Contacts of the helix formed by residues 309 - 325 (chain C) in PDB entry 4LXZ
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 THR 309 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C GLY 2.7 25.9 + - - +
274C ASP* 3.5 7.7 + - - -
275C ARG* 3.1 20.8 + - + +
308C TYR* 1.3 72.2 - - - +
310C ILE* 1.3 59.8 + - - +
311C ARG* 3.6 33.4 - - + +
312C ASN* 3.0 34.3 + - - +
313C VAL* 3.0 25.0 + - - +
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Residues in contact with ILE 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C PRO 5.3 0.2 - - - +
36C LYS* 3.9 33.7 - - + -
38C HIS* 4.2 11.0 - - + -
39C ARG* 3.8 29.0 - - + +
42C MET* 3.5 27.8 - - + +
307C GLY 4.8 0.2 - - - +
308C TYR* 3.5 14.7 + - - +
309C THR* 1.3 70.7 - - - +
311C ARG* 1.3 63.8 + - - +
313C VAL* 3.2 7.1 + - - +
314C ALA* 3.1 23.7 + - - +
341C TYR* 4.1 18.8 - - + -
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Residues in contact with ARG 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C MET* 4.1 4.3 - - - -
309C THR* 3.6 24.4 - - + +
310C ILE* 1.3 80.5 - - - +
312C ASN* 1.4 68.7 + - - +
314C ALA 3.6 0.2 + - - -
315C ARG* 3.1 50.2 + - - +
341C TYR* 3.2 33.2 - - + +
342C PHE* 3.3 23.2 - - + -
343C GLY 4.7 11.3 + - - -
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Residues in contact with ASN 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271C LEU* 3.6 21.9 - - + +
272C SER 3.9 18.4 + - - -
273C GLY* 4.7 2.8 + - - -
283C VAL* 4.4 0.2 - - - +
309C THR* 3.0 32.9 + - + +
311C ARG* 1.4 80.2 + - - +
313C VAL* 1.3 60.6 + - + +
315C ARG* 3.2 28.1 + - - +
316C CYS* 2.9 31.5 + - - +
350C ILE* 3.6 22.4 - - + +
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Residues in contact with VAL 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C ARG* 3.9 17.7 - - + +
43C THR* 4.7 0.7 - - - +
268C ALA* 4.0 12.3 - - + +
274C ASP* 5.2 0.7 - - - +
307C GLY* 3.4 39.7 - - - +
308C TYR 3.9 0.4 - - - +
309C THR 3.0 14.9 + - - +
310C ILE* 3.2 10.1 + - - +
312C ASN* 1.3 77.4 - - + +
314C ALA* 1.4 57.4 + - - +
316C CYS* 3.2 2.6 + - - +
317C TRP* 3.0 71.1 + - + +
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Residues in contact with ALA 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C ARG 4.5 0.4 + - - +
42C MET* 3.9 16.4 - - + +
43C THR* 3.3 33.5 + - - +
46C LEU* 4.1 2.9 - - + -
310C ILE 3.1 15.4 + - - +
311C ARG 3.8 4.9 - - - +
313C VAL* 1.4 75.3 - - - +
315C ARG* 1.3 59.7 + - - +
318C THR* 2.6 34.3 + - - -
342C PHE* 4.0 15.3 - - + -
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Residues in contact with ARG 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C LEU* 4.3 4.0 - - + -
283C VAL* 4.2 7.2 - - + -
311C ARG* 3.1 43.6 + - - +
312C ASN* 3.2 30.1 + - - +
313C VAL 3.3 0.2 - - - -
314C ALA* 1.3 76.9 - - - +
316C CYS* 1.4 62.6 + - - +
318C THR* 3.7 1.6 - - - -
319C TYR* 3.0 26.0 + - - +
333C LEU* 4.9 0.9 - - + -
342C PHE* 3.1 42.9 + - + +
343C GLY 5.7 0.2 + - - -
345C ASP* 3.2 17.1 + - - -
347C LYS 2.8 28.4 + - - +
348C LEU* 3.2 39.3 + - + +
349C HIS 5.1 0.4 - - - -
350C ILE* 3.8 13.8 - - - +
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Residues in contact with CYS 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268C ALA* 4.3 9.4 - - + -
271C LEU* 3.7 20.9 - - + -
283C VAL* 3.9 13.6 - - + +
286C HIS* 3.2 44.6 - - - -
312C ASN 2.9 18.8 + - - +
313C VAL 3.6 3.6 - - - +
315C ARG* 1.4 77.1 - - - +
317C TRP* 1.3 58.4 - - + +
319C TYR* 3.4 2.1 + - - +
320C GLU* 2.9 43.6 + - - +
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Residues in contact with TRP 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C ARG* 3.6 29.6 - - + -
40C ILE* 4.4 9.6 - - + -
43C THR* 3.6 25.8 - - + -
140C TRP* 3.5 57.6 - + + -
266C CYS 2.9 23.1 + - - -
268C ALA* 4.0 6.7 - - + +
304C GLY* 3.5 16.8 - - - -
305C GLY 3.6 15.7 - - - -
306C GLY 3.8 12.3 - - - -
313C VAL* 3.0 36.1 + - + +
316C CYS* 1.3 75.8 - - + +
318C THR* 1.3 56.5 + - - +
