Contacts of the helix formed by residues 275 - 283 (chain B) in PDB entry 1SVU
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 HIS 275 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197B LEU* 3.5 22.5 - - + +
201B GLU 4.2 15.0 - - - -
202B VAL* 4.5 8.1 - - + -
204B HIS* 4.8 15.3 + + - -
205B LEU* 4.3 9.2 - - + -
273B LYS 3.8 0.4 + - - -
274B LEU* 1.3 73.8 - - - +
276B PRO* 1.3 96.8 - - + +
277B ARG* 3.2 13.6 + - + +
278B GLU* 2.4 59.2 + - + +
279B CYS 2.7 8.6 + - - -
291B VAL* 5.7 4.7 - - + -
299B TYR* 4.0 1.3 - - - -
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Residues in contact with PRO 276 (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 LEU* 5.1 2.7 - - + -
275B HIS* 1.3 98.5 - - + +
277B ARG* 1.3 51.1 + - - +
279B CYS* 2.7 14.6 - - + +
280B ALA* 2.6 33.1 + - - +
291B VAL* 4.3 9.9 - - + -
295B THR* 3.5 28.3 - - - +
298B ALA* 3.7 24.9 - - + -
299B TYR* 3.1 28.9 - - + +
302B PHE* 3.8 4.1 - - + -
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Residues in contact with ARG 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B LEU* 4.0 22.9 - - + -
275B HIS* 2.7 12.8 + - + +
276B PRO* 1.3 76.9 - - - +
278B GLU* 1.3 55.8 + - - +
280B ALA* 2.6 39.0 + - - +
281B ARG* 2.7 28.1 + - - +
286B PRO 3.7 14.3 + - - -
287B ASP* 3.4 40.2 + - - +
289B TYR* 2.6 35.4 + - - +
290B LYS* 5.3 0.4 - - - +
291B VAL* 4.0 24.8 - - + +
405B UNX 3.9 17.0 - - - -
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Residues in contact with GLU 278 (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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195B LEU* 4.6 4.0 - - + +
196B LEU* 3.1 27.2 - - + +
197B LEU* 2.6 50.3 + - + +
202B VAL* 4.9 1.1 - - - -
272B ARG* 3.9 13.7 + - - -
274B LEU* 3.2 15.4 - - + -
275B HIS* 2.4 46.0 + - - +
277B ARG* 1.3 72.0 - - - +
279B CYS* 1.3 61.4 + - - +
281B ARG* 2.8 14.9 + - - +
282B VAL* 2.7 30.7 + - + +
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Residues in contact with CYS 279 (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* 3.3 35.3 - - + +
261B LYS 5.4 0.9 - - - -
262B THR* 4.5 7.2 - - - -
274B LEU* 4.4 12.0 - - - +
275B HIS 2.7 11.0 + - - -
276B PRO* 2.7 16.8 - - + +
278B GLU* 1.3 71.0 - - - +
280B ALA* 1.3 64.4 + - - +
282B VAL* 3.2 2.9 + - - +
283B MET* 3.0 19.9 + - - +
299B TYR* 3.6 35.9 - - - -
302B PHE* 4.2 15.7 - - + -
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Residues in contact with ALA 280 (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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276B PRO 2.6 6.8 + - - +
277B ARG* 2.6 41.6 + - - +
279B CYS* 1.3 69.5 - - - +
281B ARG* 1.3 52.9 + - + +
283B MET* 2.5 36.6 + - - +
285B TYR* 3.2 16.4 + - + -
286B PRO 4.6 0.7 - - - +
302B PHE* 3.1 36.5 - - + -
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Residues in contact with ARG 281 (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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159B ILE* 4.0 4.2 - - - +
194B ASP 5.3 0.8 + - - -
195B LEU* 3.1 59.8 + - + +
196B LEU 4.2 5.7 + - - -
197B LEU* 4.4 16.6 - - - +
277B ARG* 2.7 41.8 + - + +
278B GLU* 2.8 9.0 + - - +
280B ALA* 1.3 67.5 - - + +
282B VAL* 1.3 56.5 + - - +
283B MET 2.8 5.8 - - - -
284B GLY* 2.9 18.5 + - - -
285B TYR 4.0 12.3 + - - +
286B PRO 4.7 3.4 - - - +
287B ASP* 2.7 44.5 + - - +
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Residues in contact with VAL 282 (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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159B ILE* 3.2 17.9 - - - +
160B PRO* 3.7 7.9 - - + +
161B GLN* 2.5 59.1 + - + +
192B VAL* 5.5 5.8 - - + -
195B LEU* 4.2 15.9 - - + -
196B LEU* 6.4 0.2 - - + -
248B ALA* 3.3 25.8 - - + -
251B LEU* 4.0 7.0 - - + -
274B LEU* 4.5 16.2 - - + -
278B GLU* 2.7 26.5 + - + +
279B CYS 3.7 4.9 - - - +
281B ARG* 1.3 71.9 - - + +
283B MET* 1.3 53.4 + - - +
284B GLY 3.3 1.1 - - - -
307B VAL* 4.9 0.2 - - - +
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Residues in contact with MET 283 (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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161B GLN* 3.6 18.2 - - - +
163B ARG* 2.9 43.7 - - - +
251B LEU* 3.9 11.2 - - + +
279B CYS 3.0 11.6 + - - +
280B ALA 2.5 18.1 + - - +
282B VAL* 1.3 71.7 - - - +
284B GLY* 1.3 54.7 + - - +
285B TYR* 2.8 33.4 + - + -
302B PHE* 2.9 38.4 - - + +
303B GLY* 4.8 0.7 - - - -
305B SER 3.2 14.1 - - - +
306B VAL 3.7 2.0 - - - +
307B VAL* 4.3 15.9 - - - -
308B ILE 3.5 12.6 + - - -
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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