Contacts of the helix formed by residues 190 - 202 (chain T) in PDB entry 5L4K
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 GLN 190 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153T GLN* 5.7 0.4 + - - -
186T ALA* 4.0 17.5 + - - +
187T TYR* 4.4 14.9 - - + -
188T MET 3.3 1.6 - - - +
189T HIS* 1.3 87.5 + - + +
191T LEU* 1.3 64.2 + - + +
192T LEU 3.4 1.1 - - - -
193T GLY* 3.6 7.8 + - - +
194T LEU* 3.6 15.9 + - - +
225T TYR* 2.9 62.2 - - + -
253T ALA* 3.3 16.5 - - - +
256T TYR* 4.3 10.3 + - + +
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Residues in contact with LEU 191 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149T GLU* 3.8 30.1 - - + +
152T ALA* 5.4 5.2 - - + -
153T GLN* 3.2 42.6 - - + +
156T ILE* 5.7 2.2 - - + -
168T MET* 6.1 0.9 - - - +
171T LEU* 4.6 6.5 - - + -
175T TYR* 3.5 24.7 - - + +
187T TYR* 3.2 36.2 + - + +
188T MET 3.9 1.8 + - - +
190T GLN* 1.3 75.6 - - + +
192T LEU* 1.3 65.7 + - - +
194T LEU* 3.1 16.2 + - + +
195T ASN* 3.1 16.1 + - - +
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Residues in contact with LEU 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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172T LYS* 3.4 41.1 - - + -
175T TYR* 4.8 11.7 - - + -
188T MET 3.6 16.6 + - - +
189T HIS* 4.3 10.3 - - + +
191T LEU* 1.3 79.6 - - - +
193T GLY* 1.3 55.2 + - - +
195T ASN* 2.7 35.4 + - + +
196T LEU* 3.0 14.9 + - + +
211T GLU* 4.7 6.3 - - - +
214T ARG* 6.1 4.0 - - + -
215T LEU* 4.7 31.6 - - + +
226T ILE* 5.6 3.1 - - + -
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Residues in contact with GLY 193 (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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189T HIS 3.7 9.5 + - - -
190T GLN 3.6 7.2 + - - -
191T LEU 3.2 1.2 - - - -
192T LEU* 1.3 77.6 - - - +
194T LEU* 1.3 57.6 + - - +
196T LEU* 2.8 31.6 + - - +
197T LEU* 3.1 14.0 + - - +
226T ILE* 5.3 7.2 - - - -
229T PRO* 4.2 6.3 - - - +
256T TYR* 4.4 17.7 - - - -
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Residues in contact with LEU 194 (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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153T GLN* 3.8 21.5 - - - +
156T ILE* 3.5 31.6 - - + -
168T MET* 4.8 6.4 - - + +
190T GLN 3.6 13.7 + - - +
191T LEU* 3.1 13.9 + - + +
193T GLY* 1.3 73.5 - - - +
195T ASN* 1.3 63.5 + - - +
197T LEU* 3.2 10.3 + - + +
198T PHE* 2.9 26.7 + - - +
255T SER* 3.6 28.7 - - - +
256T TYR* 3.5 29.8 - - + -
259T PHE* 5.0 8.6 - - + -
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Residues in contact with ASN 195 (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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168T MET* 3.7 38.1 - - + +
172T LYS* 3.4 30.6 + - + +
191T LEU 3.1 7.3 + - - +
192T LEU* 2.7 31.4 + - + +
194T LEU* 1.3 72.3 - - - +
196T LEU* 1.3 59.8 + - - +
198T PHE* 4.0 4.2 + - - +
199T LEU* 3.2 30.7 + - - +
211T GLU* 3.4 22.5 - - - +
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Residues in contact with LEU 196 (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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192T LEU* 3.0 16.8 + - + +
193T GLY* 2.8 15.1 + - - +
195T ASN* 1.3 76.1 - - - +
197T LEU* 1.3 57.0 + - - +
198T PHE 3.1 1.6 - - - -
199T LEU* 2.7 29.1 + - + +
