Contacts of the helix formed by residues 246 - 259 (chain B) in PDB entry 1XSK
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 THR 246 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205B GLY* 4.6 0.9 - - - -
244B GLY 3.3 0.4 - - - -
245B PRO* 1.3 91.2 - - + +
247B PRO* 1.3 75.4 - - + +
248B LYS 3.8 1.7 + - - -
249B ALA* 2.9 19.8 + - - +
250B VAL* 2.9 16.4 + - - +
596B PRO* 4.9 11.7 - - + -
3008B SO4 2.9 41.6 + - - +
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Residues in contact with PRO 247 (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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201B MET* 3.3 29.7 - - + +
202B THR 4.8 7.2 - - - +
203B ASN* 5.6 2.7 - - - -
205B GLY* 5.0 4.5 - - - +
245B PRO 4.6 1.8 - - - +
246B THR* 1.3 86.6 - - - +
248B LYS* 1.3 63.1 + - - +
250B VAL* 3.1 10.0 + - + +
251B LEU* 3.0 26.3 + - - +
592B MET* 4.0 19.5 - - + +
593B MET* 4.0 20.2 - - + +
596B PRO* 3.6 29.4 - - + -
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Residues in contact with LYS 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B THR* 3.2 1.2 + - - -
247B PRO* 1.3 80.2 - - - +
249B ALA* 1.3 58.1 + - - +
251B LEU* 3.5 7.9 + - - +
252B ASP* 2.9 27.5 + - - +
583B ARG* 3.8 17.4 + - - +
584B GLY 5.9 0.2 - - - -
585B THR* 3.8 32.6 + - + +
589B ARG* 4.9 0.9 - - - +
593B MET* 3.9 28.7 - - + +
594B GLU* 2.8 40.9 + - - +
612B ASP* 3.1 18.8 + - - -
3008B SO4 3.9 31.5 + - - +
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Residues in contact with ALA 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B GLY* 3.1 28.7 - - - +
245B PRO* 4.1 2.9 - - + -
246B THR* 2.9 23.7 + - + +
248B LYS* 1.3 74.6 - - - +
250B VAL* 1.3 65.5 + - - +
252B ASP* 3.3 5.4 + - - +
253B ARG* 3.1 28.3 + - - +
583B ARG* 3.9 9.6 - - - +
3008B SO4 3.9 6.3 + - - +
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Residues in contact with VAL 250 (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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199B PHE* 3.9 24.2 - - + -
201B MET* 4.4 9.4 - - + -
205B GLY 3.4 34.1 - - - +
206B TYR* 3.7 7.2 - - - +
207B GLY* 3.8 19.1 - - - +
242B ILE* 4.1 9.2 - - + +
243B ASP 4.0 7.4 - - - +
244B GLY* 3.5 6.0 - - - +
246B THR 2.9 17.2 + - - +
247B PRO* 3.4 9.6 - - + +
249B ALA* 1.3 75.7 - - - +
251B LEU* 1.3 51.8 + - - +
253B ARG* 3.1 5.2 + - - +
254B TYR* 2.8 31.9 + - - +
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Residues in contact with LEU 251 (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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199B PHE* 4.3 14.4 - - + -
201B MET* 4.2 8.7 - - - -
247B PRO 3.0 16.1 + - - +
248B LYS* 3.7 8.7 - - - +
250B VAL* 1.3 73.5 - - - +
252B ASP* 1.3 64.4 + - - +
254B TYR* 4.1 5.4 - - + -
255B THR* 2.9 33.0 + - - +
501B GLY 3.7 10.1 - - - +
502B LEU* 4.3 12.1 - - - +
504B GLY* 3.7 31.6 - - - +
583B ARG 3.9 1.3 - - - -
584B GLY 3.8 11.7 - - - +
585B THR* 5.2 1.1 - - - -
586B PRO* 4.0 12.6 - - + -
593B MET* 3.7 33.9 - - + -
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Residues in contact with ASP 252 (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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248B LYS 2.9 14.7 + - - +
249B ALA* 3.3 14.1 - - - +
250B VAL 3.2 0.2 - - - -
251B LEU* 1.3 76.5 - - - +
253B ARG* 1.3 64.3 + - + +
256B ARG* 3.0 20.2 + - - +
260B ARG* 2.8 45.9 + - - -
583B ARG* 3.1 44.3 + - - +
