Contacts of the helix formed by residues 304 - 323 (chain A) in PDB entry 4IXU
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 SER 304 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302A ALA* 3.3 8.4 - - - +
303A THR* 1.3 84.4 + - - +
305A GLU* 1.3 64.9 + - - +
306A GLU* 3.5 10.8 + - - +
307A GLU* 3.1 36.3 + - - +
308A ALA* 3.2 9.5 + - - +
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Residues in contact with GLU 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A SER* 1.3 72.4 - - - +
306A GLU* 1.3 57.2 + - - +
308A ALA* 3.3 7.2 + - + +
309A LYS* 2.9 46.2 + - + +
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Residues in contact with GLU 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A SER* 3.1 9.3 + - - +
305A GLU* 1.3 79.6 - - - +
307A GLU* 1.3 58.3 + - + +
309A LYS* 3.4 5.7 + - - +
310A THR* 3.0 34.2 + - + +
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Residues in contact with GLU 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A PRO* 3.7 29.1 - - + +
301A LEU 4.6 0.9 - - - +
302A ALA* 3.7 10.1 - - + -
303A THR* 2.8 42.8 + - - +
304A SER* 3.1 23.8 + - - +
306A GLU* 1.3 77.1 - - + +
308A ALA* 1.3 60.7 + - - +
310A THR* 3.3 8.6 - - + +
311A THR* 2.9 29.6 + - - -
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Residues in contact with ALA 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ALA* 5.7 0.7 - - - +
262A ALA* 4.3 6.4 - - - +
297A VAL* 5.4 1.6 - - - +
299A PRO* 3.9 25.5 - - + +
302A ALA* 3.4 19.4 - - + +
304A SER 3.2 8.2 + - - +
305A GLU* 3.6 11.2 - - + +
306A GLU 3.2 0.2 - - - -
307A GLU* 1.3 76.6 - - - +
309A LYS* 1.3 63.5 + - + +
311A THR* 3.3 4.7 + - - -
312A ALA* 3.1 22.7 + - - +
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Residues in contact with LYS 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305A GLU* 2.9 30.2 + - + +
306A GLU* 4.0 4.9 - - - +
308A ALA* 1.3 80.3 - - + +
310A THR* 1.3 56.8 + - - +
312A ALA* 3.2 6.5 + - - +
313A ASN* 2.7 44.0 + - - +
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Residues in contact with THR 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A THR 5.5 2.5 - - - +
259A LEU* 4.1 17.4 + - - +
261A PRO* 4.3 6.5 - - + -
306A GLU* 3.0 21.3 + - + +
307A GLU* 3.3 19.3 - - + +
309A LYS* 1.3 76.5 - - - +
311A THR* 1.3 62.0 - - - +
313A ASN* 3.7 10.8 + - - +
314A LEU* 2.9 29.6 + - - +
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Residues in contact with THR 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A ILE* 4.1 23.0 - - + +
259A LEU 4.4 5.4 - - - -
260A ALA* 4.1 9.4 - - + -
261A PRO* 3.2 10.0 - - - +
262A ALA* 3.2 40.7 + - + +
297A VAL* 4.1 12.1 - - + -
307A GLU 2.9 17.1 + - - -
308A ALA 3.3 5.1 + - - -
309A LYS 3.2 0.6 - - - -
310A THR* 1.3 80.7 - - - +
312A ALA* 1.3 61.4 + - - +
314A LEU* 3.3 5.5 + - - +
315A ALA* 3.1 21.0 + - - +
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Residues in contact with ALA 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A ALA* 3.5 39.9 - - + +
49A ILE* 4.4 2.8 - - - +
52A ALA* 3.9 7.6 - - + -
297A VAL* 4.7 6.7 - - + +
308A ALA 3.1 13.4 + - - +
309A LYS* 3.2 10.5 + - - +
311A THR* 1.3 76.2 - - - +
313A ASN* 1.3 64.2 + - - +
315A ALA* 3.2 8.9 + - - +
316A VAL* 3.1 25.6 + - - +
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Residues in contact with ASN 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A ALA* 3.4 26.4 - - - +
57A ARG* 5.2 0.5 + - - -
309A LYS* 2.7 34.3 + - - +
310A THR* 3.7 9.8 - - - +
311A THR 3.3 0.2 - - - -
312A ALA* 1.3 72.5 - - - +
314A LEU* 1.3 57.6 + - - +
316A VAL* 3.3 5.7 + - - +
317A ASP* 2.9 34.8 + - - +
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Residues in contact with LEU 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A ILE* 4.2 2.5 - - + -
255A PHE* 3.4 52.3 - - + -
259A LEU* 3.6 28.3 - - + +
260A ALA* 3.9 11.9 - - + -
273A TYR* 3.6 34.8 - - + -
277A MET* 4.3 2.0 - - + -
310A THR 2.9 17.5 + - - +
311A THR 3.4 5.4 - - - +
313A ASN* 1.3 74.7 - - - +
315A ALA* 1.3 65.7 + - - +
317A ASP* 3.1 8.2 + - - +
318A VAL* 3.0 23.4 + - - +
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Residues in contact with ALA 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ILE* 3.8 21.1 - - + -
