Contacts of the helix formed by residues 182 - 195 (chain C) in PDB entry 5YL4
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 182 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C ASN* 3.1 33.9 - - + +
180C ALA* 3.3 2.9 - - + -
181C VAL* 1.3 76.5 - - + +
183C GLU* 1.3 63.8 + - - +
184C PRO* 3.3 3.6 - - - -
185C TYR* 3.1 19.4 + - + +
186C ASN* 3.2 12.4 + - - +
398C MET* 4.5 5.2 - - - -
404C PHE* 3.5 47.6 - - + -
408C TYR* 3.4 18.6 + - + +
255D VAL* 3.9 22.4 - - + +
256D ASN* 4.9 0.4 - - - +
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Residues in contact with GLU 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C GLY* 3.4 33.5 - - - +
173C PRO* 3.2 22.9 - - + +
178C SER* 3.1 27.9 - - - -
179C THR* 3.2 12.6 + - - -
180C ALA* 3.3 24.4 + - + +
181C VAL 3.3 0.6 - - - -
182C VAL* 1.3 76.5 - - - +
184C PRO* 1.4 59.2 - - + +
186C ASN* 3.1 2.3 + - - +
187C SER* 2.7 41.2 + - - -
501C GTP 2.5 32.2 + - - -
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Residues in contact with PRO 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173C PRO* 5.7 0.7 - - + -
180C ALA 5.1 0.2 - - - +
181C VAL 3.6 9.9 - - - +
182C VAL 3.4 3.6 - - - -
183C GLU* 1.4 94.7 - - + +
185C TYR* 1.3 57.0 + - - +
187C SER* 3.6 6.0 - - - -
188C ILE* 3.0 35.9 + - - +
391C LEU* 4.2 15.3 - - + +
394C LYS* 3.7 31.6 - - + -
395C PHE* 3.8 24.2 - - - +
398C MET* 3.9 13.7 - - + -
346D PRO* 5.8 1.3 - - + -
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Residues in contact with TYR 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182C VAL* 3.1 15.9 + - + +
184C PRO* 1.3 77.7 - - - +
186C ASN* 1.3 59.3 + - - +
188C ILE* 3.9 1.2 - - - +
189C LEU* 3.0 36.3 + - - +
395C PHE* 3.7 41.0 - + - -
398C MET* 3.1 42.9 + - + +
399C TYR* 3.2 12.9 + - + -
403C ALA 2.7 29.9 + - - -
404C PHE* 4.2 6.7 - - + -
405C VAL* 3.7 20.5 - - + +
408C TYR* 3.6 26.5 - + + +
418C PHE* 3.6 17.9 - + + -
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Residues in contact with ASN 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C ASN* 3.1 26.3 + - - +
103C TYR* 3.0 30.2 + - - +
141C PHE 3.5 10.8 - - - +
142C GLY 2.8 21.2 + - - +
143C GLY 4.2 1.0 + - - -
147C SER* 3.5 18.8 - - - +
182C VAL* 3.2 10.9 + - - +
183C GLU 3.1 6.1 + - - +
185C TYR* 1.3 78.9 - - - +
187C SER* 1.3 57.7 + - - +
189C LEU* 3.9 0.9 - - - +
190C THR* 3.0 31.7 + - - +
408C TYR* 2.7 22.3 + - - -
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Residues in contact with SER 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C PHE* 3.3 32.3 + - - +
173C PRO* 3.8 11.8 - - - +
183C GLU 2.7 28.9 + - - -
184C PRO 3.6 3.6 - - - -
186C ASN* 1.3 74.5 - - - +
188C ILE* 1.3 56.2 + - - +
190C THR* 3.4 1.9 - - - +
191C THR* 2.8 37.6 + - - -
391C LEU* 3.5 27.6 - - - -
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Residues in contact with ILE 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184C PRO 3.0 23.0 + - - +
187C SER* 1.3 74.0 - - - +
189C LEU* 1.3 67.4 + - + +
191C THR* 3.9 4.3 - - - -
192C HIS* 3.0 22.9 + - - +
391C LEU* 3.9 35.4 - - + +
392C ASP* 3.3 28.9 - - - +
395C PHE* 3.6 32.8 - - + -
421C ALA* 3.7 28.5 - - + -
422C ARG* 4.0 3.6 - - - +
425C MET* 4.0 13.6 - - + +
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Residues in contact with LEU 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C TYR* 3.6 45.8 - - + -
