Contacts of the helix formed by residues 305 - 324 (chain C) in PDB entry 4IL6
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 305 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291C TRP 3.4 20.0 - - - +
292C PHE 3.6 20.2 + - - +
294C ASN* 4.4 7.4 - - + -
304C PRO* 1.3 76.4 - - - +
306C GLY* 1.3 65.0 + - - +
307C PRO* 3.6 10.2 - - - +
308C GLU* 3.0 32.3 + - - +
309C ALA* 2.9 22.9 + - - +
361C PHE* 4.2 5.4 - - + -
400C PRO* 4.0 0.7 - - - -
423C ARG* 3.5 33.8 - - - +
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Residues in contact with GLY 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A GLY 6.0 0.2 - - - -
296A ASN* 5.8 1.3 - - - -
343A LEU* 5.0 8.1 - - - +
344A ALA* 6.2 0.9 - - - -
291C TRP* 4.4 14.5 + - - -
305C THR* 1.3 73.1 - - - +
307C PRO* 1.4 71.5 - - - +
309C ALA* 3.5 1.9 + - - +
310C SER* 3.2 21.8 + - - -
358C PHE* 4.3 7.4 - - - -
400C PRO* 3.5 26.5 - - - +
401C LEU* 6.1 0.2 - - - -
423C ARG* 5.2 0.2 - - - +
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Residues in contact with PRO 307 (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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164A GLY 5.7 0.2 - - - +
291C TRP* 4.5 14.8 - - - +
292C PHE* 4.2 25.1 - - + +
305C THR* 3.6 13.2 - - - +
306C GLY* 1.4 88.5 - - - +
308C GLU* 1.3 56.8 + - - +
310C SER* 3.4 3.6 + - - -
311C GLN* 3.0 35.6 + - - +
358C PHE* 3.5 42.7 - - + +
361C PHE* 4.3 15.5 - - + +
515C DGD 5.6 1.1 - - - +
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Residues in contact with GLU 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294C ASN* 4.0 9.6 + - - -
299C SER* 2.7 28.0 + - - -
304C PRO* 3.4 2.8 - - + +
305C THR* 3.0 33.0 + - - +
307C PRO* 1.3 76.2 - - - +
309C ALA* 1.3 57.0 + - - +
311C GLN* 3.3 2.9 + - - +
312C ALA* 2.8 30.3 + - - +
361C PHE* 3.3 30.9 - - + -
363C GLY* 4.8 0.3 - - - -
364C PRO* 5.2 1.2 - - - +
365C TRP* 2.7 30.7 + - - +
395C TYR* 3.3 25.8 - - + -
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Residues in contact with ALA 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A LEU* 3.5 11.8 - - + +
304C PRO* 4.1 4.9 - - + +
305C THR 2.9 14.9 + - - +
306C GLY 4.0 3.4 - - - +
308C GLU* 1.3 76.2 - - - +
310C SER* 1.3 57.5 + - - +
312C ALA* 3.4 5.9 + - - +
313C GLN 3.0 21.7 + - - -
395C TYR 3.3 25.8 - - - +
396C MET* 3.8 3.1 - - - -
399C ALA* 3.5 30.7 - - + -
400C PRO* 4.2 0.9 - - + -
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Residues in contact with SER 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A LEU* 4.1 23.3 - - - +
344A ALA* 5.3 0.9 + - - +
306C GLY 3.2 10.4 + - - -
308C GLU 3.2 0.6 - - - -
309C ALA* 1.3 76.5 - - - +
311C GLN* 1.3 65.1 + - - +
313C GLN* 3.3 14.5 + - - +
314C ALA* 3.4 9.2 + - - +
354C GLU* 5.9 0.2 - - - +
355C THR* 2.8 33.6 + - - -
358C PHE* 3.4 29.4 - - - -
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Residues in contact with GLN 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307C PRO 3.0 19.6 + - - +
308C GLU 3.6 6.5 - - - +
310C SER* 1.3 73.9 - - - +
312C ALA* 1.3 58.1 + - - +
314C ALA* 3.2 5.2 + - - +
315C MET* 3.0 26.7 + - - +
351C PHE* 3.6 29.3 + - + +
355C THR* 2.8 46.5 + - - +
