Contacts of the helix formed by residues 306 - 326 (chain B) in PDB entry 2NYM
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 GLU 306 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B SER* 4.5 20.9 + - - +
272B THR* 5.4 1.2 + - - -
304B VAL* 3.4 10.1 + - - +
305B ILE* 1.3 79.6 - - - +
307B PRO* 1.3 66.0 - - + +
308B SER* 3.2 12.8 - - - +
309B GLU* 2.5 44.8 + - + +
310B PHE 2.7 10.2 + - - -
344B TYR* 5.8 0.2 - - - -
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Residues in contact with PRO 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B GLU* 1.3 91.8 - - + +
308B SER* 1.3 63.6 + - - +
309B GLU 2.9 1.4 + - - -
310B PHE* 3.2 18.1 + - + +
311B VAL* 3.2 19.2 + - - +
344B TYR* 3.4 21.3 - - + +
348B LEU* 4.1 17.2 - - + -
352B ASN* 5.6 0.3 + - - -
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Residues in contact with SER 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B GLU* 3.9 16.8 - - - +
307B PRO* 1.3 77.6 - - - +
309B GLU* 1.3 65.9 + - - +
311B VAL* 4.3 10.1 - - - +
312B LYS* 4.2 16.8 - - - +
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Residues in contact with GLU 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B SER* 2.9 29.8 + - - +
270B THR* 3.5 18.9 - - - +
272B THR* 3.5 14.9 - - + +
273B GLU* 3.8 6.2 + - - +
305B ILE* 3.3 13.5 - - + -
306B GLU* 2.5 29.9 + - + +
308B SER* 1.3 76.5 + - - +
310B PHE* 1.3 64.4 + - - +
311B VAL 2.7 6.4 + - - -
312B LYS* 2.7 42.4 + - - +
313B ILE* 2.9 11.9 - - - +
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Residues in contact with PHE 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B LEU* 3.7 28.3 - - + -
305B ILE* 2.8 23.5 - - + +
306B GLU 2.7 11.1 + - - +
307B PRO* 3.7 11.4 - - + +
309B GLU* 1.3 71.0 - - - +
311B VAL* 1.3 58.7 + - + +
313B ILE* 3.4 3.8 + - + +
314B MSE 2.8 69.8 + - + +
317B LEU* 4.9 0.7 - - + -
318B PHE* 3.5 31.4 - + - -
345B ILE* 5.5 1.6 - - + -
348B LEU* 3.0 44.9 - - + -
349B ILE* 4.7 0.9 - - + -
352B ASN* 4.0 15.0 - - - -
356B ILE* 3.9 9.9 - - + -
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Residues in contact with VAL 311 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B PRO 3.2 17.9 - - - +
308B SER* 4.3 10.3 - - - +
309B GLU 2.7 4.8 + - - -
310B PHE* 1.3 72.4 - - + +
312B LYS* 1.3 65.7 + - + +
313B ILE 3.3 0.7 + - - -
314B MSE 3.6 35.2 - - + +
315B GLU* 4.6 2.8 + - - +
352B ASN* 4.4 22.2 - - - +
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Residues in contact with LYS 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B THR* 5.6 3.2 + - - +
273B GLU* 3.4 39.7 + - + +
277B MSE 4.2 8.7 - - - +
308B SER 4.2 16.4 - - - +
309B GLU* 2.7 44.0 + - - +
311B VAL* 1.3 74.7 - - + +
313B ILE* 1.3 63.5 + - + +
315B GLU* 5.7 0.2 - - - +
316B PRO* 4.5 4.7 - - - +
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Residues in contact with ILE 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B THR* 4.0 18.4 - - + -
273B GLU* 4.2 9.9 - - - +
276B VAL* 3.2 41.3 - - + -
277B MSE 3.6 15.7 - - + -
302B LEU* 5.8 0.9 - - + -
305B ILE* 4.5 2.9 - - + -
309B GLU* 2.9 28.0 - - + +
310B PHE* 3.9 6.3 - - + +
312B LYS* 1.3 83.7 - - + +
314B MSE 1.3 56.3 + - - +
315B GLU 2.6 20.1 + - - -
316B PRO* 2.6 22.2 - - - +
317B LEU* 3.2 31.4 - - + -
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Residues in contact with MSE 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B PHE* 2.8 54.0 + - + +
311B VAL* 3.6 31.0 - - + +
313B ILE* 1.3 75.2 - - - +
315B GLU* 1.3 89.9 + - + +
317B LEU* 4.3 4.7 - - - -
318B PHE* 2.8 29.4 + - - +
352B ASN* 3.7 30.7 - - - +
355B LYS* 4.7 13.9 - - + -
356B ILE* 3.8 19.5 - - + -
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Residues in contact with GLU 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B VAL 4.9 2.7 - - - +
312B LYS 5.7 0.4 - - - +
313B ILE 2.6 4.9 + - - -
314B MSE 1.3 99.8 - - + +
316B PRO* 1.3 67.0 - - + +
318B PHE 3.8 0.3 - - - -
319B ARG* 2.8 55.6 + - - +
355B LYS* 3.8 39.8 + - + +
356B ILE* 6.1 0.2 - - - -
359B ILE* 4.2 19.7 - - + +
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Residues in contact with PRO 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B MSE 3.7 28.9 - - + -
280B LEU* 4.4 10.5 - - + +
312B LYS 4.5 5.6 - - - +
313B ILE 2.6 20.9 - - - +
315B GLU* 1.3 86.9 - - + +
317B LEU* 1.3 62.1 + - - +
319B ARG* 3.3 24.9 - - + +
320B GLN* 3.2 18.4 + - - +