320C GLU* 3.5 17.5 - - - +
321C THR* 2.6 37.9 + - - -
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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
----------------------------------------------------------
43C THR* 3.5 20.4 + - - +
46C LEU* 3.5 14.8 - - + +
47C LEU* 4.1 17.3 - - + -
50C TYR* 3.6 36.3 - - + -
52C LEU* 3.9 2.9 - - + +
314C ALA 2.6 25.1 + - - -
315C ARG* 3.7 3.8 - - - -
317C TRP* 1.3 76.8 - - - +
319C TYR* 1.3 57.5 + - - +
321C THR* 3.1 9.0 + - - -
322C ALA* 3.0 25.5 + - - +
329C ILE* 3.9 7.4 - - + -
348C LEU* 4.5 1.3 - - + -
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Residues in contact with TYR 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C VAL* 3.8 19.7 - - + -
284C LYS* 4.3 20.5 - - + +
287C ALA* 3.5 33.0 - - + -
291C GLU* 5.2 6.6 + - - -
315C ARG 3.0 17.9 + - - +
316C CYS 3.8 0.7 - - - +
318C THR* 1.3 76.5 - - - +
320C GLU* 1.3 51.7 + - - +
322C ALA* 3.1 8.8 + - + +
323C VAL* 2.8 46.5 + - + +
327C CYS 5.6 1.3 - - - -
328C GLU* 6.0 1.3 - - - -
329C ILE* 4.2 20.2 - - + -
348C LEU* 3.7 22.9 - - + -
349C HIS* 3.7 24.6 - + - -
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Residues in contact with GLU 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C TRP* 4.1 14.8 - - + -
180C ILE* 4.8 0.2 - - - +
266C CYS* 3.7 10.4 - - - +
283C VAL* 6.0 0.2 - - + -
286C HIS* 2.5 35.2 + - - +
287C ALA* 3.2 32.2 + - + -
290C VAL* 3.8 20.6 - - + +
302C MET* 3.6 13.6 - - + +
316C CYS* 2.9 21.4 + - - +
317C TRP* 3.5 23.7 - - - +
318C THR 3.3 0.2 - - - -
319C TYR* 1.3 72.5 - - - +
321C THR* 1.3 59.3 + - - +
323C VAL* 3.4 7.6 + - - +
324C ALA 3.0 22.3 + - - -
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Residues in contact with THR 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C VAL* 5.3 1.3 - - + -
18C TYR* 4.5 4.7 - - + -
47C LEU* 3.8 13.9 - - + +
52C LEU* 4.5 4.0 - - + -
56C MET* 3.7 37.5 - - + -
138C VAL* 4.7 7.4 - - + +
140C TRP* 3.0 22.0 + - - -
302C MET* 5.2 0.2 - - - -
317C TRP 2.6 22.9 + - - -
318C THR 3.1 5.8 + - - -
320C GLU* 1.3 73.4 - - - +
322C ALA* 1.3 65.4 + - - +
324C ALA* 3.2 7.3 + - - +
325C LEU* 3.1 29.9 + - + +
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Residues in contact with ALA 322 (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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52C LEU* 4.1 17.2 - - + +
318C THR 3.0 11.2 + - - +
319C TYR* 3.3 11.4 - - + +
321C THR* 1.3 76.5 - - - +
323C VAL* 1.4 56.5 + - - +
325C LEU* 3.2 4.0 + - - -
326C ASP 3.0 8.0 + - - -
327C CYS* 2.9 46.9 + - - +
329C ILE* 3.8 27.1 - - + -
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Residues in contact with VAL 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287C ALA* 4.2 9.0 - - + -
290C VAL* 3.8 23.3 - - + -
291C GLU* 3.7 32.5 - - + +
294C LYS* 2.8 33.7 + - + +
319C TYR* 2.8 52.8 + - + +
320C GLU* 3.6 7.4 - - - +
321C THR 3.3 0.2 - - - -
322C ALA* 1.4 72.5 - - - +
324C ALA* 1.4 50.9 + - - +
326C ASP* 2.9 13.5 + - - +
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Residues in contact with ALA 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C LYS* 5.1 2.3 - - - +
16C VAL* 3.6 18.7 - - + +
136C MET* 3.3 45.4 - - - +
138C VAL* 4.9 2.7 - - + -
290C VAL* 4.7 0.6 - - - +
294C LYS* 3.6 10.8 + - - -
302C MET* 3.9 16.6 - - + -
320C GLU 3.0 14.4 + - - +
321C THR* 3.2 11.9 + - - +
323C VAL* 1.4 75.3 - - - +
325C LEU* 1.3 58.5 + - - +
326C ASP* 3.3 0.7 + - - +
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Residues in contact with LEU 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C LYS 5.6 4.9 - - - +
16C VAL* 3.8 20.0 - - + +
52C LEU* 3.9 43.1 - - + +
55C LYS* 3.4 43.4 - - + +
56C MET* 3.7 23.3 - - + -
321C THR* 3.1 21.0 + - + +
322C ALA 3.6 4.0 - - - +
323C VAL 3.2 0.4 - - - -
324C ALA* 1.3 74.6 - - - +
326C ASP* 1.4 69.1 + - - +
327C CYS* 3.3 9.9 + - + +
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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