358C PHE* 3.6 21.3 + - + +
359C TRP* 4.3 6.8 - - - +
361C PHE* 3.8 24.5 - - + +
365C TRP* 3.9 9.0 - - + -
366C LEU* 4.0 11.8 - - + +
370C ARG* 5.3 2.9 + - - -
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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
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308C GLU 2.8 17.3 + - - +
309C ALA 3.6 6.1 - - - +
310C SER 3.2 0.2 - - - -
311C GLN* 1.3 74.7 - - - +
313C GLN* 1.3 54.6 + - - +
315C MET* 3.5 2.0 + - - +
316C THR* 2.7 37.7 + - - -
365C TRP* 3.5 21.3 - - + -
392C ALA* 3.3 27.3 - - - +
395C TYR* 3.9 8.3 - - + -
396C MET 3.9 7.2 - - - +
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Residues in contact with GLN 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A PHE* 3.4 26.8 - - + +
340A PRO* 3.4 10.9 - - - +
341A LEU* 2.8 57.4 + - - +
343A LEU* 3.9 13.5 - - + +
309C ALA 3.0 13.5 + - - +
310C SER* 3.6 10.9 + - - +
311C GLN 3.3 0.6 - - - -
312C ALA* 1.3 74.4 - - - +
314C ALA* 1.3 64.6 + - - +
316C THR* 3.3 0.7 + - - -
317C PHE* 3.2 27.5 + - + +
396C MET* 3.8 26.9 - - + +
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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
----------------------------------------------------------
339A PHE* 3.7 33.3 - - + -
310C SER 3.4 2.0 + - - +
311C GLN 3.2 9.3 + - - +
313C GLN* 1.3 79.6 - - - +
315C MET* 1.3 56.8 + - - +
317C PHE* 3.4 1.4 + - - +
318C LEU* 2.9 31.1 + - - +
340C TYR* 5.1 1.2 - - - +
351C PHE* 3.8 31.3 - - + -
352C GLY 4.4 0.4 - - - +
355C THR* 3.9 12.6 - - + -
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Residues in contact with MET 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311C GLN 3.0 15.8 + - - +
312C ALA 3.6 4.9 - - - +
314C ALA* 1.3 74.2 - - - +
316C THR* 1.3 59.5 + - - +
318C LEU* 3.4 10.5 + - + +
319C ILE* 2.9 52.2 + - + +
351C PHE* 3.8 28.8 - - + -
365C TRP* 3.9 17.7 - - + +
366C LEU* 4.3 6.3 - - - -
369C LEU* 3.6 26.5 - - + -
380C ILE* 5.3 2.0 - - + -
384C ILE* 3.8 28.7 - - + -
388C GLN* 5.2 4.0 - - - +
392C ALA* 3.8 14.6 - - + -
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Residues in contact with THR 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312C ALA 2.7 22.1 + - - -
313C GLN 3.5 5.8 - - - -
315C MET* 1.3 76.3 - - - +
317C PHE* 1.3 61.7 + - + +
319C ILE* 3.4 9.1 + - - +
320C ARG* 2.9 26.6 + - + +
389C GLU* 4.9 4.8 + - + +
392C ALA* 3.5 22.6 + - - +
393C ALA* 3.7 6.8 + - + +
396C MET* 3.9 19.7 - - - -
48V THR* 4.0 31.2 - - + +
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Residues in contact with PHE 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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339A PHE* 3.6 26.0 - + + -
340A PRO* 3.5 33.2 - - + -
313C GLN* 3.2 20.9 + - + +
316C THR* 1.3 77.3 - - + +
318C LEU* 1.3 61.5 + - - +
320C ARG* 3.7 27.6 - - - -
321C ASP* 2.9 40.1 + - - +
340C TYR* 4.2 2.9 - - - -
396C MET* 3.6 24.5 - - + -
99U ASN* 4.8 0.2 - - - -
103U TYR* 3.8 15.9 - + - -
47V LYS 3.5 13.5 - - - -
48V THR 3.7 14.1 - - - -
50V PRO* 3.6 20.4 - - + -
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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 ALA 2.9 18.7 + - - +
