Contacts of the helix formed by residues 309 - 325 (chain B) in PDB entry 5IWG
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B GLY 2.7 27.1 + - - +
274B ASP* 3.6 8.9 + - - -
275B ARG* 3.1 18.8 + - - +
308B TYR* 1.3 71.8 - - - +
310B ILE* 1.3 59.7 + - - +
311B ARG* 3.6 34.5 - - + +
312B ASN* 3.0 46.0 + - - +
313B VAL* 3.2 11.4 + - - +
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Residues in contact with ILE 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B PRO 5.4 0.4 - - - +
36B LYS* 4.1 31.2 - - + -
38B HIS* 4.4 9.2 - - + -
39B ARG* 3.9 29.3 - - + +
42B MET* 3.6 27.9 - - + +
307B GLY 4.6 2.2 - - - +
308B TYR* 3.6 14.1 + - - +
309B THR* 1.3 74.1 - - - +
311B ARG* 1.3 65.7 + - - +
313B VAL* 3.2 7.9 + - - +
314B ALA* 3.0 23.4 + - - +
341B TYR* 4.4 13.9 - - + -
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Residues in contact with ARG 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B MET* 4.0 9.2 - - - -
309B THR* 3.6 25.6 - - + +
310B ILE* 1.3 82.8 - - - +
312B ASN* 1.3 66.2 + - - +
314B ALA 3.5 0.2 + - - -
315B ARG* 3.1 50.3 + - - +
341B TYR* 3.2 32.1 - - + +
342B PHE* 3.4 18.6 - - + -
343B GLY 4.5 5.7 + - - -
407B PEG 4.1 24.4 + - - -
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Residues in contact with ASN 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B LEU* 3.5 20.3 - - + +
272B SER 3.7 21.2 + - - -
273B GLY* 4.8 2.2 + - - -
283B VAL* 4.4 0.5 - - - +
309B THR* 3.0 31.6 + - + +
311B ARG* 1.3 79.3 + - - +
313B VAL* 1.3 59.8 + - + +
315B ARG* 3.1 29.8 + - - +
316B CYS* 2.9 30.5 + - - +
350B ILE* 3.6 23.8 - - + +
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Residues in contact with VAL 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ARG* 4.1 16.8 - - + +
43B THR* 4.6 0.9 - - - +
268B ALA* 4.1 13.2 - - + +
271B LEU* 5.7 0.4 - - + -
274B ASP* 5.3 0.2 - - - +
307B GLY* 3.5 39.5 - - - +
308B TYR 4.0 0.4 - - - +
309B THR 3.2 12.4 + - - +
310B ILE* 3.2 12.1 + - - +
312B ASN* 1.3 76.0 - - - +
314B ALA* 1.3 61.8 + - - +
316B CYS* 3.2 2.6 + - - +
317B TRP* 3.0 67.0 + - + +
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Residues in contact with ALA 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ARG 4.6 0.8 + - - +
42B MET* 4.0 15.0 - - + +
43B THR* 3.4 33.6 - - - +
46B LEU* 4.2 3.8 - - + -
310B ILE 3.0 12.9 + - - +
311B ARG 3.8 7.6 - - - +
312B ASN 3.4 0.2 - - - -
313B VAL* 1.3 76.7 - - - +
315B ARG* 1.3 59.2 + - - +
317B TRP 4.1 0.2 - - - -
318B THR* 2.8 34.6 + - - -
342B PHE* 4.1 15.5 - - + -
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Residues in contact with ARG 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B LEU* 4.3 3.6 - - + +
283B VAL* 4.1 7.4 - - + -
311B ARG* 3.1 41.6 + - - +
312B ASN* 3.1 31.6 + - - +
314B ALA* 1.3 76.5 - - - +
316B CYS* 1.3 56.7 + - - +
319B TYR* 3.0 31.5 + - - +
333B LEU* 5.1 0.7 - - + -
342B PHE* 3.1 40.7 + - + +
343B GLY 5.1 0.6 + - - -
345B ASP* 3.1 21.7 + - - -
347B LYS 2.8 27.4 + - - +
348B LEU* 3.2 43.3 + - + +
349B HIS 5.3 0.4 - - - -
350B ILE* 3.9 12.7 - - - +
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Residues in contact with CYS 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B ALA* 4.4 2.9 - - + -
271B LEU* 3.7 21.5 - - + -
283B VAL* 3.9 14.1 - - + +
286B HIS* 3.3 45.1 - - - -
312B ASN 2.9 17.5 + - - +
313B VAL* 3.6 5.6 - - - +
315B ARG* 1.3 77.9 - - - +
317B TRP* 1.3 62.9 + - + +
319B TYR* 3.3 2.3 + - - +
320B GLU* 2.9 41.3 + - - +
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Residues in contact with TRP 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ARG* 3.6 22.9 - - + -
40B ILE* 3.6 24.7 - - + -
43B THR* 3.6 23.1 - - + -
140B TRP* 3.4 51.0 - + + -
266B CYS 2.8 25.4 + - - -
268B ALA* 4.1 11.1 - - + +
304B GLY* 3.5 4.5 - - - -
305B GLY 3.5 28.7 - - - -
306B GLY 3.8 10.8 - - - -
313B VAL* 3.0 30.7 + - + +
