry 5LLU
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 VAL 172 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171A GLU* 1.3 80.0 - - + +
173A LEU* 1.4 63.6 + - - +
175A CYS* 3.4 13.8 - - - +
176A PHE* 3.3 21.1 - - + -
432A VAL* 3.8 25.4 - - + +
433A ILE* 3.8 34.3 - - + +
436A THR* 3.5 35.2 - - + +
442A THR* 5.4 1.1 - - + -
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Residues in contact with LEU 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A GLU 3.4 1.4 - - - +
172A VAL* 1.4 71.4 - - - +
174A ASP* 1.4 60.2 + - - +
175A CYS 3.1 1.8 - - - -
176A PHE* 3.0 35.7 + - + +
177A LEU* 3.0 38.2 + - + +
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Residues in contact with ASP 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A GLU* 3.3 36.6 + - + +
173A LEU* 1.4 78.3 - - - +
175A CYS* 1.4 53.9 + - - +
177A LEU* 3.9 17.7 - - - +
178A ASP* 2.9 37.8 + - - +
181A ARG* 4.4 2.8 + - - -
198A THR* 3.5 27.8 - - + +
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Residues in contact with CYS 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A GLU* 3.4 15.6 + - - -
172A VAL* 3.4 15.7 - - - +
173A LEU 3.1 0.6 - - - -
174A ASP* 1.4 77.2 - - - +
176A PHE* 1.4 56.6 + - - +
178A ASP* 3.5 6.5 + - - +
179A LEU* 3.1 29.1 + - - +
429A VAL 5.7 2.2 - - - -
432A VAL* 5.0 8.5 - - - -
433A ILE* 3.8 29.8 - - + -
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Residues in contact with PHE 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A VAL* 3.3 26.2 - - + -
173A LEU* 3.0 22.7 + - + +
175A CYS* 1.4 77.5 - - + +
177A LEU* 1.3 57.2 + - + +
179A LEU* 3.6 16.6 + - + +
180A ALA* 3.1 27.5 + - - +
412A THR* 6.2 2.5 - - + -
415A ALA* 6.1 5.6 - - + -
433A ILE* 4.6 27.6 - - + -
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Residues in contact with LEU 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A LEU* 3.0 47.8 + - + +
174A ASP* 3.9 20.4 - - - +
176A PHE* 1.3 75.0 - - + +
178A ASP* 1.4 53.6 + - - +
180A ALA* 3.3 5.5 + - - +
181A ARG* 2.8 59.1 + - - +
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Residues in contact with ASP 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A ASP* 2.9 25.6 + - - +
175A CYS* 3.5 5.9 + - - +
177A LEU* 1.4 73.0 - - - +
179A LEU* 1.4 57.4 + - - +
181A ARG* 3.1 32.5 + - - +
182A ASN* 2.8 40.2 + - - +
196A TYR* 3.4 17.1 - - - +
197A SER* 3.7 8.0 + - - -
198A THR* 3.2 36.0 + - - +
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Residues in contact with LEU 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A CYS 3.1 17.7 + - - +
176A PHE* 3.7 17.3 - - + +
178A ASP* 1.4 74.7 - - - +
180A ALA* 1.4 56.2 + - - +
182A ASN* 3.1 9.3 + - - +
183A ILE* 3.0 45.3 + - + +
224A LEU* 3.8 22.5 - - + +
418A ILE* 6.5 0.7 - - + -
419A GLY* 3.9 35.2 - - - +
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Residues in contact with ALA 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A PHE 3.1 19.2 + - - +
177A LEU* 3.5 9.2 - - + +
179A LEU* 1.4 75.3 - - - +
181A ARG* 1.4 61.2 + - - +
183A ILE* 3.3 20.3 + - - +
184A PHE* 3.4 25.8 - - + -
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Residues in contact with ARG 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A ASP* 4.4 4.6 + - - -
177A LEU* 2.8 44.0 + - - +
178A ASP* 3.1 35.2 + - - +
179A LEU 3.3 0.2 - - - -
180A ALA* 1.4 70.8 - - - +
182A ASN* 1.3 58.2 + - - +
184A PHE* 2.9 31.0 - - - +
185A PRO* 3.8 2.1 - - - +
196A TYR* 3.3 42.5 + - + -
198A THR* 4.0 17.5 + - - +
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Residues in contact with ASN 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A ASP* 2.8 25.8 + - - +
179A LEU* 3.1 8.0 + - - +
181A ARG* 1.3 72.8 - - - +
183A ILE* 1.4 62.9 + - - +
184A PHE 3.2 2.5 + - - -
185A PRO* 3.4 3.0 - - - +
195A SER* 4.7 4.3 - - - -
196A TYR* 2.9 49.4 + - - +
222A ASN* 3.1 34.3 + - - +
224A LEU* 4.6 7.9 - - + -
225A GLY* 3.1 22.8 - - - -
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Residues in contact with ILE 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A LEU* 3.0 44.2 + - + +
180A ALA* 3.3 13.9 + - - +
182A ASN* 1.4 74.1 - - - +
184A PHE* 1.4 81.2 - - + +
185A PRO* 3.5 7.1 - - - +
224A LEU* 3.6 25.4 - - + -
225A GLY* 4.3 0.6 - - - +
228A VAL* 3.5 42.0 - - + +
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Residues in contact with PHE 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A ALA* 3.4 16.8 - - + +
181A ARG* 2.9 15.5 + - - +
182A ASN 3.2 0.2 - - - -
183A ILE* 1.4 100.9 - - + +
185A PRO* 1.4 64.3 - - - +
186A SER* 3.6 1.9 + - - -
228A VAL* 5.5 5.4 - - + -
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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