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Residues in contact with ARG 253 (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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61B GLN* 5.6 1.4 - - + +
62B GLU* 2.9 54.1 + - - +
63B GLY* 3.6 17.8 - - - -
64B ILE* 4.2 8.1 - - + +
107B ASN* 5.8 3.6 - - - +
242B ILE* 3.5 16.6 - - + -
243B ASP* 2.9 25.9 + - - -
244B GLY 2.9 28.5 + - - -
249B ALA* 3.1 11.9 + - - +
250B VAL 3.5 2.7 - - - +
252B ASP* 1.3 79.1 - - + +
254B TYR* 1.3 67.1 + - - +
256B ARG* 3.1 13.4 + - - +
257B PHE* 2.8 25.3 + - - +
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Residues in contact with TYR 254 (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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197B ILE* 3.4 23.2 - - - +
199B PHE* 3.6 50.9 - + + +
209B LEU* 4.2 11.4 - - + -
242B ILE* 4.0 14.5 - - + +
250B VAL 2.8 21.1 + - - +
251B LEU* 3.7 8.1 - - + +
253B ARG* 1.3 73.8 - - - +
255B THR* 1.3 58.5 + - + +
257B PHE* 3.1 7.0 + + - +
258B THR* 2.8 61.5 + - + -
470B VAL* 3.9 18.2 - - - +
473B GLN* 4.4 5.7 + - - -
503B SER 3.5 21.7 + - - -
504B GLY* 4.0 16.6 - - - -
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Residues in contact with THR 255 (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 LEU 2.9 25.3 + - - +
254B TYR* 1.3 71.5 - - + +
256B ARG* 1.3 61.4 + - - +
257B PHE 3.1 1.8 - - - -
258B THR* 4.0 2.9 - - - -
259B GLY* 2.8 48.1 + - - +
260B ARG* 2.7 37.0 + - - +
261B PRO* 4.4 3.4 - - + -
473B GLN* 4.6 1.1 - - - +
504B GLY* 3.8 35.2 - - - +
584B GLY* 3.7 21.4 - - - +
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Residues in contact with ARG 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B GLN* 3.5 26.2 - - + +
85B ASN* 3.1 22.7 + - - +
252B ASP* 3.0 26.6 + - - +
253B ARG* 3.1 12.2 + - - +
255B THR* 1.3 77.8 + - - +
257B PHE* 1.3 56.8 + - - +
260B ARG* 3.2 35.4 - - - +
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Residues in contact with PHE 257 (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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60B PRO* 3.6 29.6 - - + -
61B GLN* 3.8 10.1 - - + -
64B ILE* 3.7 18.8 - - + -
84B LEU* 3.7 25.9 - - + -
85B ASN* 2.8 58.6 + - - -
86B ILE* 4.3 1.6 - - + -
209B LEU* 4.1 12.8 - - + -
240B PHE* 3.8 40.2 - + + -
242B ILE* 4.7 7.4 - - + -
253B ARG 2.8 12.2 + - - +
254B TYR* 3.2 9.0 - + - +
255B THR 3.1 0.2 - - - -
256B ARG* 1.3 79.0 - - - +
258B THR* 1.3 68.3 + - + +
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Residues in contact with THR 258 (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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83B PRO* 3.8 17.2 - - - +
84B LEU* 4.2 7.6 - - + -
85B ASN* 4.2 3.6 - - - -
209B LEU* 4.2 12.3 - - + -
254B TYR* 2.8 53.0 + - + +
257B PHE* 1.3 80.2 - - + +
259B GLY* 1.3 56.4 + - - +
470B VAL* 3.8 25.6 - - + -
471B GLY* 3.5 17.8 - - - -
473B GLN* 2.8 25.6 + - - -
474B LYS* 4.4 4.0 + - - -
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Residues in contact with GLY 259 (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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85B ASN* 4.1 8.3 - - - +
255B THR* 2.8 29.1 + - - +
257B PHE 3.7 1.0 - - - -
258B THR* 1.3 75.6 + - - +
260B ARG* 1.3 60.6 + - - -
473B GLN* 3.0 23.3 + - - +
474B LYS* 3.6 20.9 - - - -
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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