Contacts of the helix formed by residues 226 - 237 (chain T) in PDB entry 5GJQ
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 ILE 226 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189T HIS* 4.6 18.8 - - + +
192T LEU* 5.5 4.5 - - + -
193T GLY* 4.6 15.7 - - - +
196T LEU* 5.0 9.9 - - + -
215T LEU* 6.1 2.5 - - + -
223T ASN* 3.5 19.5 - - + -
224T VAL* 3.5 3.5 - - + +
225T TYR* 1.3 74.9 - - + +
227T LYS* 1.3 64.0 + - - +
228T HIS 3.0 2.2 - - - -
229T PRO* 3.0 18.5 - - + +
230T VAL* 3.1 17.3 - - + +
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Residues in contact with LYS 227 (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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223T ASN* 3.0 36.2 - - + +
224T VAL 3.7 11.9 - - - +
225T TYR 3.0 1.8 + - - +
226T ILE* 1.3 76.1 - - - +
228T HIS* 1.3 69.9 + - + +
230T VAL* 3.8 6.3 - - - -
231T SER* 2.8 38.2 + - - +
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Residues in contact with HIS 228 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197T LEU* 4.6 15.9 - - + -
225T TYR* 3.0 15.9 + - + +
227T LYS* 1.3 83.4 - - + +
229T PRO* 1.4 59.4 - - + +
231T SER* 5.1 0.4 - - - -
232T LEU* 2.6 42.7 + - + +
246T LEU* 5.1 11.4 - - + +
249T GLY 6.1 0.9 - - - -
250T ASN* 5.2 17.7 - - + -
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Residues in contact with PRO 229 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193T GLY* 4.0 23.3 - - - +
196T LEU* 3.8 38.6 - - + -
197T LEU* 4.1 13.7 - - + +
200T LEU* 3.5 17.2 - - + +
208T PHE* 4.4 2.7 - - + -
225T TYR* 4.1 1.1 - - + +
226T ILE* 3.0 30.3 - - - +
228T HIS* 1.4 86.0 - - + +
230T VAL* 1.3 66.1 + - - +
232T LEU* 3.3 6.2 - - + +
233T GLU* 2.8 15.9 + - - +
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Residues in contact with VAL 230 (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* 5.0 3.8 - - + -
208T PHE* 4.5 8.5 - - - -
212T LEU* 4.6 20.9 - - + -
223T ASN* 4.2 15.9 - - - -
226T ILE* 3.1 23.3 + - + +
227T LYS* 4.0 4.5 - - - +
229T PRO* 1.3 76.7 - - + +
231T SER* 1.3 56.6 + - - +
233T GLU* 2.5 29.3 + - - +
234T GLN* 2.9 17.6 + - + +
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Residues in contact with SER 231 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227T LYS* 2.8 27.0 + - - +
228T HIS* 4.4 0.4 - - - -
230T VAL* 1.3 76.2 - - - +
232T LEU* 1.3 62.0 + - - +
233T GLU 3.0 0.9 + - - -
234T GLN* 3.0 18.1 + - - +
235T TYR* 3.0 28.8 + - - -
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Residues in contact with LEU 232 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197T LEU* 4.7 13.2 - - + -
200T LEU* 3.6 25.6 - - + -
228T HIS* 2.6 29.2 + - + +
229T PRO* 3.3 3.6 - - + +
231T SER* 1.3 76.2 - - - +
233T GLU* 1.3 60.5 + - - +
235T TYR* 4.7 2.2 - - - +
236T LEU* 3.2 39.3 + - + +
243T LYS* 4.7 14.0 - - + +
246T LEU* 4.2 28.9 - - + +
247T ALA* 5.3 3.1 - - + +
263T LEU* 4.2 28.5 - - + -
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Residues in contact with GLU 233 (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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200T LEU* 4.1 15.5 - - + -
205T VAL* 6.6 0.2 - - + -
208T PHE* 3.8 31.0 - - + -
209T HIS* 4.4 11.9 - - + +
229T PRO 2.8 10.5 + - - +
230T VAL* 2.5 16.8 + - - +
232T LEU* 1.3 72.1 - - - +
234T GLN* 1.3 70.3 + - + +
236T LEU* 3.1 15.0 + - + +
237T MET* 3.0 40.3 + - + +
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Residues in contact with GLN 234 (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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396S ILE 5.3 5.8 - - - +
399S ARG* 4.5 30.7 - - + +
209T HIS* 6.5 0.7 - - + -
230T VAL* 2.9 18.1 + - + +
231T SER* 3.0 8.9 + - - +
233T GLU* 1.3 79.9 - - + +
235T TYR* 1.3 62.0 + - + +
237T MET* 2.8 33.0 - - + +
238T GLU* 3.9 1.4 + - - +
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Residues in contact with TYR 235 (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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399S ARG* 6.1 2.5 - - - -
231T SER* 3.0 24.6 + - - +
232T LEU* 4.7 2.9 - - - +
234T GLN* 1.3 80.1 - - + +
236T LEU* 1.3 56.7 + - - +
238T GLU* 2.8 13.7 + - - +
239T GLY* 2.8 25.4 + - - +
242T ASN* 4.0 29.2 - - + -
243T LYS* 4.4 11.2 - - + +
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Residues in contact with LEU 236 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200T LEU* 5.8 6.7 - - + -
232T LEU* 3.2 32.8 + - + +
233T GLU* 3.2 20.9 - - + +
235T TYR* 1.3 74.5 - - - +
237T MET* 1.3 70.8 + - + +
238T GLU* 2.5 20.2 + - - +
239T GLY 3.5 9.4 - - - +
240T SER* 5.8 0.7 - - - -
243T LYS* 4.9 9.1 - - + +
263T LEU* 6.0 5.6 - - + -
267T ILE* 5.1 20.4 - - + -
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Residues in contact with MET 237 (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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400S HIS* 5.2 18.4 - - + +
440S LYS* 5.0 9.5 - - - +
205T VAL* 5.4 13.2 - - + -
209T HIS* 5.2 12.3 - - + +
233T GLU* 3.0 36.3 + - + +
234T GLN* 2.8 22.4 - - + +
236T LEU* 1.3 86.2 - - + +
238T GLU* 1.3 59.9 + - - +
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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