Contacts of the helix formed by residues 308 - 321 (chain C) in PDB entry 4LQL
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 ASP 308 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191C THR* 3.1 31.5 - - - +
276C THR* 3.8 6.0 - - - +
304C GLY* 3.9 6.3 - - - -
305C PRO 3.1 14.0 + - - +
306C GLU 3.3 2.2 - - - -
307C GLY* 1.3 72.6 - - - +
309C PHE* 1.3 62.3 + - - +
310C LYS* 3.2 18.8 + - - +
311C MET* 3.5 15.8 + - + +
312C ALA* 3.3 19.1 + - - +
447C HIS* 3.4 38.3 + - + +
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Residues in contact with PHE 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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178C ILE* 3.8 15.0 - - + +
191C THR 4.3 4.8 + - - -
192C GLU* 6.0 0.7 - - - -
193C GLY* 5.6 8.3 - - - -
195C LYS* 6.0 8.5 - - + -
198C ALA* 5.9 7.0 - - + -
206C VAL* 6.0 5.2 - - - -
276C THR* 4.1 10.3 - - + +
307C GLY 3.4 7.3 + - - +
308C ASP* 1.3 72.0 + - - +
310C LYS* 1.3 81.2 + - + +
312C ALA* 3.4 3.5 + - - +
313C GLY* 3.0 17.5 + - - -
400C TYR* 6.2 0.4 - - - -
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Residues in contact with LYS 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191C THR 5.4 1.1 - - - +
308C ASP* 3.2 11.6 - - - +
309C PHE* 1.3 86.2 - - + +
311C MET* 1.3 52.6 + - + +
312C ALA 2.9 2.1 + - - -
313C GLY* 3.5 0.9 - - - -
314C LEU* 2.6 38.8 + - - +
393C LEU* 3.9 37.3 - - + +
400C TYR* 6.0 2.9 - - + -
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Residues in contact with MET 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303C PHE 4.1 3.5 - - - +
304C GLY* 4.3 5.6 - - - -
308C ASP* 3.5 19.4 + - + +
310C LYS* 1.3 78.5 - - + +
312C ALA* 1.3 56.2 + - - +
314C LEU* 3.6 27.8 - - + +
315C THR* 3.1 26.2 + - - -
329C LEU* 5.0 6.7 - - + +
392C THR* 5.1 2.2 - - - -
393C LEU 5.2 3.4 - - - +
447C HIS* 3.0 42.0 - - + +
448C THR 3.7 7.9 - - - +
449C VAL* 4.7 2.1 - - - +
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Residues in contact with ALA 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178C ILE* 3.7 15.3 - - + -
274C ALA* 4.0 3.8 - - + +
275C PHE 4.0 9.2 - - - +
276C THR* 4.1 4.3 - - + -
302C GLY* 3.7 5.2 - - - -
303C PHE* 3.7 4.7 - - - -
304C GLY* 3.2 27.1 - - - +
308C ASP 3.3 11.4 + - - +
309C PHE 3.5 9.4 - - - +
310C LYS 2.9 0.8 + - - -
311C MET* 1.3 74.6 - - - +
313C GLY* 1.3 58.2 + - - +
314C LEU 3.1 0.7 - - - -
315C THR* 2.7 22.9 + - - -
316C ARG 3.0 10.7 + - - -
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Residues in contact with GLY 313 (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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176C ILE* 5.2 7.5 - - - +
178C ILE* 3.5 13.2 - - - +
204C TRP* 5.7 7.6 - - - -
274C ALA* 4.8 0.2 - - - -
309C PHE 3.0 11.1 + - - -
310C LYS 3.5 2.2 - - - -
312C ALA* 1.3 76.1 - - - +
314C LEU* 1.3 62.6 + - - +
316C ARG* 3.6 8.4 - - - +
317C LEU* 3.2 31.0 + - - +
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Residues in contact with LEU 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 LYS 2.6 22.1 + - - +
311C MET* 3.6 22.4 - - + -
313C GLY* 1.3 71.6 - - - +
315C THR* 1.3 65.7 + - - +
316C ARG 3.5 0.2 + - - -
317C LEU* 4.7 6.3 - - + -
318C LEU* 3.6 30.8 + - + +
391C ILE* 3.3 34.5 - - + +
392C THR* 4.4 13.7 - - - +
393C LEU* 4.6 18.4 - - + +
402C PHE* 5.7 4.7 - - + -
449C VAL* 3.5 26.7 - - + +
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Residues in contact with THR 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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297C MET* 5.8 1.2 - - - +
