Contacts of the helix formed by residues 308 - 321 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219C VAL* 3.8 16.8 - - - -
306C TYR 3.5 0.2 + - - -
307C PRO* 1.4 70.5 - - - +
309C ILE* 1.4 63.0 + - - +
310C ALA 3.4 2.2 + - - -
311C ASP* 3.5 17.9 + - - +
312C ARG* 2.9 26.2 + - - +
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Residues in contact with ILE 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C MET* 5.3 9.2 - - + -
219C VAL* 4.1 15.3 - - + -
261C LEU* 4.4 16.8 - - + -
262C PHE* 4.3 18.4 - - + -
274C ILE* 5.5 1.8 - - + -
299C LEU* 3.8 16.6 - - + -
303C THR 4.1 19.3 - - - +
304C THR* 3.2 31.0 - - - +
306C TYR* 3.1 23.0 + - + +
307C PRO 3.5 1.0 + - - -
308C GLY* 1.4 76.0 - - - +
310C ALA* 1.3 60.3 + - - +
312C ARG* 4.6 0.4 - - - +
313C MET* 2.8 39.6 + - + +
335C ARG* 4.3 5.4 - - - +
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Residues in contact with ALA 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C LEU* 4.4 2.9 - - - -
308C GLY 3.4 0.6 - - - -
309C ILE* 1.3 82.9 - - + +
311C ASP* 1.3 59.0 + - - +
313C MET* 3.6 1.7 - - - +
314C GLN* 2.9 30.1 + - - +
329C ILE* 3.6 22.3 - - + +
331C ALA* 4.3 20.2 - - + -
335C ARG* 6.0 0.2 - - - +
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Residues in contact with ASP 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221C LEU* 4.0 20.1 - - + +
308C GLY* 3.5 18.1 + - - +
310C ALA* 1.3 81.2 - - - +
312C ARG* 1.3 58.6 + - - +
314C GLN* 3.5 7.8 - - - +
315C LYS* 2.9 29.8 + - - +
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Residues in contact with ARG 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219C VAL* 3.9 14.0 - - + +
220C ALA 2.6 37.3 + - - +
221C LEU* 3.7 26.5 + - + +
223C PHE* 4.7 5.4 - - - +
259C GLU* 2.8 28.5 + - - -
262C PHE* 3.5 39.2 - - + +
263C GLN* 4.8 5.5 - - - +
275C HIS* 5.6 0.8 - - - -
308C GLY 2.9 18.4 + - - +
309C ILE* 4.1 1.8 - - - +
311C ASP* 1.3 73.9 - - - +
313C MET* 1.3 63.4 + - - +
315C LYS* 4.0 6.0 - - - +
316C GLU* 2.7 64.6 + - - +
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Residues in contact with MET 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153C MET* 3.8 39.3 - - + -
262C PHE* 4.0 15.0 - - + -
274C ILE* 4.0 17.3 - - + +
275C HIS* 4.1 12.1 - - - -
278C THR* 3.9 12.1 - - + +
297C THR* 5.2 0.7 - - + -
299C LEU* 3.9 17.0 - - + -
309C ILE* 2.8 28.4 + - + +
310C ALA* 3.6 5.8 - - - +
312C ARG* 1.3 74.0 - - - +
314C GLN* 1.3 61.7 + - - +
316C GLU* 3.0 5.2 + - - +
317C ILE* 2.9 43.4 + - + +
329C ILE* 4.3 14.8 - - + -
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Residues in contact with GLN 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310C ALA 2.9 18.2 + - - +
311C ASP* 3.5 8.7 - - - +
313C MET* 1.3 73.1 - - - +
315C LYS* 1.3 62.6 + - + +
317C ILE* 3.0 1.0 + - - +
318C THR* 2.7 53.5 + - - +
327C ILE* 3.0 34.6 + - - +
328C LYS* 4.6 0.4 - - - +
329C ILE* 3.9 24.4 - - + +
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Residues in contact with LYS 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221C LEU* 2.9 44.2 + - + +
222C ASP* 4.6 15.0 + - - +
311C ASP 2.9 21.3 + - - +
312C ARG* 3.8 7.3 - - - +
314C GLN* 1.3 71.2 - - - +
316C GLU* 1.3 91.3 + - + +
318C THR* 3.7 6.9 - - - -
319C ALA* 3.3 20.1 + - - +
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Residues in contact with GLU 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262C PHE* 4.7 1.8 - - + -
275C HIS* 3.7 38.4 + - + -
312C ARG* 2.7 60.1 + - + +
313C MET 3.0 4.6 + - - +
314C GLN 2.9 0.2 + - - -
315C LYS* 1.3 98.0 + - - +
317C ILE* 1.3 64.1 + - - +
319C ALA* 3.4 16.0 + - - +
320C LEU* 3.2 21.9 + - - +
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Residues in contact with ILE 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275C HIS* 4.1 17.3 - - - +
278C THR* 3.6 30.7 - - + -
279C PHE* 5.4 6.1 - - + +
282C ILE* 5.8 0.7 - - + -
294C TYR* 4.0 18.6 - - + -
297C THR* 4.2 6.5 - - + +
313C MET* 2.9 36.8 + - - +
314C GLN 3.9 1.6 - - - +
316C GLU* 1.3 77.1 - - - +
318C THR* 1.3 58.8 + - - +
319C ALA 3.2 0.5 + - - -
320C LEU* 3.3 6.4 + - + +
321C ALA* 2.9 28.2 + - - +
327C ILE* 3.6 29.2 - - + -
329C ILE* 4.1 15.9 - - + -
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Residues in contact with THR 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314C GLN* 2.7 40.6 + - - +
315C LYS* 3.7 9.0 - - - -
317C ILE* 1.3 77.3 - - - +
319C ALA* 1.3 60.4 + - - +
321C ALA* 3.9 10.6 - - - +
327C ILE* 3.6 20.1 - - + +
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Residues in contact with ALA 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315C LYS 3.3 14.4 + - - +
316C GLU* 3.7 15.7 - - - +
317C ILE 3.2 0.8 - - - -
318C THR* 1.3 77.5 - - - +
320C LEU* 1.3 63.4 + - + +
321C ALA 4.2 2.8 - - - +
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Residues in contact with LEU 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A GLN* 6.0 0.3 - - - +
275C HIS* 3.9 38.4 - - + +
276C GLU* 3.5 22.2 - - - +
279C PHE* 3.4 49.0 - - + -
316C GLU 3.2 21.4 + - - +
317C ILE* 3.3 4.9 + - - +
319C ALA* 1.3 76.7 - - + +
321C ALA* 1.3 64.0 + - - +
322C PRO* 3.8 1.6 - - - +
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Residues in contact with ALA 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A ASP 3.8 5.2 - - - +
279C PHE* 4.5 0.2 - - - -
294C TYR* 3.7 20.0 - - + -
317C ILE 2.9 18.7 + - - +
318C THR 3.9 10.4 - - - +
319C ALA 3.4 3.5 - - - +
320C LEU* 1.3 79.1 - - - +
322C PRO* 1.4 76.5 - - + +
323C SER* 3.5 3.5 + - - -
325C MET* 4.2 0.4 - - + -
327C ILE* 3.4 23.6 - - + -
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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