Contacts of the helix formed by residues 300 - 310 (chain B) in PDB entry 4RUH
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 300 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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284B ILE* 3.9 3.1 - - - -
298B HIS* 3.6 1.2 - - - +
299B SER* 1.3 82.7 + - - +
301B LYS* 1.3 68.5 + - + +
302B LYS* 2.8 44.9 + - + +
303B ASP* 2.9 31.9 + - + +
304B ILE* 2.9 13.0 + - - +
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Residues in contact with LYS 301 (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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280B ILE* 3.0 30.9 + - - +
282B PHE* 3.1 45.8 + - + +
284B ILE* 3.7 30.0 - - + +
300B HIS* 1.3 82.3 - - + +
302B LYS* 1.3 60.7 + - - +
304B ILE* 4.0 3.1 - - - +
305B LEU* 3.2 34.9 + - + +
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Residues in contact with LYS 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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300B HIS* 2.8 29.0 + - + +
301B LYS* 1.3 75.7 - - - +
303B ASP* 1.3 72.3 + - - +
305B LEU* 3.7 4.9 + - - +
306B MET* 3.2 48.1 + - + +
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Residues in contact with ASP 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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298B HIS* 3.9 23.9 + - + +
300B HIS* 2.9 19.9 + - + +
302B LYS* 1.3 95.8 + - - +
304B ILE* 1.3 65.8 + - - +
306B MET* 4.2 5.8 - - - +
307B HIS* 3.2 35.3 + - + +
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Residues in contact with ILE 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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235A SER* 3.8 32.6 + - - +
282B PHE* 4.1 24.7 - - + -
284B ILE* 4.1 13.7 - - + -
287B PHE* 4.4 9.6 - - + -
296B LEU* 3.7 21.1 - - + -
298B HIS* 3.5 38.8 - - + +
300B HIS 2.9 16.8 + - - +
301B LYS* 4.0 6.5 - - - +
303B ASP* 1.3 76.5 - - - +
305B LEU* 1.3 63.2 + - + +
307B HIS* 3.6 1.0 + - - +
308B ARG* 3.2 22.7 + - - +
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Residues in contact with LEU 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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199B LEU* 3.9 31.4 - - + -
280B ILE* 4.9 13.5 - - + -
282B PHE* 3.8 40.8 - - + -
301B LYS* 3.2 29.8 + - + +
302B LYS* 4.2 4.7 - - - +
303B ASP 3.3 0.2 - - - -
304B ILE* 1.3 77.6 - - + +
306B MET* 1.3 66.5 + - + +
308B ARG* 3.0 21.5 + - - +
309B TRP* 2.9 34.5 - - + +
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Residues in contact with MET 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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302B LYS* 3.2 45.0 + - + +
303B ASP* 4.2 7.9 - - - +
305B LEU* 1.3 78.3 - - - +
307B HIS* 1.3 55.5 + - - +
308B ARG 3.0 0.2 - - - -
309B TRP* 3.0 19.7 + - + +
310B ARG* 2.4 55.5 + - + +
311B TYR* 3.2 35.6 + - + +
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Residues in contact with HIS 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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233A GLY 3.6 6.4 - - - +
234A GLY* 3.7 22.0 + - - +
235A SER* 5.0 0.9 - - - -
211B ARG* 2.6 31.6 + - - -
298B HIS* 3.2 37.9 + + + +
303B ASP* 3.2 27.8 + - + +
304B ILE 4.1 2.5 - - - +
306B MET* 1.3 78.3 - - - +
308B ARG* 1.3 52.4 + - - +
311B TYR* 3.7 46.5 - + + +
312B PRO 4.9 5.0 + - - +
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Residues in contact with ARG 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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231A VAL* 3.7 33.1 + - - +
233A GLY 4.5 4.0 - - - -
235A SER* 4.4 6.3 - - - +
198B TRP 5.1 1.8 + - - -
199B LEU* 3.3 35.6 + - - +
211B ARG* 3.1 23.9 + - - +
282B PHE* 4.1 5.9 - - - -
287B PHE* 3.3 34.8 - - - -
304B ILE* 3.2 15.2 + - - +
305B LEU* 3.0 25.5 + - - +
307B HIS* 1.3 80.4 - - - +
309B TRP* 1.3 59.8 + - + +
413B ARG 5.5 0.8 + - - +
414B GLU* 2.7 42.9 + - - +
415B GLY* 3.2 20.0 - - - +
440B ALA* 5.8 2.6 - - - +
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Residues in contact with TRP 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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208B TYR* 5.4 3.6 - - - -
210B LEU 5.8 0.5 - - - -
211B ARG* 4.2 8.5 + - - +
305B LEU* 2.9 41.3 + - + +
306B MET* 3.0 20.7 + - + +
308B ARG* 1.3 85.0 - - + +
310B ARG* 1.3 91.8 + - + +
311B TYR 3.6 2.7 - - - -
345B VAL* 3.7 12.6 - - - +
346B PRO* 5.6 0.2 - - - +
413B ARG* 3.1 92.6 + - + +
414B GLU* 3.9 10.1 - - - +
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Residues in contact with ARG 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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306B MET* 2.4 51.8 + - + +
309B TRP* 1.3 100.5 - - + +
311B TYR* 1.3 62.4 + - + +
345B VAL* 3.6 17.4 - - - +
413B ARG* 5.4 1.6 - - - +
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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