Contacts of the helix formed by residues 302 - 319 (chain D) in PDB entry 4OGB
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 ASN 302 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300D LEU 3.5 1.4 + - - -
301D ASP* 1.3 100.5 + - - +
303D TYR* 1.3 65.4 + - - +
304D SER* 3.4 13.3 + - - +
305D ASP* 2.5 55.8 + - - +
306D ARG* 3.1 26.0 + - - +
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Residues in contact with TYR 303 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189D GLU* 5.8 2.9 - - - -
259D SER* 6.0 0.2 - - - -
262D LYS* 3.7 25.3 - - + +
263D MET* 3.8 27.3 - - + -
266D ASP* 2.6 30.4 + - - -
302D ASN* 1.3 71.9 - - - +
304D SER* 1.3 60.6 + - - +
306D ARG* 4.3 10.7 - - + +
307D ILE* 2.8 65.7 + - + +
506D EDO 4.1 9.4 - - - -
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Residues in contact with SER 304 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302D ASN* 3.2 11.2 + - - +
303D TYR* 1.3 82.2 - - - +
305D ASP* 1.3 64.6 + - - +
307D ILE* 3.6 8.4 - - - +
308D GLN* 3.2 29.0 + - - +
506D EDO 6.4 0.7 - - - -
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Residues in contact with ASP 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286D MET* 3.4 26.7 - - + +
299D LEU 5.5 0.7 - - - +
300D LEU* 4.2 14.8 - - + -
301D ASP* 4.4 2.8 + - - +
302D ASN* 2.5 39.1 + - - +
304D SER* 1.3 75.7 + - - +
306D ARG* 1.3 67.4 + - - +
308D GLN* 3.4 8.4 + - - +
309D VAL* 3.1 29.7 + - - +
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Residues in contact with ARG 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184D VAL* 3.2 28.0 + - - +
185D PHE* 3.9 11.1 - - + +
186D THR* 4.3 7.9 - - - +
189D GLU* 2.8 46.9 + - - +
300D LEU* 3.0 45.0 + - + +
301D ASP* 5.1 1.0 - - - +
302D ASN 3.1 19.8 + - - +
303D TYR* 3.7 12.6 - - + +
305D ASP* 1.3 77.1 - - - +
307D ILE* 1.3 61.6 + - - +
309D VAL* 3.3 5.0 + - - +
310D LEU* 3.1 27.6 + - + +
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Residues in contact with ILE 307 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263D MET* 3.8 34.1 - - + +
266D ASP* 3.7 14.1 - - + -
267D ILE* 4.0 12.8 - - + -
303D TYR* 2.8 64.3 + - + +
304D SER* 3.6 9.0 - - - +
306D ARG* 1.3 74.9 - - - +
308D GLN* 1.3 56.6 + - + +
310D LEU* 3.3 9.5 + - + +
311D GLN* 2.7 47.6 + - + +
506D EDO 4.1 15.3 - - - -
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Residues in contact with GLN 308 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279D LEU* 5.7 2.0 - - + -
282D ASP* 3.9 30.6 + - + +
283D LEU* 4.6 3.9 - - + +
286D MET* 2.3 59.1 - - - +
304D SER* 3.2 20.2 + - - +
305D ASP* 3.7 8.8 + - - +
306D ARG 3.3 0.2 - - - -
307D ILE* 1.3 78.5 - - + +
309D VAL* 1.3 56.2 + - - +
311D GLN* 3.4 14.1 - - - +
312D ASN* 3.0 46.8 + - - +
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Residues in contact with VAL 309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181D LEU* 4.8 3.1 - - + -
185D PHE* 3.8 20.9 - - + -
283D LEU* 5.5 2.0 - - + -
286D MET* 3.4 29.2 - - - -
298D LEU* 4.4 6.3 - - + -
300D LEU* 3.8 19.1 - - + -
305D ASP 3.1 15.4 + - - +
306D ARG 3.6 7.2 - - - +
308D GLN* 1.3 77.1 - - - +
310D LEU* 1.3 50.8 + - - +
312D ASN* 3.3 4.4 + - - +
313D MET* 2.7 36.1 + - + +
384D TRP* 3.9 22.5 - - + -
387D LEU* 4.4 9.0 - - + -
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Residues in contact with LEU 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176D LEU* 4.5 2.9 - - + -
185D PHE* 3.7 35.9 - - + -
189D GLU* 4.2 31.2 - - + +
193D ALA* 4.2 16.8 - - + -
263D MET* 4.7 5.2 - - - -
267D ILE* 4.0 24.2 - - + -
306D ARG* 3.1 15.8 + - + +
307D ILE* 3.6 17.0 - - + +
309D VAL* 1.3 73.4 - - - +
311D GLN* 1.3 65.5 + - - +
313D MET* 3.3 15.3 + - + +
314D VAL* 3.0 29.8 + - - +
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Residues in contact with GLN 311 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266D ASP* 3.0 33.7 + - - +
267D ILE* 4.0 14.8 - - + +
270D ALA* 3.7 18.5 - - + +
271D THR* 5.8 0.5 - - - +
279D LEU* 4.1 14.3 - - + +
307D ILE* 2.7 33.8 + - + +
