Contacts of the helix formed by residues 303 - 322 (chain B) in PDB entry 4EG8
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 303 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B ALA* 4.0 0.7 - - - -
302B VAL* 1.3 77.2 - - - +
304B PRO* 1.3 75.1 - - - +
305B TYR* 3.7 10.2 + - - +
306B ASP* 3.1 32.6 + - - +
307B PHE* 2.9 21.0 + - - +
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Residues in contact with PRO 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B VAL* 5.1 1.3 - - + -
294B ALA* 4.6 14.1 - - + +
297B ALA* 3.7 19.9 - - + -
302B VAL 3.8 1.8 - - - +
303B SER* 1.3 88.9 - - - +
305B TYR* 1.3 56.3 + - + +
307B PHE* 3.6 0.3 - - - +
308B THR* 2.8 36.3 + - + +
457B HIS 6.2 0.2 - - - +
459B TRP* 3.5 44.9 - - + +
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Residues in contact with TYR 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B SER* 3.1 8.0 - - - +
304B PRO* 1.3 80.5 - - - +
306B ASP* 1.3 80.8 + - - +
308B THR* 3.1 7.4 + - - -
309B THR* 2.8 51.9 + - + +
331B ARG* 5.3 4.5 - - - -
333B THR* 6.2 4.3 - - + -
459B TRP* 3.6 17.3 - + + -
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Residues in contact with ASP 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B VAL* 4.4 10.0 - - + +
303B SER* 3.1 27.6 + - - +
305B TYR* 1.3 96.1 - - - +
307B PHE* 1.3 66.8 + - - +
309B THR* 3.3 4.8 + - - -
310B ALA* 2.9 27.1 + - - +
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Residues in contact with PHE 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B VAL* 3.6 25.6 - - + -
252B ASN* 5.1 2.2 - - - -
293B VAL* 4.1 24.7 - - + -
296B ALA* 3.4 33.7 - - + -
297B ALA* 3.7 20.9 - - + -
300B LYS* 4.1 19.1 - - + -
302B VAL* 3.9 13.8 - - + +
303B SER 2.9 16.3 + - - +
304B PRO 3.6 3.8 - - - +
306B ASP* 1.3 78.2 - - - +
308B THR* 1.3 60.4 + - - +
310B ALA* 3.4 5.0 - - + +
311B VAL* 2.9 45.1 + - + +
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Residues in contact with THR 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B VAL* 3.9 13.7 - - + +
288B GLU* 3.5 38.9 + - + +
293B VAL* 3.4 29.8 - - + -
304B PRO 2.8 20.9 + - - +
305B TYR* 3.1 14.9 + - - -
307B PHE* 1.3 73.5 - - - +
309B THR* 1.3 59.4 + - - +
311B VAL* 4.2 0.8 - - - +
312B ALA* 2.9 31.5 + - - +
331B ARG* 3.8 5.1 + - - -
333B THR* 4.4 1.9 - - - +
459B TRP* 3.9 9.3 - - + -
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Residues in contact with THR 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B TYR* 2.8 42.8 + - + +
306B ASP* 3.8 5.6 - - - -
308B THR* 1.3 76.2 + - - +
310B ALA* 1.3 58.0 + - - +
312B ALA* 3.6 2.1 + - - +
313B GLY* 3.1 23.9 + - - -
331B ARG* 3.2 29.4 + - - +
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Residues in contact with ALA 310 (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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306B ASP 2.9 19.2 + - - +
307B PHE* 3.4 7.0 - - + +
309B THR* 1.3 74.9 - - - +
311B VAL* 1.3 65.0 + - + +
313B GLY* 3.3 3.3 + - - -
314B GLU* 3.1 26.8 + - - +
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Residues in contact with VAL 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B VAL* 3.6 43.3 - - + +
253B ALA 4.1 6.7 - - - +
307B PHE* 2.9 39.1 + - + +
308B THR 4.2 0.9 - - - +
310B ALA* 1.3 73.0 - - + +
312B ALA* 1.3 67.8 + - - +
313B GLY 3.1 1.3 - - - -
314B GLU* 2.9 35.2 + - + +
315B PHE* 3.0 32.5 + - + -
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Residues in contact with ALA 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B VAL* 4.6 1.2 - - - +
286B THR* 4.1 17.5 - - + +
288B GLU* 3.6 19.7 - - - +
308B THR 2.9 19.6 + - - +
309B THR 3.7 4.7 - - - +
311B VAL* 1.3 75.0 - - - +
313B GLY* 1.3 58.0 + - - +
315B PHE* 3.2 4.2 + - - +
316B LYS* 2.9 35.3 + - - +
329B PHE* 3.9 3.6 - - + -
331B ARG* 3.6 20.6 - - + +
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Residues in contact with GLY 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B THR 3.1 14.5 + - - -
310B ALA* 3.6 4.9 - - - -
