Contacts of the helix formed by residues 300 - 310 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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284A ILE* 3.8 4.7 - - - -
298A HIS* 3.4 2.2 - - - +
299A SER* 1.3 102.3 + - - +
301A LYS* 1.3 66.5 + - - +
302A LYS* 3.4 4.9 - - + +
303A ASP* 3.3 25.6 + - - +
304A ILE* 3.0 24.4 + - - +
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Residues in contact with LYS 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A ASP* 5.9 1.8 - - - +
280A ILE* 2.5 35.8 + - - +
282A PHE* 3.2 45.8 + - + +
284A ILE* 3.9 24.0 - - + +
300A HIS* 1.3 72.6 - - - +
302A LYS* 1.3 66.0 + - - +
304A ILE* 3.1 14.2 + - - +
305A LEU* 3.1 24.2 + - + +
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Residues in contact with LYS 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A HIS* 3.4 3.5 - - + +
301A LYS* 1.3 80.0 - - - +
303A ASP* 1.3 82.3 + - - +
305A LEU* 3.1 9.8 + - - +
306A MET* 2.7 69.1 + - + +
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Residues in contact with ASP 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298A HIS* 3.9 20.4 - - + +
299A SER* 5.6 0.7 + - - -
300A HIS* 3.3 28.9 + - + +
302A LYS* 1.3 102.1 + - - +
304A ILE* 1.3 62.0 + - - +
306A MET* 3.6 8.5 - - - +
307A HIS* 2.9 39.8 + - + +
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Residues in contact with ILE 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282A PHE* 4.3 13.5 - - + -
284A ILE* 3.6 17.7 - - + -
287A PHE* 3.9 18.6 - - + -
296A LEU* 3.6 21.1 - - + -
298A HIS* 3.5 43.1 - - + +
300A HIS 3.0 20.0 + - - +
301A LYS 3.1 6.7 + - - +
303A ASP* 1.3 75.7 - - - +
305A LEU* 1.3 63.2 + - + +
307A HIS* 3.4 3.3 + - - +
308A ARG* 3.1 24.5 + - + +
235B SER* 3.3 22.1 + - - +
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Residues in contact with LEU 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A LEU* 3.9 24.0 - - + -
280A ILE* 4.0 27.8 - - + -
282A PHE* 3.6 35.9 - - + -
301A LYS* 3.1 22.6 + - + +
302A LYS* 3.1 9.1 + - - +
304A ILE* 1.3 74.2 - - - +
306A MET* 1.3 59.7 + - - +
308A ARG* 3.1 14.1 + - - +
309A TRP* 2.9 33.5 + - - +
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Residues in contact with MET 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302A LYS* 2.7 61.9 + - + +
303A ASP* 3.6 11.0 - - - +
305A LEU* 1.3 72.7 - - - +
307A HIS* 1.3 58.1 + - - +
309A TRP* 3.1 2.2 + - - -
310A ARG* 2.7 66.7 + - - +
311A TYR* 3.1 50.1 + - + +
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Residues in contact with HIS 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A ARG* 2.4 29.0 + - - -
298A HIS* 3.3 32.9 + + + +
303A ASP* 2.9 32.6 + - + +
304A ILE 3.7 2.9 - - - +
305A LEU 3.3 0.2 - - - -
306A MET* 1.3 77.0 - - + +
308A ARG* 1.3 53.7 - - - +
311A TYR* 3.8 38.3 - + + +
312A PRO 5.1 4.2 - - - +
233B GLY 3.4 7.4 - - - +
234B GLY* 3.6 25.2 - - - +
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Residues in contact with ARG 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A TRP 5.0 3.0 + - - -
199A LEU* 3.4 34.7 + - - +
211A ARG* 3.1 14.4 + - - +
282A PHE* 4.0 5.1 - - - -
287A PHE* 3.3 35.1 - - - -
304A ILE* 3.1 15.7 + - - +
305A LEU* 3.4 17.7 - - - +
306A MET 3.1 0.2 - - - -
307A HIS* 1.3 80.2 - - - +
309A TRP* 1.3 59.5 + - + +
413A ARG 5.7 0.9 + - - +
414A GLU* 2.9 32.6 + - - +
415A GLY* 3.0 36.0 - - - +
440A ALA* 5.7 3.4 - - - +
230B GLY 4.5 0.2 - - - +
231B VAL* 3.5 39.1 + - - +
233B GLY 4.6 2.0 - - - -
235B SER* 4.8 5.2 - - - +
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Residues in contact with TRP 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A LEU 5.7 1.0 - - - -
211A ARG* 4.0 16.5 + - - +
305A LEU 2.9 16.2 + - - +
306A MET* 4.7 1.3 - - - -
308A ARG* 1.3 80.7 - - + +
310A ARG* 1.3 63.7 + - + +
311A TYR 3.5 1.7 + - - -
345A VAL* 4.1 4.2 - - - +
346A PRO* 5.5 1.0 - - - +
413A ARG* 3.9 45.1 + - + +
414A GLU 4.3 8.5 - - - +
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Residues in contact with ARG 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A GLU* 3.2 27.8 + - - +
306A MET* 2.7 57.1 + - - +
309A TRP* 1.3 76.3 - - + +
311A TYR* 1.3 68.8 + - + -
345A VAL* 3.4 14.7 - - - +
346A PRO* 5.8 0.2 - - - -
413A ARG* 5.1 16.2 - - - +
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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