Contacts of the helix formed by residues 306 - 318 (chain B) in PDB entry 1SA4
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 GLY 306 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253B PHE* 4.7 7.7 - - - -
301B SER 4.1 0.8 + - - -
302B PHE* 2.7 29.5 + - - -
305B ALA* 1.3 72.1 - - - +
307B LEU* 1.3 57.7 + - - +
308B LEU 3.2 0.2 - - - -
309B PRO* 3.1 15.8 - - - +
310B LEU* 3.5 17.8 + - - +
372B ILE* 3.6 24.0 - - - +
399B PRO* 4.4 4.3 - - - +
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Residues in contact with LEU 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B THR* 3.5 50.5 - - + +
253B PHE* 3.6 11.4 - - + -
256B LEU* 3.7 23.6 - - + -
273B LEU* 4.6 1.8 - - + -
277B VAL* 3.6 23.3 - - + -
303B TRP 3.5 11.8 + - - +
304B GLN* 2.9 34.0 + - - +
306B GLY* 1.3 78.0 - - - +
308B LEU* 1.3 58.5 + - - +
310B LEU* 3.3 8.8 + - + +
311B LEU* 2.8 35.2 + - + +
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Residues in contact with LEU 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B LEU* 3.8 27.8 - - + -
277B VAL* 4.0 16.6 - - + -
278B THR* 4.2 4.9 - - + -
288B PHE* 4.9 2.7 - - + -
304B GLN 3.9 11.2 - - - +
305B ALA* 3.1 15.7 + - - +
307B LEU* 1.3 75.1 - - - +
309B PRO* 1.3 67.4 - - + +
311B LEU* 3.8 8.4 - - + +
312B HIS* 2.9 30.0 + - - +
328B TRP* 4.1 10.9 - - + -
329B MET* 3.7 29.8 + - + +
330B PHE* 3.6 32.8 - - + -
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Residues in contact with PRO 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B ALA 3.1 12.3 - - - +
306B GLY 3.1 13.7 - - - +
308B LEU* 1.3 91.9 - - + +
310B LEU* 1.3 60.6 + - - +
312B HIS* 3.4 2.3 + - - +
313B ARG* 3.1 24.1 + - - +
328B TRP* 3.5 46.4 - - + -
372B ILE* 3.8 18.4 - - + -
399B PRO* 3.9 26.3 - - + +
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Residues in contact with LEU 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B PHE* 4.0 20.6 - - + -
256B LEU* 3.6 22.0 - - + -
257B ALA* 4.0 29.4 - - + +
260B VAL* 4.3 16.6 - - + +
306B GLY 3.5 16.2 - - - +
307B LEU* 3.3 8.7 + - + +
308B LEU 3.2 0.6 - - - -
309B PRO* 1.3 75.3 - - - +
311B LEU* 1.3 59.9 + - - +
313B ARG* 3.4 10.0 + - - +
314B ALA* 2.9 27.9 + - - +
399B PRO* 3.8 20.2 - - + +
400B VAL* 3.7 28.9 - - + -
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Residues in contact with LEU 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B LEU* 3.8 18.6 - - + -
270B LEU* 4.0 35.2 - - + +
273B LEU* 4.2 13.5 - - + -
274B LEU* 3.8 43.3 - - + +
277B VAL* 3.9 15.5 - - + -
307B LEU 2.8 21.9 + - - +
308B LEU* 3.8 7.2 - - + +
310B LEU* 1.3 73.4 - - - +
312B HIS* 1.3 59.1 + - - +
314B ALA* 3.2 3.7 + - + +
315B LEU* 2.8 44.8 + - + +
329B MET* 5.3 1.3 - - + -
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Residues in contact with HIS 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B LEU 2.9 18.5 + - - +
309B PRO 3.5 5.6 - - - +
310B LEU 3.3 0.2 - - - -
311B LEU* 1.3 76.3 - - - +
313B ARG* 1.3 59.8 + - + +
316B HIS* 2.8 35.3 + - + +
323B LEU* 3.3 38.4 - - + +
324B SER 3.0 29.4 + - - -
327B HIS 4.6 4.3 + - - -
328B TRP* 3.8 22.0 - + + -
329B MET* 5.1 7.2 - - + +
376B PHE* 3.6 12.8 - + - -
377B GLY 5.0 0.4 - - - -
378B SER* 3.2 36.3 + - - -
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Residues in contact with ARG 313 (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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260B VAL* 3.8 30.8 + - + +
265B GLU* 5.5 3.9 + - - +
309B PRO 3.1 14.5 + - - +
310B LEU* 3.7 9.8 - - - +
312B HIS* 1.3 80.0 - - + +
314B ALA* 1.3 66.9 + - - +
316B HIS* 3.7 7.2 - - + +
317B ALA* 3.0 25.2 + - + +
398B HIS* 4.1 25.1 + - - -
399B PRO* 5.3 6.3 - - - +
400B VAL* 4.3 7.9 - - - +
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Residues in contact with ALA 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B LEU* 5.5 1.3 - - + -
260B VAL* 6.2 0.2 - - - +
265B GLU* 4.1 33.0 + - + +
270B LEU* 4.0 22.9 - - + -
310B LEU 2.9 18.3 + - - +
311B LEU* 3.5 8.5 - - + +
313B ARG* 1.3 77.4 - - - +
315B LEU* 1.3 62.1 + - - +
317B ALA* 3.3 14.2 + - - +
318B GLN* 3.5 21.0 + - - +
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Residues in contact with LEU 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A TYR* 3.9 19.7 - - + +
270B LEU* 4.1 31.0 - - + +
274B LEU* 4.5 10.3 - - + -
311B LEU* 2.8 28.7 + - + +
314B ALA* 1.3 72.3 - - - +
316B HIS* 1.3 57.5 - - - +
318B GLN* 3.0 30.4 + - - +
319B GLY 3.3 0.3 + - - -
320B ASP* 3.2 31.1 + - + +
323B LEU* 3.9 15.9 - - + -
329B MET* 4.1 24.0 - - + -
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Residues in contact with HIS 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B HIS* 2.8 24.4 + - + +
313B ARG* 3.7 8.1 - - + +
315B LEU* 1.3 77.5 - - - +
317B ALA* 1.3 59.8 + - - +
319B GLY* 3.0 17.9 + - - +
320B ASP 4.6 4.8 + - - +
323B LEU* 3.4 18.0 - - + +
378B SER* 4.4 18.3 + - - -
379B GLY* 5.5 7.7 + - - -
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Residues in contact with ALA 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B GLU* 5.4 5.4 - - - +
266B ARG* 5.7 0.7 + - - -
313B ARG* 3.0 17.7 + - + +
314B ALA* 3.5 8.3 - - - +
315B LEU 3.2 0.2 - - - -
316B HIS* 1.3 79.1 - - - +
318B GLN* 1.3 60.8 - - + +
319B GLY 3.2 1.4 + - - -
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Residues in contact with GLN 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B ARG* 3.6 55.8 + - - +
270B LEU* 3.2 32.6 - - - +
314B ALA* 3.5 12.9 + - - +
315B LEU* 3.0 21.7 + - - +
317B ALA* 1.3 79.8 - - + +
319B GLY* 1.3 59.1 + - - +
320B ASP* 3.4 1.8 - - + +
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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