Contacts of the helix formed by residues 182 - 195 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A ASN* 3.1 34.8 - - + +
180A ALA* 3.5 1.1 - - + -
181A VAL* 1.3 78.8 - - - +
183A GLU* 1.3 63.6 + - - +
184A PRO* 3.3 4.3 - - - -
185A TYR* 3.0 19.9 + - + +
186A ASN* 3.2 10.8 + - - +
398A MET* 4.6 5.2 - - - -
404A PHE* 3.6 47.3 - - + -
408A TYR* 3.4 15.7 + - + +
255B VAL* 4.3 15.0 - - + +
256B ASN* 4.2 10.5 - - - +
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Residues in contact with GLU 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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142A GLY* 3.4 24.3 - - - +
173A PRO* 3.2 26.9 - - + +
174A ALA 4.4 2.1 + - - +
175A PRO* 5.2 0.7 - - - +
178A SER* 2.7 29.8 + - - -
180A ALA* 3.5 24.8 - - + +
181A VAL 3.4 0.4 - - - -
182A VAL* 1.3 77.0 - - - +
184A PRO* 1.3 62.9 - - + +
186A ASN* 3.8 1.1 - - - +
187A SER* 2.7 38.5 + - - -
501A GTP 2.4 39.4 + - - +
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Residues in contact with PRO 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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173A PRO* 5.7 0.9 - - + -
181A VAL 3.7 10.5 - - - +
182A VAL 3.4 3.8 - - - -
183A GLU* 1.3 94.5 - - + +
185A TYR* 1.3 59.7 + - - +
187A SER* 3.9 2.4 - - - +
188A ILE* 3.2 31.5 + - - +
391A LEU* 4.3 15.7 - - + +
394A LYS* 3.9 36.8 - - + -
395A PHE* 3.8 11.8 - - - +
398A MET* 3.5 21.3 - - + -
346B PRO* 5.7 2.0 - - + -
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Residues in contact with TYR 185 (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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182A VAL* 3.0 13.3 + - + +
184A PRO* 1.3 79.1 - - - +
186A ASN* 1.3 63.6 + - - +
188A ILE* 3.4 1.7 + - - +
189A LEU* 3.0 30.1 + - + +
395A PHE* 3.7 27.9 - + - -
398A MET* 3.2 47.9 + - + -
399A TYR* 3.2 19.5 + - + -
403A ALA 2.8 31.1 + - - -
404A PHE* 4.2 9.2 - - + -
405A VAL* 3.9 12.9 - - + +
408A TYR* 3.6 26.9 - + + +
418A PHE* 3.6 25.1 - + + -
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Residues in contact with ASN 186 (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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101A ASN 2.8 28.1 + - - -
103A TYR* 3.3 22.9 + - - -
141A PHE 3.4 14.8 - - - +
142A GLY 2.7 23.1 + - - +
143A GLY 3.9 3.6 + - - -
147A SER* 3.6 13.2 - - - +
182A VAL* 3.2 10.6 + - - +
183A GLU 3.8 3.8 - - - +
185A TYR* 1.3 75.1 - - - +
187A SER* 1.3 62.0 + - - +
189A LEU* 3.8 1.2 - - - +
190A THR* 3.0 26.2 + - - +
408A TYR* 2.7 27.3 + - - -
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Residues in contact with SER 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A PHE* 3.3 35.3 + - - +
173A PRO* 3.6 13.9 - - - +
183A GLU 2.7 24.4 + - - -
184A PRO 3.9 1.8 - - - -
186A ASN* 1.3 74.6 - - - +
188A ILE* 1.3 56.1 + - - +
190A THR* 3.5 2.1 - - - +
191A THR* 2.8 37.5 + - - -
391A LEU* 3.5 27.6 - - - -
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Residues in contact with ILE 188 (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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184A PRO 3.2 26.7 + - - +
187A SER* 1.3 76.5 - - - +
189A LEU* 1.3 69.0 + - + +
191A THR* 3.9 4.8 - - - -
192A HIS* 3.0 23.4 + - - +
391A LEU* 3.8 36.3 - - + +
392A ASP* 3.4 26.0 - - - +
395A PHE* 3.6 32.3 - - + -
421A ALA* 3.9 20.6 - - + -
422A ARG* 4.0 11.9 - - - +
425A MET* 3.8 14.7 - - + +
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Residues in contact with LEU 189 (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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103A TYR* 3.7 41.5 - - + -