200T LEU* 3.1 10.8 + - - +
208T PHE* 3.8 46.1 - - + +
211T GLU* 3.8 29.6 - - + -
212T LEU* 4.3 13.9 - - + +
226T ILE* 4.1 26.5 - - + -
229T PRO* 4.1 12.6 - - + -
230T VAL* 4.9 0.7 - - + -
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Residues in contact with LEU 197 (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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193T GLY 3.1 13.8 + - - +
194T LEU* 3.2 11.9 + - + +
196T LEU* 1.3 75.6 - - - +
198T PHE* 1.3 57.7 + - - +
200T LEU* 2.9 32.1 + - + +
201T SER* 3.1 10.6 + - - -
229T PRO* 3.8 31.6 - - + -
232T LEU* 3.8 19.1 - - + -
250T ASN* 5.4 0.4 - - - +
256T TYR* 3.7 50.9 - - + +
259T PHE* 3.7 21.4 - - + -
260T ILE* 4.1 15.4 - - + +
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Residues in contact with PHE 198 (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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161T ILE* 4.3 14.8 - - + -
164T PHE* 3.7 22.7 - + - -
165T GLU* 4.4 29.4 - - + -
168T MET* 3.9 26.9 - - + -
194T LEU 2.9 17.2 + - - +
195T ASN* 4.0 5.4 - - - +
196T LEU 3.0 0.2 + - - -
197T LEU* 1.3 77.5 - - - +
199T LEU* 1.3 79.2 + - + +
201T SER* 3.7 1.8 + - - -
202T GLN* 3.2 50.7 + - + +
204T ARG* 4.6 7.4 - - - -
259T PHE* 3.6 28.3 - + + -
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Residues in contact with LEU 199 (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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172T LYS* 5.5 0.7 - - - +
195T ASN* 3.2 26.9 - - - +
196T LEU* 2.7 17.0 + - - +
198T PHE* 1.3 85.0 - - + +
200T LEU* 1.3 62.9 + - - +
202T GLN* 3.8 3.8 + - - +
203T ASN 3.5 1.9 + - - -
204T ARG* 3.2 62.9 + - + +
205T VAL* 4.6 0.9 + - - -
207T GLU* 4.4 14.4 - - + -
208T PHE* 4.4 19.3 - - + +
211T GLU* 3.8 28.9 - - + -
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Residues in contact with LEU 200 (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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196T LEU 3.1 9.7 + - - +
197T LEU* 2.9 34.2 + - + +
199T LEU* 1.3 75.2 - - - +
201T SER* 1.3 56.8 + - - +
202T GLN 3.0 4.7 - - - -
203T ASN* 2.8 28.0 + - - +
205T VAL* 5.3 3.6 - - + -
208T PHE* 3.6 27.6 - - + -
229T PRO 4.1 15.7 - - - +
232T LEU* 4.2 15.3 - - + +
233T GLU* 3.9 23.3 - - + +
236T LEU* 4.6 16.2 - - + +
260T ILE* 5.1 2.0 - - + -
263T LEU* 3.9 25.3 - - + +
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Residues in contact with SER 201 (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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197T LEU 3.1 7.1 + - - -
198T PHE* 3.7 3.8 + - - -
199T LEU 3.6 0.2 - - - -
200T LEU* 1.3 77.1 - - - +
202T GLN* 1.3 67.0 + - - +
203T ASN* 3.3 11.1 + - - +
259T PHE* 3.5 31.8 - - - -
260T ILE* 6.3 0.9 - - - +
262T ILE* 3.9 30.5 - - - +
263T LEU* 4.1 20.8 - - - +
266T THR* 5.3 1.8 + - - -
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Residues in contact with GLN 202 (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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161T ILE* 4.3 28.0 - - - +
198T PHE* 3.2 47.5 + - + +
199T LEU* 4.1 6.5 - - - +
200T LEU 3.0 1.4 - - - -
201T SER* 1.3 82.6 + - - +
203T ASN* 1.3 72.3 + - - +
204T ARG* 3.3 35.9 + - + +
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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