Contacts of the helix formed by residues 308 - 321 (chain I) in PDB entry 3LUE
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 308 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219I VAL* 3.8 16.8 - - - -
307I PRO* 1.4 71.0 - - - +
309I ILE* 1.4 62.7 + - - +
310I ALA 3.4 3.1 + - - -
311I ASP* 3.5 17.0 + - - +
312I ARG* 2.9 26.2 + - - +
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Residues in contact with ILE 309 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153I MET* 5.3 9.4 - - + -
219I VAL* 4.0 15.0 - - + +
261I LEU* 4.4 17.7 - - + -
262I PHE* 4.3 19.7 - - + -
274I ILE* 5.5 1.1 - - + -
299I LEU* 3.8 17.7 - - + -
303I THR 4.1 19.7 - - - +
304I THR* 3.2 30.3 - - - +
306I TYR* 3.1 23.1 + - + +
307I PRO 3.4 1.0 + - - -
308I GLY* 1.4 77.0 - - - +
310I ALA* 1.3 61.7 + - - +
312I ARG* 4.6 0.2 - - - -
313I MET* 2.8 39.0 + - + +
335I ARG* 4.3 4.7 - - - +
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Residues in contact with ALA 310 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299I LEU* 4.4 2.9 - - - -
308I GLY 3.4 0.4 - - - -
309I ILE* 1.3 83.6 - - - +
311I ASP* 1.3 59.9 + - - +
313I MET* 3.6 1.7 - - - +
314I GLN* 2.9 30.3 + - - +
329I ILE* 3.6 24.5 - - + +
331I ALA* 4.3 19.1 - - + -
335I ARG* 6.0 0.4 - - - +
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Residues in contact with ASP 311 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221I LEU* 4.0 20.5 - - + +
308I GLY* 3.5 17.7 + - - +
310I ALA* 1.3 79.3 - - - +
312I ARG* 1.3 58.0 - - - +
314I GLN* 3.5 8.4 + - - +
315I LYS* 2.9 29.5 + - - +
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Residues in contact with ARG 312 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219I VAL* 3.9 14.6 - - + +
220I ALA 2.6 36.4 + - - +
221I LEU* 3.7 26.0 + - + +
223I PHE* 4.7 5.4 - - - +
259I GLU* 2.8 29.1 + - - -
262I PHE* 3.5 39.6 - - + +
263I GLN* 4.8 5.7 - - - +
275I HIS* 5.6 0.4 - - - -
308I GLY 2.9 17.9 + - - +
309I ILE 4.1 1.8 - - - +
311I ASP* 1.3 74.5 - - - +
313I MET* 1.3 63.6 + - - +
315I LYS* 4.0 6.6 - - - +
316I GLU* 2.7 64.4 + - - +
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Residues in contact with MET 313 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153I MET* 3.8 39.3 - - + -
262I PHE* 4.0 14.4 - - + -
274I ILE* 4.0 16.2 - - + +
275I HIS* 4.1 12.3 - - - -
278I THR* 3.9 13.0 - - + +
297I THR* 5.2 1.1 - - + -
299I LEU* 3.9 16.2 - - + -
309I ILE* 2.8 27.6 + - + +
310I ALA* 3.6 5.2 - - - +
312I ARG* 1.3 74.6 - - - +
314I GLN* 1.3 63.0 + - - +
316I GLU* 3.0 5.1 + - - +
317I ILE* 2.9 43.8 + - + +
329I ILE* 4.3 15.3 - - + -
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Residues in contact with GLN 314 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310I ALA 2.9 18.3 + - - +
311I ASP* 3.5 9.4 - - - +
313I MET* 1.3 73.4 - - - +
315I LYS* 1.3 63.0 + - - +
317I ILE 3.0 0.2 + - - -
318I THR* 2.7 53.5 + - - +
327I ILE* 3.0 33.4 + - - +
328I LYS* 4.6 0.2 - - - +
329I ILE* 3.9 25.4 - - + +
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Residues in contact with LYS 315 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221I LEU* 2.9 44.0 + - + +
222I ASP* 4.6 14.5 + - - +
311I ASP 2.9 20.6 + - - +
312I ARG* 3.8 6.2 - - - +
314I GLN* 1.3 72.8 - - - +
316I GLU* 1.3 90.3 + - + +
318I THR* 3.7 7.6 - - - -
319I ALA* 3.3 19.8 + - - +
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Residues in contact with GLU 316 (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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262I PHE* 4.7 1.3 - - + -
275I HIS* 3.7 37.9 + - + -
312I ARG* 2.7 60.8 + - + +
313I MET 3.0 4.9 + - - +
315I LYS* 1.3 98.4 + - - +
317I ILE* 1.3 64.0 + - - +
319I ALA* 3.4 16.1 + - - +
320I LEU* 3.2 22.1 + - - +
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Residues in contact with ILE 317 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275I HIS* 4.1 16.2 - - - +
278I THR* 3.6 31.0 - - + -
279I PHE* 5.4 5.8 - - + +
282I ILE* 5.8 0.7 - - + -
294I TYR* 4.0 19.1 - - + -
297I THR* 4.2 7.2 - - + +
313I MET* 2.9 37.5 + - - +
314I GLN 3.9 2.0 - - - +
316I GLU* 1.3 76.8 - - - +
318I THR* 1.3 58.4 + - - +
319I ALA 3.2 0.5 + - - -
320I LEU* 3.3 6.6 + - + +
321I ALA* 2.9 28.6 + - - +
327I ILE* 3.6 28.3 - - + -
329I ILE* 4.1 15.5 - - + -
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Residues in contact with THR 318 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314I GLN* 2.7 41.5 + - - +
315I LYS* 3.7 7.9 - - - -
317I ILE* 1.3 77.6 - - - +
319I ALA* 1.3 58.8 + - - +
321I ALA* 3.9 10.8 - - - +
327I ILE* 3.6 19.1 - - + +
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Residues in contact with ALA 319 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315I LYS* 3.3 13.8 + - + +
316I GLU* 3.7 15.5 - - - +
317I ILE 3.2 1.2 - - - -
318I THR* 1.3 77.3 - - - +
320I LEU* 1.3 63.4 + - + +
321I ALA 3.6 2.6 + - - +
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Residues in contact with LEU 320 (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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246G GLN* 6.0 0.2 - - - +
275I HIS* 3.9 37.7 - - + +
276I GLU* 3.5 22.0 - - - +
279I PHE* 3.4 48.7 - - + -
316I GLU 3.2 20.3 + - - +
317I ILE* 3.3 6.0 + - - +
319I ALA* 1.3 77.9 - - + +
321I ALA* 1.3 62.5 + - - +
322I PRO* 3.8 1.7 - - - +
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Residues in contact with ALA 321 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244G ASP 3.8 5.4 - - - +
279I PHE* 4.4 0.4 - - - -
294I TYR* 3.7 18.4 - - + -
317I ILE 2.9 18.9 + - - +
318I THR 3.9 10.2 - - - +
319I ALA 3.4 3.0 - - - +
320I LEU* 1.3 78.7 - - - +
322I PRO* 1.4 77.8 - - + +
323I SER* 3.5 3.5 + - - -
325I MET* 4.2 0.9 - - + -
327I ILE* 3.4 23.8 - - + -
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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