308D GLN* 3.4 22.2 - - - +
310D LEU* 1.3 72.7 - - - +
312D ASN* 1.3 58.0 + - - +
314D VAL* 3.8 1.6 - - - +
315D HIS* 2.9 30.7 + - - +
506D EDO 3.4 23.1 + - - -
509D EDO 3.4 18.2 + - - -
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Residues in contact with ASN 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279D LEU* 3.5 48.5 + - - +
280D LEU 4.4 0.4 - - - +
283D LEU* 3.8 42.4 - - + +
308D GLN* 3.0 28.9 + - - +
309D VAL 3.8 2.9 - - - +
311D GLN* 1.3 74.3 - - - +
313D MET* 1.3 55.2 + - - +
315D HIS* 3.6 5.0 - - - +
316D CYS* 2.6 38.6 + - - +
380D LEU* 4.0 14.1 - - - +
384D TRP* 4.3 5.6 - - + -
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Residues in contact with MET 313 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172D THR* 4.1 13.5 - - + +
175D LEU* 3.5 28.2 - - + +
176D LEU* 3.6 46.7 - - + -
181D LEU* 3.5 31.2 - - + -
185D PHE* 4.1 10.5 - - + -
193D ALA* 5.2 1.1 - - - -
309D VAL* 2.7 21.3 + - + +
310D LEU* 3.5 14.6 - - + +
312D ASN* 1.3 73.8 - - - +
314D VAL* 1.3 57.8 + - - +
316D CYS* 3.1 6.0 + - - +
317D ALA* 2.9 24.6 + - - +
384D TRP* 3.7 19.8 - - + -
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Residues in contact with VAL 314 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168D VAL* 4.5 6.0 - - + +
172D THR* 3.9 17.0 - - + +
193D ALA* 4.0 16.6 - - + +
196D ALA 5.3 0.7 - - - -
197D SER* 3.8 33.7 - - - +
200D HIS* 5.4 2.5 - - + -
267D ILE* 3.6 28.7 - - + -
271D THR* 4.3 15.9 - - + -
310D LEU 3.0 16.7 + - - +
311D GLN 4.0 1.1 - - - +
313D MET* 1.3 72.4 - - + +
315D HIS* 1.3 61.5 + - - +
317D ALA* 3.2 1.9 + - - +
318D ASP* 2.8 28.1 + - + +
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Residues in contact with HIS 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270D ALA 4.2 13.4 + - - +
271D THR* 4.6 13.7 + - - +
273D MET* 3.8 20.0 - - - -
276D HIS* 3.0 34.7 + - + +
279D LEU* 3.8 24.9 - - + -
311D GLN 2.9 19.5 + - - +
312D ASN* 3.6 6.1 - - - +
314D VAL* 1.3 75.6 - - - +
316D CYS* 1.3 63.5 + - - +
318D ASP* 3.2 11.5 + - - +
319D LEU* 3.0 44.7 + - + +
380D LEU* 3.7 23.6 - - + -
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Residues in contact with CYS 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175D LEU* 3.9 7.9 - - + -
312D ASN* 2.6 22.3 + - - +
313D MET* 3.2 10.8 - - - +
315D HIS* 1.3 74.0 - - - +
317D ALA* 1.3 62.6 + - - +
319D LEU 3.1 12.6 + - - -
320D SER 3.1 10.2 + - - -
380D LEU* 3.7 35.9 - - - -
381D TRP* 3.3 28.4 - - + -
384D TRP* 3.8 32.3 - - - -
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Residues in contact with ALA 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167D ASP* 5.2 0.7 - - - +
168D VAL* 3.8 16.5 - - + +
171D SER* 3.7 23.4 - - - -
172D THR* 3.4 28.9 - - - +
175D LEU* 4.0 4.6 - - + +
313D MET 2.9 14.0 + - - +
314D VAL 3.2 6.5 + - - +
316D CYS* 1.3 72.6 - - - +
318D ASP* 1.3 62.2 + - - +
320D SER* 2.7 29.0 + - - -
321D ASN* 5.5 0.7 + - - -
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Residues in contact with ASP 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159D TYR* 4.1 14.4 + - - -
164D HIS* 3.1 12.0 + - - -
168D VAL* 3.9 9.3 - - + +
200D HIS* 3.2 7.9 + - - +
271D THR* 3.9 27.4 - - + +
273D MET* 6.1 0.2 - - - +
314D VAL 2.8 16.2 + - - +
315D HIS* 3.3 14.4 + - - +
317D ALA* 1.3 74.3 - - - +
319D LEU* 1.3 68.1 + - + +
320D SER 3.3 2.3 + - - -
321D ASN* 4.9 3.3 + - - +
502D 2SR 4.6 13.9 - - - +
512D ZN 2.2 35.4 - - - -
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Residues in contact with LEU 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273D MET* 4.1 7.6 - - - -
276D HIS* 4.6 0.2 - - - +
315D HIS* 3.0 45.2 + - + +
316D CYS 3.1 5.1 + - - +
318D ASP* 1.3 82.0 - - + +
320D SER* 1.3 60.5 + - - +
321D ASN* 3.5 2.5 - - - -
322D PRO* 3.7 5.1 - - - +
372D PHE* 4.1 8.5 - - + -
376D ILE* 3.8 28.5 - - + +
377D VAL* 3.6 22.3 - - + +
380D LEU* 3.9 16.4 - - + -
381D TRP* 3.2 12.3 + - - -
502D 2SR 3.5 38.6 - - + -
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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