185C TYR 3.0 26.8 + - - +
187C SER 3.4 0.2 - - - -
188C ILE* 1.3 78.5 - - + +
190C THR* 1.3 58.3 + - - +
192C HIS* 3.3 3.2 + - + +
193C THR* 3.0 32.7 + - + +
395C PHE* 5.6 0.7 - - + -
408C TYR* 3.8 19.5 - - + -
413C MET* 3.8 24.0 - - + -
417C GLU* 3.9 23.6 - - + +
418C PHE* 4.3 17.0 - - + -
421C ALA* 4.1 9.6 - - + -
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Residues in contact with THR 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C TYR* 3.6 7.8 - - - -
139C HIS* 4.5 10.0 - - + -
141C PHE* 3.7 26.9 - - + +
146C GLY 4.5 0.2 + - - -
147C SER* 2.9 39.6 + - - -
150C THR* 4.7 0.2 - - - -
151C SER* 4.0 2.1 + - - -
186C ASN 3.0 21.8 + - - +
187C SER* 3.4 8.3 - - - +
189C LEU* 1.3 73.3 - - - +
191C THR* 1.3 69.4 + - - +
193C THR* 3.7 2.5 - - - -
194C THR* 2.9 41.3 + - - -
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Residues in contact with THR 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C PHE* 3.8 25.0 - - + -
187C SER 2.8 23.6 + - - -
188C ILE* 3.9 3.4 - - - -
189C LEU 3.3 0.2 - - - -
190C THR* 1.3 78.3 - - - +
192C HIS* 1.3 61.8 + - - +
194C THR* 4.1 1.9 - - - -
195C LEU* 3.2 26.9 + - + +
267C PHE* 4.9 8.5 - - + -
388C TRP* 3.9 22.6 - - + -
391C LEU* 5.6 0.3 - - - +
425C MET* 3.4 31.9 - - + -
428C LEU* 4.8 5.6 - - + -
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Residues in contact with HIS 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188C ILE 3.0 18.4 + - - +
189C LEU* 3.5 3.4 - - + +
191C THR* 1.3 78.9 - - - +
193C THR* 1.3 78.6 + - + +
195C LEU* 3.4 12.8 + - - +
196C GLU* 4.9 2.1 + - - +
417C GLU 4.8 2.9 - - - -
420C GLU* 3.1 34.7 + - + +
421C ALA* 3.4 36.1 - - + +
424C ASP* 2.8 41.8 + - + +
425C MET* 4.6 3.7 - - - -
100E LYS* 5.6 6.7 + - - -
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Residues in contact with THR 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C TYR* 2.7 30.9 + - + +
151C SER* 3.2 18.6 - - - +
155C GLU* 4.6 10.1 - - - +
189C LEU* 3.0 17.1 + - + +
190C THR 3.6 1.2 + - - -
192C HIS* 1.3 95.5 - - + +
194C THR* 1.3 58.4 + - - +
195C LEU 3.5 0.2 - - - -
196C GLU* 4.9 2.8 + - - +
197C HIS* 3.3 23.0 + - - -
100E LYS* 6.3 2.5 - - - -
104E LYS* 3.8 22.4 - - - +
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Residues in contact with THR 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C THR* 4.9 1.8 - - + +
151C SER* 3.7 17.8 + - - +
154C MET* 3.4 32.0 - - + +
168C GLU* 3.4 33.9 + - - +
190C THR* 2.9 29.5 + - - -
191C THR* 4.4 2.5 - - - -
193C THR* 1.3 76.6 - - - +
195C LEU* 1.3 56.6 + - - +
196C GLU 3.4 1.8 - - - -
197C HIS* 2.8 24.8 + - - -
198C SER* 3.2 5.4 + - - -
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Residues in contact with LEU 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191C THR* 3.2 21.8 + - + +
192C HIS* 3.4 10.4 + - - +
193C THR 3.5 0.2 - - - -
194C THR* 1.3 77.3 - - - +
196C GLU* 1.3 59.9 + - + +
198C SER* 3.7 3.9 - - - +
263C PRO 5.3 0.7 - - - +
264C ARG* 3.3 49.6 - - + +
266C HIS* 3.4 36.4 - - + -
267C PHE* 3.5 36.3 - - + -
424C ASP* 3.7 13.9 - - - +
425C MET* 5.8 1.6 - - - -
428C LEU* 4.4 16.2 - - + -
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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