Contacts of the helix formed by residues 301 - 316 (chain B) in PDB entry 3RU0
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 LYS 301 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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296B LEU* 2.9 36.0 + - + +
297B LYS* 4.7 0.4 - - - +
299B HIS* 3.9 28.5 - - + +
300B TRP* 1.3 73.4 - - - +
302B TRP* 1.3 58.3 + - - +
303B GLU 3.4 2.5 - - - -
304B GLN* 3.3 29.0 + - - +
305B VAL* 3.1 29.2 + - - +
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Residues in contact with TRP 302 (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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191B GLN* 4.0 23.6 - - + -
297B LYS* 3.9 27.8 - - + -
300B TRP* 3.1 55.6 + + + -
301B LYS* 1.3 68.5 - - - +
303B GLU* 1.3 66.9 + - - +
305B VAL* 3.3 9.9 + - + +
306B LEU* 2.9 26.5 + - - +
333B CYS 4.9 2.2 - - - -
336B ASP* 4.3 8.1 - - + -
337B ALA* 3.6 31.3 - - + +
340B ASN* 3.4 48.5 + - + +
341B LEU* 3.9 24.5 - - + -
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Residues in contact with GLU 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A SER* 5.8 0.2 - - - -
64A GLN* 3.9 27.9 + - - +
301B LYS 3.4 0.6 - - - -
302B TRP* 1.3 77.2 - - - +
304B GLN* 1.3 59.9 + - + +
306B LEU* 3.4 1.8 + - - +
307B ALA* 3.0 28.8 + - - +
341B LEU* 3.7 29.0 - - + +
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Residues in contact with GLN 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B LYS* 5.3 2.6 + - - -
296B LEU* 3.2 31.8 - - + +
301B LYS* 3.3 37.1 + - - +
302B TRP 3.3 0.2 - - - -
303B GLU* 1.3 76.1 - - + +
305B VAL* 1.3 64.7 + - - +
307B ALA* 3.6 6.7 + - - +
308B MET* 3.1 28.5 + - + +
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Residues in contact with VAL 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B ILE* 4.1 8.1 - - + +
296B LEU* 3.7 10.7 - - + +
297B LYS* 3.5 35.4 - - + +
301B LYS 3.1 18.3 + - - +
302B TRP* 3.5 16.4 - - + +
304B GLN* 1.3 75.3 - - - +
306B LEU* 1.3 58.0 - - - +
308B MET* 3.2 4.8 + - - +
309B CYS* 2.8 42.2 + - - -
333B CYS* 3.7 31.0 - - + +
337B ALA* 3.9 5.2 - - + -
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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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66A ARG* 3.8 24.0 - - - +
302B TRP 2.9 17.5 + - - +
303B GLU 3.8 3.1 - - - +
305B VAL* 1.3 76.0 - - - +
307B ALA* 1.3 55.9 + - - +
309B CYS* 4.4 2.2 - - - -
310B GLN* 2.7 60.7 + - + +
334B ALA* 4.1 15.0 - - + +
337B ALA* 3.9 7.9 - - + -
338B CYS* 3.8 25.6 - - - +
341B LEU* 3.9 20.6 - - + -
343B LEU* 3.9 13.2 - - + -
350B TYR* 4.1 9.6 - - + -
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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
----------------------------------------------------------
303B GLU 3.0 18.2 + - - +
304B GLN* 3.8 7.9 - - - +
305B VAL 3.3 0.2 - - - -
306B LEU* 1.3 76.9 - - - +
308B MET* 1.3 62.7 + - + +
310B GLN* 3.8 13.1 + - - +
311B ALA* 3.4 19.2 + - - +
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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
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289B SER* 3.8 23.3 - - - +
292B LYS* 3.9 21.1 - - + -
293B ILE* 3.8 28.3 - - + -
296B LEU* 3.9 22.7 - - + -
304B GLN 3.1 18.2 + - - +
305B VAL* 3.8 3.1 - - - +
307B ALA* 1.3 76.2 - - + +
309B CYS* 1.3 63.6 + - - +
