Contacts of the helix formed by residues 253 - 270 (chain I) in PDB entry 5IIO
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 ASN 253 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251I ASN* 2.9 11.6 + - - +
252I HIS* 1.3 86.4 - - - +
254I LEU* 1.3 64.1 + - - +
255I HIS 3.3 3.4 - - - +
256I ILE* 3.2 22.8 + - + +
257I THR* 3.0 22.2 + - - +
286I LEU* 3.2 31.9 + - + +
289I PHE* 4.1 7.3 + - - +
291I LYS 3.3 20.6 + - - -
292I PRO* 3.5 2.6 - - - +
293I VAL* 2.8 37.2 + - - +
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Residues in contact with LEU 254 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251I ASN* 3.5 28.3 - - + +
252I HIS 3.8 1.6 - - - -
253I ASN* 1.3 76.1 - - - +
255I HIS* 1.3 64.3 + - - +
256I ILE 3.0 1.6 + - - -
257I THR* 3.4 7.4 - - - +
258I GLU* 3.0 51.5 + - + +
287I LYS* 6.1 0.9 - - - -
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Residues in contact with HIS 255 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253I ASN* 3.3 0.8 - - - +
254I LEU* 1.3 78.8 - - - +
256I ILE* 1.3 61.9 + - + +
258I GLU* 3.6 14.9 - - - +
259I LYS* 3.7 21.7 - - - +
316I ILE* 3.7 15.9 - - + +
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Residues in contact with ILE 256 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253I ASN* 3.2 31.8 + - + +
254I LEU 3.0 0.4 - - - -
255I HIS* 1.3 81.6 - - + +
257I THR* 1.3 66.0 + - - +
258I GLU 3.3 1.6 - - - -
259I LYS* 3.2 6.9 + - - +
260I LEU* 3.1 28.2 + - + +
286I LEU* 3.6 25.1 - - + -
293I VAL* 4.6 6.1 - - + +
313I ILE* 3.5 34.8 - - + -
316I ILE* 3.8 26.5 - - + +
317I LEU* 3.8 18.8 - - + -
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Residues in contact with THR 257 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251I ASN* 3.3 16.8 + - - +
253I ASN 3.0 20.3 + - - +
254I LEU* 3.3 7.1 + - - +
256I ILE* 1.3 76.9 - - - +
258I GLU* 1.3 58.4 + - - +
260I LEU* 3.0 8.4 + - - +
261I GLU* 2.8 36.5 + - - +
283I ILE* 3.8 27.4 - - + +
286I LEU* 3.6 33.0 - - + -
287I LYS* 4.1 14.6 - - + +
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Residues in contact with GLU 258 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254I LEU* 3.0 43.2 + - + +
255I HIS* 3.6 21.2 - - - +
257I THR* 1.3 78.6 + - - +
259I LYS* 1.3 73.6 + - + +
261I GLU* 3.8 14.9 + - - +
262I VAL* 3.5 23.0 + - - +
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Residues in contact with LYS 259 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255I HIS* 3.7 18.8 - - - +
256I ILE 3.2 7.3 + - - +
257I THR 3.1 0.4 - - - -
258I GLU* 1.3 87.2 + - + +
260I LEU* 1.3 64.7 + - - +
262I VAL* 3.3 14.7 + - - +
263I LEU* 3.4 8.0 + - - +
316I ILE* 3.7 29.4 - - + -
320I GLY* 3.2 31.2 + - - -
321I HIS* 4.3 4.1 - - - +
322I LEU* 4.3 16.4 - - + +
325I LEU* 3.6 26.5 - - + +
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Residues in contact with LEU 260 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256I ILE* 3.1 23.4 + - + +
257I THR* 3.0 7.7 + - - +
259I LYS* 1.3 76.7 - - - +
261I GLU* 1.3 51.6 + - - +
263I LEU* 3.0 8.5 + - + +
264I ALA* 2.7 33.3 + - - +
279I TYR* 4.0 24.8 - - + -
282I ALA* 5.2 0.4 - - + -
283I ILE* 3.8 23.3 - - + +
286I LEU* 3.7 29.6 - - + -
309I MET* 4.2 21.5 - - + -
312I LYS* 4.6 12.3 - - + -
313I ILE* 4.8 5.2 - - + -
316I ILE* 5.0 3.4 - - + -
322I LEU* 4.4 17.0 - - + -
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Residues in contact with GLU 261 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257I THR* 2.8 19.1 + - - +
258I GLU* 3.9 14.8 - - - +
259I LYS 3.2 0.2 - - - -
260I LEU* 1.3 74.4 - - - +
262I VAL* 1.3 59.3 + - - +
264I ALA* 3.6 2.5 - - + +
265I LYS* 2.8 37.2 + - - +
283I ILE* 3.6 23.5 - - + +
287I LYS* 3.0 34.0 + - - -