311B VAL 3.1 0.4 - - - -
312B ALA* 1.3 73.2 - - - +
314B GLU* 1.3 58.5 + - - +
316B LYS* 3.2 10.2 + - - +
317B LYS* 2.8 32.7 + - - +
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Residues in contact with GLU 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B ALA* 3.7 26.0 - - - +
255B PRO* 3.8 16.2 - - + +
310B ALA* 3.1 16.9 + - - +
311B VAL* 2.9 30.9 + - - +
313B GLY* 1.3 74.9 - - - +
315B PHE* 1.3 55.8 + - - +
317B LYS* 3.5 7.5 + - - +
318B CYS* 3.0 27.4 + - - +
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Residues in contact with PHE 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B TYR* 3.5 40.6 - + + -
250B TYR 4.5 6.1 - - - -
251B VAL* 4.8 2.0 - - - -
253B ALA 3.5 21.5 - - - -
255B PRO* 3.6 23.3 - - + -
259B HIS* 3.5 39.0 - + + -
286B THR* 4.2 10.8 - - + -
311B VAL* 3.0 33.4 + - + -
312B ALA 3.6 6.7 - - - +
314B GLU* 1.3 73.8 - - - +
316B LYS* 1.3 67.5 + - - +
318B CYS* 3.1 12.5 + - - +
319B PHE* 3.2 29.9 + + + -
329B PHE* 3.8 17.5 - - + -
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Residues in contact with LYS 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B ALA* 2.9 21.1 + - - +
313B GLY* 3.6 7.9 - - - +
315B PHE* 1.3 76.4 - - - +
317B LYS* 1.3 64.2 + - - +
319B PHE* 3.4 3.9 + - - +
320B GLU* 3.1 35.7 + - - +
329B PHE* 3.4 55.6 + - + +
331B ARG* 4.5 16.9 - - - +
801B DMS 5.9 0.3 - - - -
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Residues in contact with LYS 317 (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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313B GLY 2.8 17.3 + - - +
314B GLU* 3.7 7.6 - - - +
316B LYS* 1.3 77.9 - - - +
318B CYS* 1.3 57.1 + - - +
320B GLU* 3.4 15.5 + - + +
321B GLN* 3.0 41.8 + - + +
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Residues in contact with CYS 318 (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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255B PRO* 4.1 22.7 - - + -
260B VAL* 3.7 29.8 - - - -
314B GLU 3.0 14.8 + - - +
315B PHE 3.1 8.9 + - - +
317B LYS* 1.3 76.7 - - - +
319B PHE* 1.3 66.0 + - + +
321B GLN* 3.2 8.2 + - - +
322B MET* 2.9 32.4 + - - +
566B VAL* 4.8 12.1 - - - -
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Residues in contact with PHE 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B TYR* 3.7 14.8 - + - -
255B PRO* 5.8 0.2 - - + -
259B HIS* 4.3 12.8 - - + -
260B VAL* 4.6 2.0 - - - -
263B THR* 3.3 26.7 - - + -
284B THR* 3.8 30.7 - - + -
315B PHE* 3.2 31.0 + + - +
316B LYS* 4.0 3.1 - - - +
318B CYS* 1.3 90.2 - - + +
320B GLU* 1.3 65.6 + - - +
322B MET* 3.7 1.2 + - + -
323B ASP 3.3 2.8 + - - -
324B TYR* 3.2 52.3 + + + +
329B PHE* 3.9 21.5 - + + -
801B DMS 3.9 17.4 + - + -
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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
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316B LYS* 3.1 31.9 + - - +
317B LYS* 3.6 15.9 + - + +
319B PHE* 1.3 75.7 - - - +
321B GLN* 1.3 64.2 + - + +
323B ASP* 2.9 16.6 + - - +
801B DMS 4.0 16.6 - - - +
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Residues in contact with GLN 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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317B LYS* 3.0 30.6 + - + +
318B CYS* 3.5 9.2 - - - +
320B GLU* 1.3 76.5 - - + +
322B MET* 1.3 59.1 + - - +
323B ASP* 3.2 3.6 + - - +
566B VAL* 4.3 23.1 - - + -
570B GLU* 4.0 6.1 - - - +
574B TYR* 3.1 43.5 + - - -
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Residues in contact with MET 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B VAL* 4.0 23.6 - - + -
318B CYS* 2.9 26.6 + - - +
319B PHE 3.9 2.2 - - - +
320B GLU 3.2 0.2 - - - -
321B GLN* 1.3 73.3 - - - +
323B ASP* 1.3 61.9 + - - +
324B TYR* 3.6 34.4 + - + +
565B PRO* 3.9 7.6 - - + +
566B VAL* 3.2 49.1 - - + +
569B ALA* 4.2 2.0 - - + -
574B TYR* 3.6 23.5 - - + -
577B LEU* 5.3 3.8 - - - -
578B LYS* 2.8 37.9 + - - -
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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