185A TYR 3.0 23.7 + - - +
186A ASN 3.8 0.2 - - - +
188A ILE* 1.3 81.2 - - + +
190A THR* 1.3 61.0 + - - +
192A HIS* 3.4 3.2 + - + +
193A THR* 3.1 26.0 + - - -
395A PHE* 5.4 0.2 - - + -
408A TYR* 4.0 13.7 - - + -
413A MET* 3.4 36.8 - - + -
417A GLU* 3.9 28.7 - - + +
418A PHE* 4.4 15.5 - - + -
421A ALA* 4.2 8.3 - - + -
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Residues in contact with THR 190 (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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103A TYR* 3.6 6.7 - - - -
139A HIS* 4.8 7.1 - - + -
141A PHE* 4.3 20.6 - - + +
146A GLY 4.7 0.9 + - - -
147A SER* 2.7 43.7 + - - -
150A THR* 4.8 0.3 - - - -
151A SER* 3.6 5.6 + - - -
186A ASN 3.0 22.4 + - - +
187A SER* 3.5 11.0 - - - +
189A LEU* 1.3 73.0 - - - +
191A THR* 1.3 63.8 + - - +
194A THR* 2.6 46.5 + - - -
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Residues in contact with THR 191 (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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141A PHE* 3.7 26.2 - - - -
187A SER 2.8 22.2 + - - -
188A ILE* 3.9 2.9 - - - -
190A THR* 1.3 78.2 - - - +
192A HIS* 1.3 62.1 + - - +
194A THR* 4.8 2.2 - - - -
195A LEU* 3.0 42.0 + - + +
267A PHE* 4.6 3.8 - - + -
388A TRP* 3.9 22.1 - - + -
425A MET* 3.6 26.2 - - + -
428A LEU* 4.9 1.3 - - + -
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Residues in contact with HIS 192 (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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188A ILE 3.0 18.3 + - - +
189A LEU 3.5 2.2 - - - +
191A THR* 1.3 79.7 - - - +
193A THR* 1.3 73.2 + - - +
194A THR 3.6 0.2 + - - -
195A LEU* 3.8 7.8 + - - +
196A GLU* 5.1 2.1 + - - +
417A GLU* 4.8 8.3 - - + -
420A GLU* 3.2 32.5 + - + -
421A ALA* 3.4 39.2 - - + +
424A ASP* 2.9 45.8 + - + +
425A MET* 4.8 2.8 - - + -
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Residues in contact with THR 193 (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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103A TYR* 3.2 22.1 + - - +
107A HIS* 4.5 5.2 - - + +
151A SER* 4.1 14.1 - - - +
155A GLU* 3.4 32.2 - - + +
189A LEU 3.1 14.8 + - - -
192A HIS* 1.3 89.8 - - + +
194A THR* 1.3 59.0 + - - +
196A GLU 5.4 0.2 - - - -
197A HIS* 3.4 21.7 + - - -
417A GLU* 4.1 8.4 + - - +
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Residues in contact with THR 194 (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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139A HIS* 6.3 0.2 - - - -
150A THR* 4.9 1.9 - - + +
151A SER* 3.5 14.2 + - - -
154A MET* 3.8 31.6 - - + +
168A GLU* 3.6 35.1 + - - +
190A THR* 2.6 34.9 + - - -
191A THR* 4.3 2.7 - - - -
193A THR* 1.3 78.5 - - - +
195A LEU* 1.3 57.0 + - - +
196A GLU 3.5 1.3 - - - -
197A HIS* 2.9 23.8 + - - -
198A SER* 3.2 6.5 + - - -
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Residues in contact with LEU 195 (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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191A THR* 3.0 25.1 + - + +
192A HIS* 3.8 8.3 + - - +
193A THR 3.5 1.8 - - - -
194A THR* 1.3 76.1 - - - +
196A GLU* 1.3 67.1 - - + +
197A HIS 3.2 1.6 + - - -
198A SER* 3.4 6.6 + - - +
264A ARG* 3.4 45.1 - - + +
266A HIS* 3.3 44.8 - - + -
267A PHE* 3.7 26.9 - - + -
424A ASP* 3.9 14.6 - - - +
425A MET* 6.0 1.8 - - - -
428A LEU* 4.3 13.2 - - + -
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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