Contacts of the helix formed by residues 231 - 244 (chain I) in PDB entry 5LN3
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 GLY 231 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187I ILE* 5.1 9.8 - - - +
190I LEU* 6.3 1.8 - - - -
229I GLY 3.5 1.4 - - - -
230I THR* 1.3 81.5 - - - +
232I LYS* 1.4 58.8 + - - +
233I THR 3.4 0.9 - - - -
234I LEU* 3.8 16.1 - - - +
235I LEU* 3.0 31.7 + - - +
353I PHE* 3.6 21.7 - - - -
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Residues in contact with LYS 232 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224I LEU* 3.5 40.8 - - + +
226I GLY* 3.5 30.8 + - - +
227I PRO 4.3 1.1 - - - +
228I PRO* 4.6 2.0 - - - +
229I GLY* 3.7 22.6 - - - +
230I THR* 4.9 2.7 - - + +
231I GLY* 1.4 78.3 - - - +
233I THR* 1.3 60.6 + - - +
235I LEU* 3.4 3.3 + - - +
236I ALA* 3.2 22.7 + - - +
283I PHE* 5.0 4.0 - - + -
286I GLU* 4.3 5.3 + - - -
330I ALA* 4.2 13.2 - - + +
331I THR* 2.9 31.9 + - - +
332I ASN* 3.9 1.4 - - - +
353I PHE* 3.8 30.4 - - + -
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Residues in contact with THR 233 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229I GLY* 3.2 36.8 - - - +
230I THR 4.2 0.7 - - - +
232I LYS* 1.3 77.0 - - - +
234I LEU* 1.3 76.5 + - + +
236I ALA* 3.4 7.7 + - - +
237I LYS* 3.3 30.4 + - - +
249I ARG* 3.6 28.5 + - - +
283I PHE* 5.5 3.6 - - - -
278J ASN* 5.1 8.9 + - - +
310J ARG* 4.3 8.1 + - - +
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Residues in contact with LEU 234 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182I GLU* 5.7 1.4 - - - +
183I THR 5.5 0.2 - - - +
187I ILE* 3.8 27.1 - - + -
230I THR* 3.1 26.9 - - - +
231I GLY* 3.7 14.1 + - - +
232I LYS 3.3 0.4 - - - -
233I THR* 1.3 83.9 - - + +
235I LEU* 1.3 62.0 + - - +
237I LYS* 3.3 25.5 + - - +
238I ALA* 3.3 23.0 + - - +
396I LYS* 3.8 32.5 - - - +
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Residues in contact with LEU 235 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184I TYR* 5.0 11.0 - - + -
187I ILE* 5.4 5.1 - - + +
193I GLN* 5.3 7.2 - - + +
194I ILE* 4.0 35.2 - - + -
197I ILE* 3.9 37.5 - - + -
224I LEU* 3.9 28.3 - - + -
231I GLY 3.0 20.3 + - - +
232I LYS* 3.6 3.4 - - - +
233I THR 3.3 0.2 - - - -
234I LEU* 1.3 79.2 - - - +
236I ALA* 1.3 60.0 + - - +
238I ALA* 3.4 6.3 - - + +
239I VAL* 3.0 24.4 + - + +
242I GLN* 5.8 2.9 - - - +
351I ILE* 5.8 0.2 - - + -
353I PHE* 4.7 9.0 - - + -
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Residues in contact with ALA 236 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224I LEU* 5.2 3.6 - - + +
232I LYS 3.2 8.0 + - - +
233I THR* 3.7 9.6 - - - +
234I LEU 3.4 0.2 - - - -
235I LEU* 1.3 77.6 - - - +
237I LYS* 1.3 63.6 + - - +
239I VAL* 3.2 25.4 + - - +
240I ALA* 3.4 7.3 + - - +
247I PHE* 4.2 13.0 - - + -
249I ARG* 5.2 4.0 - - - +
283I PHE* 3.7 36.1 - - + -
328I ILE* 4.8 5.4 - - + -
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Residues in contact with LYS 237 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180I PRO* 3.8 20.4 - - + +
182I GLU* 4.3 28.3 - - + +
233I THR* 3.3 19.1 + - - +
234I LEU* 3.3 26.6 + - - +
236I ALA* 1.3 78.6 - - - +
238I ALA* 1.3 63.2 + - - +
240I ALA* 3.6 15.7 + - - +