302C GLY* 3.6 4.9 - - - -
303C PHE 3.4 21.2 + - - -
311C MET 3.1 14.6 + - - -
312C ALA 2.7 14.5 + - - -
314C LEU* 1.3 79.9 - - - +
316C ARG* 1.3 61.6 + - - +
318C LEU* 4.5 1.4 - - - +
319C LYS* 3.4 28.4 + - - +
328C ALA* 4.6 3.0 - - - -
329C LEU* 3.3 33.3 + - - +
449C VAL* 4.3 7.0 - - - +
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Residues in contact with ARG 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C ILE* 4.1 19.3 - - + -
273C ASP* 4.8 8.5 - - - -
274C ALA* 4.6 8.1 - - + -
300C GLY 4.9 3.1 - - - +
302C GLY* 3.7 14.9 - - - +
312C ALA 3.0 9.8 + - - +
313C GLY* 3.6 11.0 - - - +
315C THR* 1.3 73.4 - - - +
317C LEU* 1.3 56.3 + - - +
318C LEU 2.6 1.4 + - - -
319C LYS* 2.6 36.3 + - - -
320C ILE* 2.8 13.8 + - + -
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Residues in contact with LEU 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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169C ALA* 4.5 6.4 - - + +
173C SER* 2.9 32.0 + - - +
176C ILE* 4.9 1.8 - - + +
313C GLY 3.2 18.8 + - - +
314C LEU* 4.3 7.9 - - + +
316C ARG* 1.3 76.3 - - - +
318C LEU* 1.3 54.4 + - + +
320C ILE* 3.2 12.6 - - - +
321C ALA* 2.6 36.3 + - - +
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Residues in contact with LEU 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 LEU* 3.6 27.3 + - + +
315C THR 4.5 1.1 - - - +
316C ARG 2.6 5.7 + - - -
317C LEU* 1.3 75.5 - - + +
319C LYS* 1.3 61.0 + - - +
320C ILE 3.1 0.9 - - - -
321C ALA* 2.9 30.4 + - - +
322C ALA* 3.2 8.0 + - - +
327C THR* 3.6 20.6 - - + +
391C ILE* 6.4 1.6 - - + -
449C VAL* 4.2 18.2 - - + -
451C THR* 4.8 5.4 - - - +
454C LEU* 4.1 11.5 - - + +
459C LEU* 6.2 4.0 - - + -
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Residues in contact with LYS 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297C MET* 2.6 46.0 + - - +
298C ILE 5.7 0.7 - - - -
300C GLY* 4.2 32.4 - - - +
301C TYR 4.1 6.7 + - - +
302C GLY* 5.2 1.1 - - - -
315C THR* 3.4 21.2 + - - +
316C ARG 2.6 12.1 + - - +
318C LEU* 1.3 74.3 - - - +
320C ILE* 1.3 59.1 + - - +
322C ALA* 3.2 21.4 + - - +
323C ASP* 4.2 1.6 + - - -
324C ASN 5.2 0.5 + - - -
325C LYS 5.6 1.6 - - - +
327C THR* 3.1 37.7 - - + +
328C ALA* 4.2 6.0 - - - +
329C LEU 5.6 0.4 - - - +
353C ASP* 3.6 14.3 - - - +
355C THR* 4.2 4.7 - - - -
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Residues in contact with ILE 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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3C LYS* 5.2 12.1 - - + +
165C HIS 5.5 0.5 - - - +
168C VAL* 5.2 7.0 - - + +
169C ALA* 4.8 7.5 - - + +
172C GLU* 3.4 39.7 - - + -
173C SER* 5.5 1.6 - - - +
176C ILE* 6.1 3.8 - - + -
316C ARG* 2.8 11.8 + - + +
317C LEU* 3.2 22.2 - - - +
319C LYS* 1.3 78.7 - - - +
321C ALA* 1.3 53.3 + - - +
322C ALA 3.4 2.2 + - - -
323C ASP* 5.0 5.7 + - - -
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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
----------------------------------------------------------
165C HIS* 4.5 28.8 - - + +
166C VAL* 5.2 4.3 - - + +
169C ALA* 4.3 16.6 - - + -
317C LEU 2.6 17.9 + - - +
318C LEU* 2.9 9.5 + - - +
320C ILE* 1.3 74.8 - - - +
322C ALA* 1.3 58.8 + - - +
323C ASP 4.1 0.2 - - - -
453C ALA 5.3 0.3 - - - +
454C LEU* 3.6 26.0 - - + +
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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