Contacts of the helix formed by residues 280 - 285 (chain D) in PDB entry 2R7I
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 ARG 280 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249A LEU* 4.9 11.1 + - - +
253A ASP* 3.2 26.5 + - - +
278A ARG* 3.3 42.1 - - - +
302A ASP* 2.6 41.7 + - - +
305A LEU 4.7 5.5 + - - -
306A ARG* 3.3 49.1 - - - +
307A TYR* 5.9 1.4 - - - -
278D ARG 3.5 0.2 + - - -
279D LYS* 1.3 72.7 - - - +
281D TRP* 1.3 67.1 + - - +
282D GLU* 3.7 16.2 - - + +
283D ARG* 3.0 27.6 + - + +
284D PHE* 4.1 1.4 - - - -
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Residues in contact with TRP 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227D PHE* 3.8 17.4 - + + -
232D PHE* 4.0 22.4 - + - -
248D VAL* 4.2 19.5 - - + -
249D LEU* 4.5 13.5 - - + -
279D LYS 5.2 6.0 + - - -
280D ARG* 1.3 73.5 - - - +
282D GLU* 1.3 63.7 + - - +
283D ARG 2.9 1.7 + - - -
284D PHE* 2.9 29.2 + + - +
285D VAL* 3.6 8.7 - - - +
298D LEU* 3.4 41.3 - - + -
301D LEU* 3.8 18.6 - - + -
302D ASP* 3.3 42.7 + - + +
305D LEU* 3.9 24.5 - - + -
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Residues in contact with GLU 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302A ASP* 4.6 0.6 - - - +
303A LYS* 3.4 30.1 + - - +
306A ARG* 2.7 45.6 + - - +
280D ARG* 3.7 18.6 - - + +
281D TRP* 1.3 79.3 - - - +
283D ARG* 1.3 59.9 + - + +
284D PHE 3.1 0.4 - - - -
285D VAL* 3.1 34.5 + - + +
298D LEU* 5.2 4.7 - - + +
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Residues in contact with ARG 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247D LYS 5.0 1.8 + - - -
248D VAL* 6.3 0.2 - - - +
279D LYS* 3.7 43.9 - - + +
280D ARG* 3.0 22.0 + - + +
281D TRP 2.9 0.6 + - - -
282D GLU* 1.3 80.7 - - + +
284D PHE* 1.3 81.2 + - + +
285D VAL 3.4 2.9 - - - +
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Residues in contact with PHE 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227D PHE* 3.7 23.2 - - + +
229D LYS* 5.1 14.6 - - + -
232D PHE* 4.1 20.4 - + - -
248D VAL* 3.8 36.3 - - + -
279D LYS* 4.5 7.0 - - + -
280D ARG 4.1 4.9 - - - -
281D TRP* 2.9 42.9 + + - +
283D ARG* 1.3 109.1 - - + +
285D VAL* 1.3 62.4 + - - +
286D HIS* 3.9 8.0 + - - -
289D ASN* 3.1 20.6 + - - -
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Residues in contact with VAL 285 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227D PHE* 4.1 6.3 - - + -
281D TRP 3.6 17.7 - - - +
282D GLU* 3.1 21.8 + - - +
283D ARG 4.8 2.1 - - - +
284D PHE* 1.3 81.8 - - - +
286D HIS* 1.3 69.1 + - - +
289D ASN* 3.6 10.1 - - - +
290D GLN* 4.2 21.8 - - + -
293D VAL* 3.8 29.8 - - + -
298D LEU* 5.3 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