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Residues in contact with LEU 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B VAL* 5.1 2.0 - - + -
280B LEU* 4.1 14.5 - - + +
283B TRP* 6.2 0.2 - - + -
298B LEU* 3.3 35.2 - - + -
302B LEU* 3.5 44.0 - - + -
310B PHE* 4.9 2.2 - - + -
313B ILE* 3.2 28.5 + - + -
314B MSE 3.2 5.1 + - - +
315B GLU 3.2 1.0 - - - -
316B PRO* 1.3 79.7 - - - +
318B PHE* 1.3 73.8 + - + +
320B GLN* 2.8 22.8 + - + +
321B LEU* 3.1 22.0 + - + -
339B TYR* 5.7 0.4 - - - +
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Residues in contact with PHE 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B LEU* 4.7 2.5 - - + -
310B PHE* 3.5 28.9 - + - -
314B MSE 2.8 22.0 + - - +
315B GLU* 4.2 1.3 - - - +
317B LEU* 1.3 87.1 - - + +
319B ARG* 1.3 66.3 + - - +
321B LEU* 3.7 17.5 - - + -
322B ALA* 3.0 22.9 + - - +
339B TYR* 5.8 1.1 - + + -
340B TRP* 5.1 2.9 - + - -
345B ILE* 4.3 11.9 - - + -
349B ILE* 3.2 42.8 - - + -
356B ILE* 4.0 20.9 - - + -
359B ILE* 3.9 11.8 - - + +
360B MSE 3.0 39.8 - - + +
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Residues in contact with ARG 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B GLU* 2.8 54.2 + - - +
316B PRO* 3.3 41.5 - - + +
317B LEU 3.0 0.4 - - - -
318B PHE* 1.3 78.8 - - - +
320B GLN* 1.3 57.9 + - - +
322B ALA* 3.0 17.2 - - + +
323B LYS* 3.8 12.0 + - + +
359B ILE* 3.7 25.6 - - + +
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Residues in contact with GLN 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B LEU* 4.1 18.7 - - + +
283B TRP* 3.1 61.6 - - + +
291B GLU* 4.2 3.4 + - - -
316B PRO 3.2 9.7 + - - +
317B LEU* 2.8 11.4 + - + +
319B ARG* 1.3 75.5 - - - +
321B LEU* 1.3 56.4 + - + +
322B ALA 2.7 4.5 - - - -
323B LYS* 2.4 55.5 + - - +
324B CYS* 3.0 15.0 + - - -
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Residues in contact with LEU 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B TRP* 6.2 0.2 - - + -
295B LEU* 3.6 29.8 - - + -
298B LEU* 6.1 0.4 - - + -
317B LEU* 3.1 19.7 + - + +
318B PHE* 3.8 27.4 - - + +
320B GLN* 1.3 78.2 - - - +
322B ALA* 1.3 63.0 + - - +
324B CYS* 2.9 7.3 + - - +
325B VAL* 2.9 30.2 + - + +
336B ALA* 4.4 11.4 - - + +
339B TYR* 3.8 44.0 - - + -
340B TRP* 5.3 1.3 - - + -
360B MSE 3.3 26.0 - - + -
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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
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318B PHE 3.0 14.4 + - - +
319B ARG* 3.0 22.2 - - + +
320B GLN 2.6 0.2 + - - -
321B LEU* 1.3 79.7 - - - +
323B LYS* 1.3 59.2 + - + +
325B VAL* 3.5 2.2 + - - +
326B SER* 3.3 22.3 + - - -
359B ILE* 3.8 22.0 - - + +
360B MSE 3.9 12.5 - - - -
363B SER* 3.5 14.5 - - - +
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Residues in contact with LYS 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B ARG* 4.0 15.7 - - + +
320B GLN* 2.4 37.4 + - - +
322B ALA* 1.3 71.8 - - + +
324B CYS* 1.3 64.0 + - - +
326B SER* 2.9 20.2 + - - -
327B SER* 3.0 12.7 + - - -
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Residues in contact with CYS 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B TRP* 3.5 32.8 - - - -
291B GLU* 4.0 14.4 - - - -
295B LEU* 4.0 14.1 - - - -
320B GLN* 3.0 18.8 + - - -
321B LEU* 2.9 11.4 + - - +
323B LYS* 1.3 77.3 - - - +
325B VAL* 1.3 63.1 + - - +
327B SER* 3.1 18.5 + - - -
332B VAL* 4.1 9.0 - - + -
333B ALA* 3.3 11.8 + - - -
336B ALA* 3.4 20.2 - - + -
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Residues in contact with VAL 325 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B LEU* 2.9 17.7 + - + +
322B ALA* 3.7 8.1 - - - +
324B CYS* 1.3 75.7 - - - +
326B SER* 1.3 59.9 + - - +
327B SER 2.8 9.4 + - - +
333B ALA* 3.7 12.5 - - - +
336B ALA* 4.4 4.5 - - + -
337B LEU* 3.1 43.7 - - + -
340B TRP* 4.5 11.9 - - + -
360B MSE 4.9 1.8 - - - -
363B SER* 4.3 13.9 - - - +
364B LEU* 3.8 27.1 - - + -
376B ILE* 5.7 3.3 - - - +
380B ILE* 4.3 12.0 - - + +
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Residues in contact with SER 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B ALA 3.3 5.0 + - - -
323B LYS* 2.9 15.1 + - - -
325B VAL* 1.3 76.3 - - - +
327B SER* 1.3 60.4 + - - -
328B PRO* 3.9 3.8 - - - +
363B SER* 3.0 32.7 + - - -
366B ARG* 3.5 39.5 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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