311B ALA* 3.4 5.2 + - - +
312B ILE* 3.1 30.3 + - + +
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Residues in contact with CYS 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B ILE* 3.8 29.2 - - - -
305B VAL* 2.8 25.8 + - - +
306B LEU 3.9 1.8 - - - +
308B MET* 1.3 73.1 - - - +
310B GLN* 1.3 57.1 + - - +
312B ILE* 3.2 3.3 + - - +
313B ILE* 2.9 35.4 + - - +
330B VAL* 3.5 31.9 - - + +
333B CYS* 3.8 11.0 - - - -
334B ALA* 3.8 24.0 - - + -
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Residues in contact with GLN 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ARG* 2.4 43.0 + - - +
306B LEU* 2.7 39.5 + - + +
307B ALA* 3.8 13.1 + - - +
309B CYS* 1.3 70.0 - - - +
311B ALA* 1.3 51.7 + - - +
313B ILE* 3.4 2.7 + - - +
314B SER* 2.7 39.0 + - - -
350B TYR* 3.4 25.6 + - - +
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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
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307B ALA 3.4 9.7 + - - +
308B MET* 3.4 10.6 + - - +
309B CYS 3.3 0.2 - - - -
310B GLN* 1.3 78.5 - - - +
312B ILE* 1.3 58.4 + - + +
314B SER* 3.3 5.8 + - - -
315B SER* 3.0 33.5 + - - -
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Residues in contact with ILE 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B VAL* 4.1 29.4 - - + -
289B SER* 3.5 34.1 - - - +
293B ILE* 3.7 23.1 - - + -
308B MET* 3.1 16.7 + - + +
309B CYS 3.7 6.3 - - - +
311B ALA* 1.3 77.4 - - + +
313B ILE* 1.3 63.0 + - - +
315B SER* 3.3 7.2 + - - +
316B ASN* 3.2 25.5 + - - +
327B GLN* 4.1 7.1 - - - +
330B VAL* 4.0 17.9 - - + -
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Residues in contact with ILE 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B CYS 2.9 22.5 + - - +
310B GLN* 4.0 3.1 - - - +
312B ILE* 1.3 78.7 - - - +
314B SER* 1.3 64.0 + - - +
316B ASN* 3.5 1.2 + - - +
317B SER* 3.4 20.1 + - - -
327B GLN* 4.6 13.1 + - - +
330B VAL* 3.7 20.0 - - + +
331B LEU* 3.9 13.0 - - + -
334B ALA* 3.8 16.4 - - + -
349B PHE* 5.4 0.9 - - + -
350B TYR* 3.3 37.9 - - + -
353B ARG* 3.7 36.2 + - - +
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Residues in contact with SER 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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310B GLN 2.7 25.3 + - - -
311B ALA* 3.3 7.6 + - - -
313B ILE* 1.3 76.8 - - - +
315B SER* 1.3 63.0 + - - +
316B ASN 3.2 0.9 + - - -
317B SER* 3.3 21.9 + - - -
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Residues in contact with SER 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 ALA 3.0 20.3 + - - -
312B ILE* 3.3 10.0 + - - -
313B ILE 3.4 0.2 - - - -
314B SER* 1.3 78.3 + - - +
316B ASN* 1.3 71.1 + - - +
317B SER 3.6 0.6 + - - -
318B GLU* 5.1 1.9 + - - +
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Residues in contact with ASN 316 (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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282B VAL* 3.9 20.8 + - - +
285B GLU* 6.1 0.4 - - - +
286B VAL* 3.4 30.7 - - - +
312B ILE* 3.2 20.6 + - - +
313B ILE 4.0 1.8 - - - -
314B SER 3.2 0.6 - - - -
315B SER* 1.3 90.1 + - - +
317B SER* 1.3 58.3 + - - +
318B GLU 3.2 3.1 - - - -
319B ARG* 3.2 7.9 + - + +
320B LEU* 2.9 35.5 + - + +
327B GLN* 4.1 15.2 + - - +
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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