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Residues in contact with VAL 262 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258I GLU 3.5 16.1 + - - +
259I LYS* 3.3 8.9 + - - +
260I LEU 3.3 0.4 - - - -
261I GLU* 1.3 76.7 - - + +
263I LEU* 1.3 62.9 - - - +
265I LYS* 3.5 9.3 + - - +
266I ALA* 3.1 23.0 + - - +
325I LEU* 4.1 17.9 - - + -
328I ILE* 3.9 22.0 - - + -
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Residues in contact with LEU 263 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259I LYS 3.4 2.0 + - - +
260I LEU* 3.0 12.0 + - + +
262I VAL* 1.3 77.9 - - - +
264I ALA* 1.3 63.4 + - - +
266I ALA* 3.5 5.4 + - + +
267I TYR* 3.1 50.5 + - + -
279I TYR* 3.7 27.6 - - + +
312I LYS* 4.4 6.3 - - + -
322I LEU* 3.9 24.7 - - + -
324I LYS* 4.2 25.8 - - + -
325I LEU* 3.6 19.0 - - + +
328I ILE* 4.3 15.5 - - + -
1L G 5.2 0.2 - - - +
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Residues in contact with ALA 264 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260I LEU 2.7 18.8 + - - +
261I GLU* 3.1 6.3 + - + +
263I LEU* 1.3 74.5 - - - +
265I LYS* 1.3 61.0 + - - +
267I TYR* 3.5 2.8 + - - +
268I SER* 3.0 23.9 + - - -
276I ALA* 3.6 14.4 - - + +
279I TYR* 3.6 28.2 - - + -
280I ALA* 4.7 3.1 - - + +
283I ILE* 4.0 13.5 - - + -
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Residues in contact with LYS 265 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261I GLU* 2.8 23.1 + - - +
262I VAL* 3.8 7.4 - - - +
264I ALA* 1.3 73.0 - - - +
266I ALA* 1.3 62.8 + - - +
268I SER* 3.1 8.8 + - - -
269I VAL* 3.0 32.2 + - + +
332I VAL* 6.2 1.1 - - + -
336I GLU* 3.1 40.4 - - - +
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Residues in contact with ALA 266 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262I VAL 3.1 18.6 + - - +
263I LEU* 3.6 8.5 - - + +
265I LYS* 1.3 74.7 - - - +
267I TYR* 1.3 63.3 + - + +
269I VAL* 3.3 2.8 - - - +
270I GLN* 3.2 34.1 + - - +
328I ILE* 4.2 24.5 - - + -
332I VAL* 4.0 27.3 - - + +
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Residues in contact with TYR 267 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263I LEU* 3.1 38.9 + - + +
264I ALA* 3.7 4.0 - - - +
266I ALA* 1.3 78.2 - - + +
268I SER* 1.3 61.0 + - - +
270I GLN* 3.3 14.8 + - - +
271I GLY 3.3 4.2 + - - -
272I ASP* 2.9 46.5 + - + +
275I ARG* 3.6 26.5 - - + -
276I ALA* 4.1 12.6 - - + +
279I TYR* 3.5 39.3 - + - -
324I LYS* 5.1 6.9 - - - +
1L G 3.0 16.1 + - - -
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Residues in contact with SER 268 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264I ALA 3.0 15.0 + - - -
265I LYS* 3.1 12.7 + - - -
267I TYR* 1.3 76.1 - - - +
269I VAL* 1.3 60.7 + - - +
271I GLY* 3.1 18.4 + - - -
272I ASP 4.6 2.5 - - - -
273I LYS* 5.4 2.1 + - - +
276I ALA* 3.8 16.8 - - - +
346I THR* 4.3 4.3 + - - -
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Residues in contact with VAL 269 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265I LYS* 3.0 17.8 + - + +
266I ALA 3.3 12.8 - - - +
268I SER* 1.3 73.8 - - - +
270I GLN* 1.3 62.2 + - + +
271I GLY 3.1 4.9 - - - -
332I VAL* 3.9 29.4 - - + +
335I LEU* 4.1 21.5 - - + +
336I GLU* 3.6 37.7 - - + +
339I SER* 3.8 13.0 + - - +
346I THR* 2.8 23.0 + - - +
349I ALA* 5.2 0.9 - - - +
350I GLN* 4.6 0.3 + - - -
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Residues in contact with GLN 270 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266I ALA* 3.2 26.3 + - - +
267I TYR* 3.7 19.7 - - - +
268I SER 3.2 0.8 - - - -
269I VAL* 1.3 77.9 - - - +
271I GLY* 1.3 59.7 + - - +
272I ASP* 3.4 3.8 + - + +
328I ILE* 5.6 0.6 - - - +
329I SER* 4.0 19.2 - - - +
331I SER* 4.9 2.0 + - - -
332I VAL* 3.7 26.7 - - + +
335I LEU* 4.2 15.3 - - + -
346I THR* 3.3 3.4 - - - -
350I GLN* 3.5 14.4 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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