Contacts of the helix formed by residues 302 - 316 (chain B) in PDB entry 1SXQ
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201B GLU* 3.2 15.7 - - - +
202B PHE* 3.4 18.8 - - - -
300B VAL* 3.6 0.9 - - - +
301B ASN* 1.3 82.3 - - + +
303B ARG* 1.3 65.3 + - - +
304B ALA* 3.8 13.0 - - - +
305B GLU* 2.9 31.2 + - - +
306B LEU 3.1 16.6 + - - -
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Residues in contact with ARG 303 (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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200B VAL* 2.8 39.4 + - - +
201B GLU* 2.8 45.4 + - - +
202B PHE* 4.4 6.1 - - - +
204B PHE* 3.1 18.9 + - - +
205B ASP* 3.6 31.7 + - - +
206B THR* 4.3 8.1 - - + -
227B PRO 5.1 2.2 + - - -
302B ASN* 1.3 76.4 - - - +
304B ALA* 1.3 62.5 + - - +
306B LEU* 3.1 4.0 + - - +
307B ILE* 3.0 43.0 + - + +
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Residues in contact with ALA 304 (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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302B ASN* 3.3 13.9 + - - +
303B ARG* 1.3 79.2 - - - +
305B GLU* 1.3 64.4 + - + +
307B ILE* 3.4 11.4 + - - +
308B ASP* 3.0 24.3 + - - +
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Residues in contact with GLU 305 (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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299B TYR 4.7 1.9 - - - +
300B VAL* 3.8 10.1 - - + +
301B ASN* 2.8 49.4 + - - +
302B ASN* 2.9 24.1 + - - +
304B ALA* 1.3 77.8 - - + +
306B LEU* 1.3 58.0 + - - +
308B ASP* 3.4 6.4 + - - +
309B ARG* 2.9 43.8 + - - +
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Residues in contact with LEU 306 (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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184B VAL* 4.9 18.4 - - + -
202B PHE* 3.1 49.4 - - + +
206B THR* 5.1 6.1 - - + -
208B LEU* 5.2 1.8 - - + -
210B ILE* 5.3 0.7 - - + -
254B LEU* 4.7 8.7 - - + -
281B LEU* 3.5 35.2 - - + -
300B VAL* 3.8 15.6 - - + +
302B ASN 3.1 13.4 + - - +
303B ARG* 3.1 7.8 + - - +
305B GLU* 1.3 73.1 - - - +
307B ILE* 1.3 62.6 + - + +
309B ARG* 3.2 1.2 + - - +
310B VAL* 2.9 44.0 + - + +
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Residues in contact with ILE 307 (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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205B ASP 4.7 1.6 - - - +
206B THR* 3.4 44.2 - - + +
208B LEU* 4.1 17.8 - - + +
303B ARG* 3.0 41.3 + - + +
304B ALA* 3.7 8.7 - - - +
306B LEU* 1.3 78.4 - - + +
308B ASP* 1.3 57.8 + - - +
310B VAL* 3.4 2.1 + - - +
311B ASN* 2.9 47.7 + - - +
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Residues in contact with ASP 308 (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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304B ALA 3.0 17.7 + - - +
305B GLU* 3.7 7.1 - - - +
307B ILE* 1.3 77.6 - - - +
309B ARG* 1.3 66.6 + - - +
311B ASN* 3.2 11.7 + - - +
312B GLU* 2.9 32.5 + - - +
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Residues in contact with ARG 309 (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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281B LEU* 3.8 26.0 - - + -
296B ALA 3.9 1.2 + - - -
297B ARG* 2.8 44.7 + - - +
299B TYR 2.8 28.9 + - - -
300B VAL* 3.8 10.6 - - + +
305B GLU* 2.9 36.1 + - - +
306B LEU 3.2 4.2 + - - +
308B ASP* 1.3 84.0 + - - +
310B VAL* 1.3 57.7 + - - +
312B GLU* 3.2 22.2 + - - +
313B LEU* 3.0 38.3 + - + +
319B LEU* 5.8 1.3 - - - -
323B MET* 5.4 4.7 - - + -
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Residues in contact with VAL 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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183B ASP* 4.1 18.8 - - + +
184B VAL* 3.7 22.7 - - + -
208B LEU* 3.8 21.3 - - + -
251B ILE* 5.0 4.5 - - + -
252B ALA* 4.5 4.0 - - + -
281B LEU* 4.0 9.4 - - + -
306B LEU* 2.9 33.1 + - + +
307B ILE 3.8 3.6 - - - +
309B ARG* 1.3 73.4 - - - +
311B ASN* 1.3 61.8 + - - +
313B LEU* 3.2 8.2 + - - +
314B LYS* 2.9 47.2 + - + +
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Residues in contact with ASN 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B LEU* 4.1 14.7 - - - +
307B ILE* 2.9 39.8 + - - +
308B ASP* 3.2 11.8 + - - +
310B VAL* 1.3 76.1 - - - +
312B GLU* 1.3 58.4 + - - +
314B LYS* 3.3 14.1 + - - +
315B HIS* 3.0 29.5 + - - +
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Residues in contact with GLU 312 (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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308B ASP* 2.9 18.5 + - - +
309B ARG* 3.5 25.9 + - - +
310B VAL 3.2 0.2 - - - -
311B ASN* 1.3 77.7 - - - +
313B LEU* 1.3 56.7 + - - +
315B HIS* 3.3 8.5 + - + +
316B SER* 3.0 30.9 + - - -
319B LEU* 3.5 26.6 - - + +
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Residues in contact with LEU 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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251B ILE* 3.7 16.8 - - + -
252B ALA* 4.3 17.3 - - + -
279B VAL* 4.0 28.3 - - + -
281B LEU* 4.3 13.0 - - + -
309B ARG* 3.0 22.4 + - + +
310B VAL* 3.2 8.9 + - - +
312B GLU* 1.3 74.6 - - - +
314B LYS* 1.3 63.7 + - - +
316B SER 3.3 18.8 + - - +
317B ASP* 4.3 1.4 + - - -
319B LEU* 4.0 9.9 - - + -
320B ARG* 3.8 38.1 - - + +
323B MET* 3.9 23.6 - - - -
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Residues in contact with LYS 314 (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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183B ASP* 2.8 32.6 + - - +
208B LEU* 4.9 3.6 - - + -
251B ILE* 3.2 28.8 - - + +
310B VAL* 2.9 32.7 + - + +
311B ASN* 3.7 16.6 - - - +
313B LEU* 1.3 76.4 - - - +
315B HIS* 1.3 61.3 + - - +
316B SER 5.0 0.9 - - - -
317B ASP 5.1 0.5 + - - -
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Residues in contact with HIS 315 (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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311B ASN 3.0 18.0 + - - +
312B GLU* 3.7 9.1 + - - +
313B LEU 3.2 0.2 - - - -
314B LYS* 1.3 79.0 - - - +
316B SER* 1.3 65.5 + - - +
317B ASP 4.0 1.5 + - - -
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Residues in contact with SER 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B GLU* 3.0 13.8 + - - -
313B LEU 3.3 11.0 - - - +
314B LYS 3.5 0.2 - - - -
315B HIS* 1.3 84.9 - - - +
317B ASP* 1.3 63.2 + - - +
318B VAL* 3.5 9.7 + - - +
319B LEU* 3.0 32.2 + - - +
320B ARG 3.1 17.0 + - - -
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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
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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