316B CYS* 1.3 77.9 - - + +
318B THR* 1.3 54.5 + - - +
320B GLU* 3.4 17.9 - - - +
321B THR* 2.7 37.8 + - - -
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Residues in contact with THR 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B THR* 3.4 21.4 + - - +
46B LEU* 3.6 13.2 - - + +
47B LEU* 3.7 18.1 + - + -
50B TYR* 3.6 37.0 - - + -
52B LEU* 3.9 5.7 - - + +
314B ALA 2.8 22.6 + - - -
315B ARG* 3.7 3.8 - - - -
317B TRP* 1.3 76.1 - - - +
319B TYR* 1.3 62.3 + - - +
321B THR* 3.3 8.0 + - - -
322B ALA* 3.1 17.8 + - - +
329B ILE* 3.9 7.6 - - + -
348B LEU* 4.5 1.6 - - + -
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Residues in contact with TYR 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B VAL* 3.6 19.7 - - + -
284B LYS* 4.5 15.2 - - - +
287B ALA* 3.5 33.2 - - + -
291B GLU* 4.5 9.7 + - - -
315B ARG 3.0 18.4 + - - +
318B THR* 1.3 76.4 - - - +
320B GLU* 1.3 57.7 + - - +
322B ALA* 3.2 7.2 + - + +
323B VAL* 2.9 38.7 + - + +
327B CYS 5.6 0.7 - - - -
328B GLU* 2.7 41.3 + - - -
329B ILE* 4.2 13.7 - - + -
348B LEU* 3.8 17.0 - - + +
349B HIS* 3.8 28.6 + + - -
405B PEG 6.2 0.2 - - - -
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Residues in contact with GLU 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B TRP* 3.9 18.1 - - + -
266B CYS* 3.7 10.9 - - - +
286B HIS* 2.6 33.3 + - - +
287B ALA* 3.2 33.6 + - + +
290B VAL* 3.9 20.8 - - + +
302B MET* 3.7 5.4 - - + +
316B CYS* 2.9 22.3 + - - +
317B TRP* 3.4 21.8 - - - -
319B TYR* 1.3 71.9 - - - +
321B THR* 1.3 60.2 + - - +
323B VAL* 3.4 7.2 + - - +
324B ALA* 3.0 27.2 + - - +
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Residues in contact with THR 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B VAL* 5.6 0.4 - - + -
18B TYR* 4.5 4.0 - - + -
47B LEU* 3.8 11.6 - - + +
52B LEU* 4.2 7.0 - - + -
56B MET* 3.7 38.1 - - + -
138B VAL* 4.8 5.7 - - + +
140B TRP* 2.9 22.7 + - - -
302B MET* 5.3 0.2 - - - -
317B TRP 2.7 20.7 + - - -
318B THR 3.3 8.5 + - - -
320B GLU* 1.3 74.1 - - - +
322B ALA* 1.3 63.3 + - - +
324B ALA* 3.2 8.7 + - + +
325B LEU* 3.0 29.8 + - + +
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Residues in contact with ALA 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B LEU* 3.9 9.5 - - + +
318B THR 3.1 12.8 + - - +
319B TYR* 3.2 12.3 + - + +
321B THR* 1.3 74.8 - - - +
323B VAL* 1.3 61.7 + - - +
325B LEU* 3.2 3.7 + - - +
326B ASP 3.1 4.9 + - - -
327B CYS* 3.1 47.1 + - - +
329B ILE* 4.0 32.3 - - + -
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Residues in contact with VAL 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B ALA* 4.2 10.5 - - + -
290B VAL* 3.8 21.8 - - + -
291B GLU* 3.4 38.1 - - + +
294B LYS* 2.8 31.4 + - + -
319B TYR* 2.9 45.8 + - + +
320B GLU* 3.6 9.9 - - - +
321B THR 3.2 0.2 - - - -
322B ALA* 1.3 76.3 - - - +
324B ALA* 1.3 53.1 + - - +
326B ASP* 3.0 9.2 + - - +
327B CYS 4.7 2.9 - - - +
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Residues in contact with ALA 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B LYS* 5.1 2.1 - - - +
16B VAL* 3.5 19.9 - - + +
136B MET* 3.4 36.9 - - - +
138B VAL* 4.9 2.5 - - + -
290B VAL* 4.7 0.4 - - - +
294B LYS* 3.3 18.9 + - - +
302B MET* 3.9 18.2 - - + -
320B GLU 3.0 13.2 + - - +
321B THR* 3.2 11.2 + - - +
323B VAL* 1.3 74.8 - - - +
325B LEU* 1.3 56.4 + - - +
326B ASP* 4.8 0.2 - - - +
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Residues in contact with LEU 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B LYS 5.8 2.0 - - - +
16B VAL* 3.8 26.2 - - + -
52B LEU* 3.9 43.7 - - + +
55B LYS* 3.3 42.7 - - + +
56B MET* 3.9 8.1 - - + -
321B THR* 3.0 28.2 + - + +
322B ALA 3.6 7.0 - - - +
323B VAL 3.2 0.2 - - - -
324B ALA* 1.3 74.1 - - - +
326B ASP* 1.3 69.3 + - - +
327B CYS* 3.4 11.5 + - - +
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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