Contacts of the helix formed by residues 180 - 192 (chain T) in PDB entry 5IYB
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 LYS 180 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177T ARG* 3.3 12.9 + - - +
179T ASP* 1.3 77.9 + - - +
181T GLN* 1.3 61.8 + - + +
182T HIS 3.7 0.2 - - - -
183T VAL* 3.7 6.5 + - - +
184T LEU* 3.1 40.4 + - + +
216T ILE* 5.4 16.8 - - + +
219T GLU* 5.3 11.0 + - - -
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Residues in contact with GLN 181 (chain T).
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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80R LYS* 3.9 27.8 - - - +
179T ASP 2.5 13.3 + - - +
180T LYS* 1.3 74.7 - - + +
182T HIS* 1.3 55.9 + - - +
184T LEU* 3.3 17.4 + - - +
185T ASP* 2.7 46.9 + - - +
188T PHE* 5.7 0.3 - - - -
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Residues in contact with HIS 182 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179T ASP* 3.1 26.9 + - - +
181T GLN* 1.3 74.8 - - - +
183T VAL* 1.3 65.0 + - - +
185T ASP* 3.7 11.3 + - + +
186T MET* 3.1 52.4 + - + +
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Residues in contact with VAL 183 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175T ARG* 4.4 14.8 - - + +
177T ARG* 5.2 5.6 - - - -
179T ASP* 2.6 35.5 + - + +
180T LYS* 4.1 8.3 - - - +
181T GLN 3.3 0.4 - - - -
182T HIS* 1.3 72.9 - - - +
184T LEU* 1.3 53.3 + - - +
186T MET* 3.2 23.4 - - + +
187T LEU* 2.8 32.4 + - + +
206T THR* 4.5 12.9 - - + +
208T GLN* 3.1 39.0 - - - +
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Residues in contact with LEU 184 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80R LYS* 5.8 2.9 - - + -
180T LYS* 3.1 30.2 + - + +
181T GLN* 3.5 16.4 - - - +
183T VAL* 1.3 75.7 - - - +
185T ASP* 1.3 60.2 + - - +
187T LEU* 3.3 25.0 - - + +
188T PHE* 2.9 66.9 + - + -
216T ILE* 4.3 18.1 - - + +
220T ILE* 4.3 14.8 - - + -
235T LEU* 4.6 0.7 - - + -
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Residues in contact with ASP 185 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76R GLY* 5.4 2.4 - - - -
80R LYS* 4.1 20.9 + - - -
181T GLN* 2.7 34.8 + - - +
182T HIS* 3.7 15.8 + - + +
183T VAL 3.4 0.2 - - - -
184T LEU* 1.3 71.9 - - - +
186T MET* 1.3 59.9 + - + +
188T PHE* 3.7 13.0 + - - +
189T SER* 2.9 25.7 + - - -
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Residues in contact with MET 186 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175T ARG* 3.9 24.0 - - - +
182T HIS* 3.1 42.6 + - + +
183T VAL* 3.2 28.3 - - + +
185T ASP* 1.3 77.2 - - + +
187T LEU* 1.3 56.8 + - - +
189T SER* 3.1 10.9 + - - -
190T ALA* 2.8 27.6 + - - +
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Residues in contact with LEU 187 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183T VAL* 2.8 16.3 + - + +
184T LEU* 3.0 23.7 + - + +
186T MET* 1.3 73.6 - - - +
188T PHE* 1.3 59.5 + - - +
190T ALA* 3.2 6.1 + - + +
191T PHE* 2.9 46.4 + - + -
202T LEU* 3.7 32.1 - - + -
205T ILE* 4.8 4.0 - - + -
206T THR* 3.9 23.8 - - + -
213T LEU* 4.1 21.5 - - + -
216T ILE* 4.6 8.1 - - + -
217T LEU* 5.7 0.7 - - + -
235T LEU* 3.8 20.6 - - + -
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Residues in contact with PHE 188 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75R PHE* 4.2 20.5 - + + +
76R GLY* 3.4 37.7 - - - +
79R ALA* 3.5 31.2 - - + -
80R LYS* 4.8 8.5 - - + -
181T GLN* 5.7 0.4 - - - -
184T LEU* 2.9 60.9 + - + +
185T ASP* 3.9 13.2 - - - +
187T LEU* 1.3 71.9 - - - +
189T SER* 1.3 57.5 + - - +
191T PHE* 3.2 6.6 + - - +
192T GLU* 3.0 26.2 + - - +
220T ILE* 4.0 10.5 - - + -
235T LEU* 3.6 28.7 - - + -
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Residues in contact with SER 189 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185T ASP 2.9 14.4 + - - -
186T MET* 3.1 13.7 + - - -
188T PHE* 1.3 77.6 - - - +
190T ALA* 1.3 62.8 + - - +
192T GLU* 3.1 21.3 + - - +
193T LYS* 3.6 5.2 + - - +
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Residues in contact with ALA 190 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186T MET 2.8 12.0 + - - +
187T LEU* 3.3 15.0 - - + +
189T SER* 1.3 76.5 - - - +
191T PHE* 1.3 54.7 + - + +
193T LYS* 2.8 17.1 + - - +
197T TYR* 2.3 34.0 + - + +
205T ILE* 4.1 25.1 - - + -
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Residues in contact with PHE 191 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75R PHE* 4.6 17.3 - - + -
187T LEU* 2.9 49.1 + - + -
188T PHE* 3.2 9.8 + - - +
190T ALA* 1.3 72.2 - - + +
192T GLU* 1.3 57.8 + - - +
193T LYS 3.2 0.4 - - - -
194T HIS 3.0 21.1 - - - +
195T GLN* 4.7 6.6 - - - -
197T TYR* 3.6 30.1 - + + -
202T LEU* 4.2 21.1 - - + -
217T LEU* 5.0 2.5 - - + -
233T TRP 3.7 22.7 - - - -
234T GLU* 4.0 2.9 - - - -
235T LEU* 3.5 53.6 - - + -
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Residues in contact with GLU 192 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75R PHE* 3.7 33.6 - - + +
118R TRP* 5.6 5.8 - - - -
188T PHE 3.0 11.5 + - - +
189T SER* 3.2 17.3 - - - +
190T ALA 3.0 0.6 - - - -
191T PHE* 1.3 76.1 - - - +
193T LYS* 1.3 60.6 + - - +
194T HIS 5.1 0.2 - - - -
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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