315C MET* 3.6 13.5 - - + +
317C PHE* 1.3 75.5 - - - +
319C ILE* 1.3 60.1 + - - +
322C GLN* 2.8 43.3 + - - +
328C VAL* 3.9 20.8 - - + +
340C TYR* 3.8 30.7 - - + -
341C LEU* 4.1 17.0 - - + -
351C PHE* 3.9 22.9 - - + -
380C ILE* 3.4 35.0 - - + -
384C ILE* 4.5 1.3 - - + -
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Residues in contact with ILE 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 MET* 2.9 40.9 + - + +
316C THR* 3.6 6.1 - - - +
318C LEU* 1.3 77.8 - - - +
320C ARG* 1.3 65.0 + - - +
322C GLN* 3.8 6.3 - - - +
323C LYS* 2.9 35.8 + - + +
384C ILE* 3.7 42.8 - - + -
389C GLU* 3.5 52.7 - - + +
392C ALA* 5.1 0.4 - - + -
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Residues in contact with ARG 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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316C THR* 2.9 22.3 + - + +
317C PHE* 3.7 18.1 - - + +
319C ILE* 1.3 77.2 - - - +
321C ASP* 1.3 88.7 + - - +
323C LYS* 3.3 10.5 + - - +
324C LEU* 3.2 34.3 + - + +
389C GLU* 6.0 0.7 - - - -
42U TYR* 5.1 1.2 + - - -
98U TYR 4.4 6.3 + - - -
99U ASN* 3.6 20.6 - - - +
103U TYR* 4.2 8.5 - - - -
48V THR 4.1 12.8 - - - +
49V ASN* 3.0 43.3 + - - +
50V PRO* 3.9 14.6 - - - +
51V SER* 3.6 16.7 + - - +
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Residues in contact with ASP 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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317C PHE* 2.9 22.2 + - - +
318C LEU 4.1 0.4 - - - +
320C ARG* 1.3 105.5 + - - +
322C GLN* 1.3 64.1 + - - +
324C LEU* 3.0 17.9 + - - +
325C GLY 3.2 0.9 + - - -
326C ALA* 3.0 27.0 + - + +
328C VAL* 5.1 0.2 - - + -
340C TYR* 2.5 40.5 + - + +
98U TYR* 4.2 6.7 - - - +
99U ASN* 2.7 27.8 + - - +
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Residues in contact with GLN 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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318C LEU* 2.8 27.7 + - - +
319C ILE* 3.8 4.2 - - - +
321C ASP* 1.3 73.6 - - - +
323C LYS* 1.3 65.1 + - - +
325C GLY* 3.0 15.2 + - - -
326C ALA* 3.7 19.9 + - - +
328C VAL* 3.8 19.3 - - + +
380C ILE* 2.9 26.7 + - - +
381C LYS* 3.3 37.7 + - - +
384C ILE* 4.3 4.9 - - - +
47U LYS* 4.3 4.2 + - - -
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Residues in contact with LYS 323 (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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319C ILE* 2.9 26.8 + - + +
320C ARG* 3.3 13.0 + - - +
322C GLN* 1.3 75.8 - - - +
324C LEU* 1.3 58.7 + - + +
325C GLY 3.2 0.2 - - - -
389C GLU* 2.6 37.0 + - - +
43U PRO* 6.1 0.2 - - - +
47U LYS* 3.1 27.7 + - - +
88V ILE* 6.3 0.4 - - - +
91V VAL* 4.6 11.5 - - - +
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Residues in contact with LEU 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320C ARG* 3.2 29.9 + - + +
321C ASP* 3.0 20.9 + - - +
323C LYS* 1.3 77.6 - - + +
325C GLY* 1.3 56.2 - - - +
326C ALA 3.7 0.4 - - - -
32U ILE* 3.7 30.5 - - + +
42U TYR* 3.5 41.1 - - + +
43U PRO* 3.9 20.4 - - + +
47U LYS* 3.3 21.9 - - + +
98U TYR* 3.2 29.2 - - + +
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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