241I ASN 4.1 1.0 + - - -
247I PHE* 5.5 5.6 - - + -
249I ARG* 4.6 13.9 - - - +
278J ASN* 3.6 26.2 + - + +
279J GLN* 4.9 7.6 - - + +
281J ASP* 4.8 4.2 + - - +
282J GLY* 4.1 19.8 - - - +
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Residues in contact with ALA 238 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182I GLU* 3.6 15.5 - - + +
183I THR* 4.0 5.0 - - - +
184I TYR* 3.8 37.0 - - + +
234I LEU 3.3 10.7 + - - +
235I LEU* 3.4 12.3 - - + +
237I LYS* 1.3 80.7 - - - +
239I VAL* 1.4 61.9 + - - +
241I ASN* 3.4 19.6 - - - +
242I GLN* 3.6 13.4 - - - +
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Residues in contact with VAL 239 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197I ILE* 4.6 30.7 - - + +
198I LYS* 6.4 1.8 - - + -
201I VAL* 4.9 8.7 - - + -
202I GLU* 5.7 3.8 - - + +
235I LEU* 3.0 13.2 + - + +
236I ALA* 3.2 18.5 + - - +
238I ALA* 1.4 79.1 - - - +
240I ALA* 1.4 58.7 + - - +
242I GLN* 3.3 18.8 + - - +
243I THR* 2.9 48.4 + - + +
247I PHE* 5.1 2.7 - - + -
281I ILE* 5.4 3.6 - - + -
328I ILE* 4.1 20.2 - - + -
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Residues in contact with ALA 240 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179I ALA* 4.6 2.9 - - - -
180I PRO* 3.7 23.1 - - + -
236I ALA 3.4 2.8 + - - +
237I LYS* 3.8 8.1 - - - +
238I ALA 3.3 0.6 - - - -
239I VAL* 1.4 80.7 - - - +
241I ASN* 1.3 59.8 + - - +
243I THR* 3.2 16.8 + - - -
244I SER* 3.3 11.8 + - - -
245I ALA 4.4 6.8 - - - +
247I PHE* 3.6 39.3 - - + -
281I ILE* 5.5 2.5 - - - -
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Residues in contact with ASN 241 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179I ALA* 3.6 26.0 - - - +
180I PRO* 3.0 28.4 + - - +
181I GLN 3.8 8.7 + - - -
182I GLU 3.4 15.4 + - - +
183I THR* 5.0 6.1 + - - -
237I LYS 4.1 1.9 + - - +
238I ALA 3.4 12.3 + - - +
240I ALA* 1.3 74.8 - - - +
242I GLN* 1.4 68.0 - - + +
244I SER* 3.8 11.1 + - - -
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Residues in contact with GLN 242 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183I THR* 5.4 2.0 - - - +
184I TYR* 3.1 42.2 + - + +
194I ILE* 6.0 0.6 - - - +
198I LYS* 2.7 30.2 + - - +
202I GLU* 3.0 33.6 - - - +
235I LEU* 5.8 3.2 - - - +
238I ALA* 3.6 16.4 + - - +
239I VAL* 3.4 23.6 - - + +
241I ASN* 1.4 63.9 - - + +
243I THR* 1.3 62.8 + - + +
244I SER* 3.4 9.0 + - - -
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Residues in contact with THR 243 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201I VAL* 3.7 29.4 - - + -
202I GLU* 4.2 22.9 - - + -
205I LEU* 3.4 27.9 - - + +
239I VAL* 2.9 24.6 + - + +
240I ALA* 3.2 13.2 + - - -
242I GLN* 1.3 78.9 - - + +
244I SER* 1.3 65.8 + - - +
245I ALA* 3.4 3.4 + - - +
281I ILE* 3.9 20.2 - - + +
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Residues in contact with SER 244 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178I LYS* 3.3 20.0 + - - +
179I ALA* 5.9 5.8 - - - +
240I ALA 3.3 11.2 + - - -
241I ASN 3.8 8.7 + - - -
242I GLN 3.4 12.9 + - - -
243I THR* 1.3 76.0 - - - +
245I ALA* 1.4 59.0 + - - +
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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