252A ILE* 4.0 9.4 - - + +
294A LEU* 3.6 30.5 - - + +
297A VAL* 4.2 4.9 - - + -
311A THR 3.1 13.1 + - - +
312A ALA 3.2 8.9 + - - +
314A LEU* 1.3 77.5 - - - +
316A VAL* 1.3 61.8 + - - +
318A VAL* 3.2 4.3 + - - +
319A ILE* 3.1 29.7 + - - +
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Residues in contact with VAL 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ILE* 3.4 35.0 - - + +
52A ALA* 3.7 15.5 - - + +
54A LEU* 3.9 24.6 - - + +
57A ARG* 3.4 44.0 - - + +
312A ALA 3.1 13.7 + - - +
313A ASN* 3.6 8.1 - - - +
314A LEU 3.2 0.2 - - - -
315A ALA* 1.3 75.7 - - - +
317A ASP* 1.3 57.0 + - - +
319A ILE* 3.2 2.0 + - - +
320A ALA* 2.8 28.2 + - - +
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Residues in contact with ASP 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ARG* 2.7 39.0 + - - +
273A TYR* 2.6 32.2 + - + +
277A MET* 3.7 19.3 - - + +
313A ASN* 2.9 18.4 + - - +
314A LEU* 3.1 12.0 + - - +
316A VAL* 1.3 77.4 - - - +
318A VAL* 1.3 61.8 + - - +
320A ALA* 3.9 0.5 - - - +
321A SER* 3.0 27.4 + - - -
325A GLN* 6.1 0.2 - - - -
268B VAL* 4.3 5.9 - - - +
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Residues in contact with VAL 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A LEU* 5.0 1.8 - - + -
250A PHE* 3.6 34.8 - - + -
252A ILE* 5.0 0.2 - - + -
255A PHE* 3.5 35.4 - - + -
276A GLY 5.3 0.7 - - - +
277A MET* 3.9 10.1 - - + -
280A ALA* 3.6 8.8 - - + +
292A LEU* 5.2 1.1 - - + -
294A LEU* 4.0 15.0 - - + -
314A LEU 3.0 19.3 + - - +
315A ALA* 3.2 8.3 + - - +
317A ASP* 1.3 76.1 - - - +
319A ILE* 1.3 64.9 + - + +
322A SER* 2.8 36.4 + - - +
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Residues in contact with ILE 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ILE* 4.3 7.4 - - + -
54A LEU* 3.7 28.5 - - + -
58A LEU* 4.2 6.5 - - + -
114A VAL* 4.3 17.5 - - + -
116A LEU* 3.7 29.2 - - + -
292A LEU* 3.9 17.9 - - + -
294A LEU* 4.0 17.7 - - + -
315A ALA 3.1 16.9 + - - +
316A VAL 3.8 2.5 - - - +
318A VAL* 1.3 77.5 - - - +
320A ALA* 1.3 63.4 + - - +
322A SER* 3.2 13.4 + - - -
323A PHE* 3.2 37.0 + - + -
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Residues in contact with ALA 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A LEU* 5.1 0.6 - - + +
57A ARG* 3.7 23.8 - - + +
58A LEU* 4.4 6.9 - - + +
61A LEU* 3.3 17.0 - - + +
316A VAL 2.8 20.7 + - - +
317A ASP 4.0 0.9 - - - +
319A ILE* 1.3 73.9 - - - +
321A SER* 1.3 61.7 + - - +
323A PHE 3.1 2.1 + - - -
324A GLY 3.1 7.3 + - - -
325A GLN* 2.9 45.9 + - + +
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Residues in contact with SER 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A MET* 3.3 19.0 + - - +
280A ALA* 3.5 21.1 - - - +
281A GLU* 3.2 32.4 + - - +
284A HIS* 3.5 6.1 - - - +
317A ASP 3.0 18.8 + - - -
320A ALA* 1.3 76.7 - - - +
322A SER* 1.3 61.9 + - - +
324A GLY* 3.2 11.8 + - - -
325A GLN* 3.5 18.6 + - - +
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Residues in contact with SER 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248A LEU* 3.7 12.6 - - - +
280A ALA* 3.3 21.8 - - - +
283A ILE* 4.6 1.6 - - - -
284A HIS* 3.3 18.8 + - - +
289A LEU* 3.5 22.1 - - - +
292A LEU* 3.5 28.1 - - - +
318A VAL* 2.8 21.9 + - - +
319A ILE 3.2 6.7 + - - -
321A SER* 1.3 76.8 - - - +
323A PHE* 1.3 60.2 + - - +
324A GLY 3.5 0.2 - - - -
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Residues in contact with PHE 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A VAL* 3.7 18.8 - - + -
58A LEU* 4.1 22.7 - - + -
61A LEU* 4.0 15.0 - - + +
63A CYS* 4.2 11.0 - - - -
112A SER* 3.6 31.9 - - - -
113A CYS 5.6 0.2 - - - -
114A VAL* 3.4 34.1 - - + -
284A HIS* 3.4 13.2 - - - -
289A LEU* 3.7 27.6 - - + -
291A ALA 5.9 0.2 - - - -
292A LEU* 4.2 11.9 - - + -
319A ILE* 3.2 24.5 + - + +
320A ALA 3.1 7.8 + - - +
321A SER 3.1 0.6 - - - -
322A SER* 1.3 81.4 - - - +
324A GLY* 1.3 55.2 + - - +
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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
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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