Contacts of the helix formed by residues 304 - 322 (chain B) in PDB entry 3SN5
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 304 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B GLN* 2.7 37.4 + - - +
301B MET 2.9 19.4 - - - +
302B ILE 3.2 1.9 - - - -
303B ARG* 1.3 85.6 - - - +
305B PRO* 1.4 69.0 - - + +
306B GLU* 3.2 3.8 - - + +
307B ALA* 3.2 14.2 + - + +
308B MET* 3.0 8.1 + - - +
407B PHE* 3.4 33.8 - - + +
409B TYR* 5.8 0.9 - - + -
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Residues in contact with PRO 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B ILE 4.3 3.8 - - - +
303B ARG 3.6 10.1 - - - +
304B ASN* 1.4 82.6 - - - +
306B GLU* 1.3 57.5 + - + +
308B MET* 3.7 7.5 - - + +
309B LYS* 3.0 31.8 + - - +
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Residues in contact with GLU 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B ASN* 3.2 4.0 - - + -
305B PRO* 1.3 80.4 - - + +
307B ALA* 1.4 61.5 + - - +
309B LYS* 3.9 4.9 - - - +
310B ALA* 3.3 23.9 + - - +
409B TYR* 3.3 34.0 + - + +
410B ASP* 5.5 1.9 - - - +
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Residues in contact with ALA 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B GLN 4.4 1.6 - - - +
301B MET* 4.0 16.6 - - - +
304B ASN* 3.2 22.5 + - + +
306B GLU* 1.4 74.4 - - - +
308B MET* 1.3 65.2 + - - +
310B ALA* 3.6 1.6 + - - +
311B ALA* 3.1 26.2 + - - +
349B ILE* 3.8 10.3 - - + +
407B PHE* 4.5 2.0 - - + -
409B TYR* 3.6 36.2 - - + -
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Residues in contact with MET 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B MET* 3.3 31.6 + - - +
302B ILE* 4.5 12.6 - - + +
304B ASN 3.0 10.4 + - - +
305B PRO* 3.7 9.0 - - + +
307B ALA* 1.3 77.1 - - - +
309B LYS* 1.4 54.0 + - - +
311B ALA* 3.4 2.3 + - - +
312B THR* 2.7 42.6 + - - +
462B LEU* 3.7 28.5 - - + -
465B PHE 5.9 0.9 - - - +
467B LEU* 4.4 35.7 - - + +
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Residues in contact with LYS 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B PRO 3.0 19.1 + - - +
306B GLU* 3.9 5.6 - - - +
307B ALA 3.4 0.2 - - - -
308B MET* 1.4 76.8 - - - +
310B ALA* 1.4 61.3 + - - +
312B THR* 3.6 6.0 + - - -
313B GLU* 3.2 23.6 + - - +
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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
----------------------------------------------------------
306B GLU 3.3 15.5 + - - +
307B ALA 3.9 1.1 - - - +
309B LYS* 1.4 74.9 - - - +
311B ALA* 1.4 59.6 + - - +
313B GLU* 3.4 6.6 + - - +
314B GLU* 3.0 28.4 + - - +
345B VAL* 3.9 15.6 - - + +
409B TYR* 3.7 31.6 - - + +
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Residues in contact with ALA 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B MET* 3.8 26.7 - - - -
307B ALA 3.1 18.3 + - - +
308B MET 3.8 3.4 - - - +
310B ALA* 1.4 72.7 - - - +
312B THR* 1.4 59.0 + - - +
314B GLU* 3.3 4.0 + - - +
315B VAL* 3.0 35.0 + - - +
345B VAL* 3.8 8.6 - - - +
346B LEU* 4.0 11.0 - - + -
349B ILE* 3.9 12.1 - - + -
462B LEU* 4.1 4.9 - - + -
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Residues in contact with THR 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B MET* 2.7 31.2 + - - +
309B LYS* 3.7 7.2 - - - -
311B ALA* 1.4 73.9 - - - +
313B GLU* 1.3 58.6 + - - +
315B VAL* 3.5 2.8 + - - +
316B LYS* 2.9 32.3 + - + +
462B LEU* 3.5 28.3 - - + +
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Residues in contact with GLU 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B LYS 3.2 14.3 + - - +
310B ALA* 3.7 7.2 - - - +
312B THR* 1.3 78.4 - - - +
314B GLU* 1.3 59.5 + - - +
