Contacts of the helix formed by residues 277 - 287 (chain H) in PDB entry 1R4N
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 277 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261H PHE* 3.5 4.9 - - - -
275H GLY 3.5 5.6 + - - +
276H VAL* 1.3 75.2 - - - +
278H TYR* 1.3 69.9 + - - +
279H ARG* 3.4 16.1 + - + +
280H LEU* 2.7 39.2 + - + +
281H THR* 2.9 12.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 278 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G GLU* 5.8 4.0 - - - -
254H PRO* 3.8 21.8 + - - +
257H ILE* 3.3 38.2 - - + +
258H GLN* 3.7 25.7 - - - +
261H PHE* 3.2 41.5 - + + -
277H THR* 1.3 73.4 + - - +
279H ARG* 1.3 58.2 + - - +
281H THR* 2.7 24.1 + - - -
282H GLN* 3.0 33.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 279 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G GLU* 3.3 24.8 + - - +
14G ASP* 4.3 9.4 + - - +
17G LEU* 3.4 37.9 + - - +
18G ARG* 2.5 64.0 + - - +
21G GLY* 4.7 2.0 - - - -
22G ASP* 2.8 41.0 + - - +
277H THR* 3.1 14.6 + - + +
278H TYR* 1.3 81.8 - - - +
280H LEU* 1.3 57.5 + - - +
282H GLN* 3.5 8.4 + - - -
283H GLY 3.1 7.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 280 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G ARG* 4.9 3.4 - - - +
225H PRO* 3.7 19.1 - - + -
226H GLU* 3.9 20.9 - - + +
229H ILE* 3.6 13.9 - - + -
275H GLY 3.4 23.6 - - - +
277H THR* 2.7 31.0 + - + +
279H ARG* 1.3 71.8 - - - +
281H THR* 1.3 65.4 + - - +
282H GLN 3.0 1.8 - - - -
283H GLY* 3.0 3.8 + - - +
284H VAL* 2.9 42.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 281 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229H ILE* 3.3 21.9 - - + +
257H ILE* 4.0 12.1 - - + -
260H ILE* 3.7 19.3 - - + +
261H PHE* 3.0 59.7 - - + +
276H VAL* 4.2 1.7 - - - +
277H THR 2.9 6.2 + - - -
278H TYR 2.7 7.9 + - - -
280H LEU* 1.3 76.4 - - - +
282H GLN* 1.3 60.6 + - - +
285H VAL* 2.9 33.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 282 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G ASP* 3.7 19.6 - - - +
15G ARG* 6.1 0.4 - - - +
18G ARG* 3.6 7.2 + - - +
257H ILE* 3.6 37.5 - - + +
278H TYR* 3.0 36.0 + - + +
279H ARG* 3.5 9.6 - - - +
281H THR* 1.3 76.2 - - - +
283H GLY* 1.3 60.2 + - - +
285H VAL* 3.2 4.2 + - - -
286H LYS* 2.7 53.2 + - + +
288H ILE* 3.5 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 283 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G ARG* 3.8 13.5 - - - -
279H ARG 3.1 5.3 + - - -
280H LEU* 3.0 9.8 + - - -
282H GLN* 1.3 77.9 - - - +
284H VAL* 1.3 52.6 + - - +
287H ARG* 2.7 36.0 + - - -
288H ILE* 3.2 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 284 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213H PHE* 5.5 3.1 - - + -
226H GLU* 4.2 18.6 - - + +
229H ILE* 3.4 39.5 - - + -
230H GLU* 3.7 31.6 - - + +
233H ARG* 4.6 1.3 - - - -
280H LEU* 2.9 31.9 + - + +
283H GLY* 1.3 72.4 - - - +
285H VAL* 1.3 60.2 + - - +
287H ARG* 2.6 35.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 285 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229H ILE* 4.1 7.0 - - + -
233H ARG* 3.9 29.1 + - - +
249H LEU* 4.6 5.4 - - + -
251H GLY* 4.1 26.9 - - - +
257H ILE* 5.0 6.3 - - + -
260H ILE* 3.9 39.9 - - + -
281H THR* 2.9 26.7 + - + +
282H GLN* 3.8 4.0 - - - +
284H VAL* 1.3 81.3 - - - +
286H LYS* 1.3 63.8 + - + +
287H ARG* 3.6 3.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 286 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15G ARG* 4.5 22.0 - - - +
8H ATP 5.8 1.8 - - - +
84H ASP* 4.9 5.3 + - - -
86H SER* 5.8 0.4 + - - -
251H GLY* 2.9 37.7 - - - +
252H ASP* 2.6 36.8 + - - +
257H ILE* 4.3 6.3 - - - -
282H GLN* 2.7 34.7 + - - +
285H VAL* 1.3 75.8 - - + +
287H ARG* 1.3 71.9 + - - +
288H ILE* 3.2 15.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 287 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211H VAL 5.4 7.4 + - - -
212H ASN* 4.8 11.9 - - - +
230H GLU* 2.9 35.7 + - - -
233H ARG* 4.4 18.4 - - - +
234H MET* 5.0 2.6 - - - +
283H GLY 2.7 18.1 + - - -
284H VAL* 2.6 36.8 + - - +
285H VAL 3.3 4.2 - - - +
286H LYS* 1.3 76.8 - - - +
288H ILE* 1.3 62.1 + - - +
289H ILE* 3.9 9.4 + - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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