316B LYS* 3.4 9.8 + - - +
317B ARG* 2.9 40.7 + - + +
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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
----------------------------------------------------------
310B ALA 3.0 17.2 + - - +
311B ALA* 3.3 8.0 + - - +
313B GLU* 1.3 74.8 - - - +
315B VAL* 1.3 54.6 + - + +
317B ARG* 3.3 9.1 + - - +
318B THR* 2.7 38.3 + - - +
342B ASP 5.3 1.1 - - - +
343B LEU* 3.3 32.3 - - + +
344B PRO* 3.3 14.4 - - - +
345B VAL* 3.1 32.0 + - + +
346B LEU* 3.0 30.8 + - + +
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Residues in contact with VAL 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B ALA 3.0 20.5 + - - +
312B THR 4.0 3.4 - - - +
314B GLU* 1.3 71.8 - - + +
316B LYS* 1.3 59.3 + - - +
318B THR* 3.9 5.5 - - - -
319B LEU* 3.0 35.8 + - + +
343B LEU* 5.3 2.5 - - + -
346B LEU* 4.0 14.1 - - + -
459B ILE* 3.8 42.0 - - + +
462B LEU* 3.7 24.2 - - + -
463B SER* 3.7 22.9 - - - +
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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 THR* 2.9 22.3 + - + +
313B GLU* 3.6 12.3 - - - +
315B VAL* 1.3 76.4 - - - +
317B ARG* 1.4 55.1 + - - +
319B LEU* 3.7 5.5 + - - +
320B GLU* 3.2 29.0 + - - +
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Residues in contact with ARG 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B GLU* 2.9 28.7 + - - +
314B GLU* 3.4 9.2 - - - +
316B LYS* 1.4 73.5 - - - +
318B THR* 1.3 58.9 + - - +
320B GLU* 3.4 5.8 + - - +
321B ASN* 3.1 49.8 + - - +
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Residues in contact with THR 318 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B GLU* 2.7 27.2 + - - +
315B VAL* 3.9 4.9 - - - -
317B ARG* 1.3 69.6 - - - +
319B LEU* 1.3 65.5 + - - +
321B ASN* 3.5 8.8 + - - +
322B ALA* 3.1 22.7 + - - +
335B LEU* 4.4 21.8 - - + -
339B GLU* 4.2 20.5 - - + +
342B ASP 4.8 3.0 + - - +
343B LEU* 3.2 31.5 - - + +
459B ILE* 6.0 1.3 - - + -
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Residues in contact with LEU 319 (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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315B VAL* 3.0 30.4 + - + +
316B LYS* 4.1 4.5 - - - +
318B THR* 1.3 73.1 - - - +
320B GLU* 1.3 64.5 + - - +
322B ALA* 3.3 3.5 + - - -
323B GLY 3.1 4.0 + - - -
324B GLN* 2.9 53.6 + - + +
326B VAL* 3.8 16.6 - - + -
333B ILE* 3.8 27.4 - - + -
335B LEU* 4.0 18.8 - - + -
459B ILE* 4.4 4.0 - - + -
463B SER* 3.4 25.6 - - - +
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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
----------------------------------------------------------
316B LYS 3.2 18.6 + - - +
317B ARG* 3.7 6.5 - - - +
318B THR 3.3 0.2 - - - -
319B LEU* 1.3 74.0 - - - +
321B ASN* 1.4 62.5 + - - +
323B GLY* 3.1 19.2 + - - -
324B GLN 5.0 1.8 - - - +
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Residues in contact with ASN 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B ARG* 3.1 35.7 + - - +
318B THR* 3.9 6.0 - - - +
319B LEU 3.4 0.2 - - - -
320B GLU* 1.4 77.6 - - - +
322B ALA* 1.3 57.6 + - - +
323B GLY 3.3 1.4 + - - -
339B GLU* 5.1 0.8 - - - +
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Residues in contact with ALA 322 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B THR 3.1 17.4 + - - +
319B LEU 3.9 4.0 - - - +
320B GLU 3.3 0.4 - - - -
321B ASN* 1.3 74.6 - - - +
323B GLY* 1.3 56.1 + - - +
324B GLN* 2.9 26.5 + - + -
334B CYS 4.8 0.4 - - - +
335B LEU* 3.8 15.5 - - + -
339B GLU* 3.4 34.5 - - + +
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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