Contacts of the helix formed by residues 304 - 313 (chain B) in PDB entry 2R7D
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 304 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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302B GLY* 3.5 3.0 - - - -
303B ASP* 1.3 92.1 - - - +
305B LEU* 1.3 61.4 + - - +
306B PRO* 3.5 11.4 - - - +
307B ALA* 3.3 19.6 + - - +
308B MSE 2.9 29.5 + - - +
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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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240B LEU* 3.8 17.4 - - + +
241B PRO* 3.8 13.9 - - + -
304B THR* 1.3 72.3 - - - +
306B PRO* 1.3 69.0 - - + +
308B MSE 3.4 21.4 + - + -
309B TRP* 2.8 33.1 + - - +
410B VAL* 4.2 32.3 - - + -
412B VAL* 4.3 11.9 - - + -
422B LEU* 4.6 6.7 - - + -
424B PRO* 4.4 16.4 - - + -
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Residues in contact with PRO 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B THR* 3.5 13.5 - - - +
305B LEU* 1.3 95.2 - - + +
307B ALA* 1.3 55.0 + - - +
309B TRP* 3.6 1.4 - - + +
310B ALA* 2.9 31.5 + - - +
410B VAL* 5.1 1.6 - - + -
411B VAL 3.3 24.9 - - - +
412B VAL* 3.7 21.1 - - - +
438B PRO* 4.3 9.6 - - + -
439B GLY* 3.8 20.2 - - - +
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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
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300B VAL* 4.6 6.3 - - + +
301B ALA 4.2 5.8 - - - +
302B GLY* 3.3 39.5 - - - +
304B THR* 3.3 20.2 + - - +
305B LEU 3.1 0.2 - - - -
306B PRO* 1.3 78.2 - - - +
308B MSE 1.3 60.5 + - - +
310B ALA* 3.4 4.2 + - - +
311B ARG* 3.0 30.7 + - - +
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Residues in contact with MSE 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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237B SER* 4.0 19.3 - - - +
238B ILE* 4.1 13.5 - - - +
239B ASP* 2.4 42.8 - - - +
240B LEU* 4.3 12.4 - - + +
241B PRO* 5.3 0.2 - - + -
303B ASP* 3.6 26.5 - - - +
304B THR 2.9 18.4 + - - +
305B LEU* 3.8 27.1 - - + +
307B ALA* 1.3 74.7 - - - +
309B TRP* 1.3 57.9 + - - +
311B ARG* 3.4 15.1 - - - +
312B ARG* 2.9 30.0 + - - +
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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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240B LEU* 4.3 13.4 - - + +
305B LEU 2.8 18.7 + - - +
306B PRO 3.6 4.5 - - - +
308B MSE 1.3 79.3 - - - +
310B ALA* 1.3 64.7 + - - +
311B ARG 3.1 0.9 + - - -
312B ARG* 3.2 42.4 + - - +
313B LYS* 3.5 30.5 + - + +
412B VAL* 3.3 45.0 - - + +
413B ASP* 3.9 17.3 + - + +
420B THR* 3.7 13.4 - - + +
422B LEU* 4.1 25.4 - - + -
429B ASP* 3.4 38.1 - - + -
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Residues in contact with ALA 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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298B ARG* 4.1 18.1 + - - +
300B VAL* 4.8 6.1 - - + -
306B PRO 2.9 19.0 + - - +
307B ALA* 4.0 4.3 - - - +
309B TRP* 1.3 78.0 - - + +
311B ARG* 1.3 58.4 + - - +
313B LYS* 3.8 19.6 + - - +
314B THR* 3.3 25.3 - - - +
412B VAL 5.5 1.3 - - - +
413B ASP* 6.2 2.0 - - - -
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Residues in contact with ARG 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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236B LEU* 3.9 31.9 - - + +
237B SER* 2.9 39.3 + - - +
238B ILE* 3.8 5.8 - - + -
300B VAL* 3.1 43.5 + - + +
301B ALA 4.2 0.4 - - - -
302B GLY 2.6 33.6 + - - +
303B ASP* 4.9 1.8 - - - +
307B ALA* 3.0 18.3 + - - +
308B MSE 3.4 14.1 - - - +
309B TRP 3.0 0.2 - - - -
310B ALA* 1.3 76.1 - - - +
312B ARG* 1.3 60.6 + - - +
313B LYS 3.0 1.8 - - - -
314B THR* 2.7 29.9 + - - +
315B LEU* 3.0 27.7 - - + +
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Residues in contact with ARG 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B ILE* 4.4 16.8 - - + +
240B LEU* 3.7 22.4 - - + +
308B MSE 2.9 15.7 + - - +
309B TRP* 3.2 49.7 + - - +
311B ARG* 1.3 76.8 - - - +
313B LYS* 1.3 63.8 + - + +
314B THR 3.2 0.6 + - - -
315B LEU* 3.5 32.4 + - + +
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Residues in contact with LYS 313 (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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297B THR* 4.6 2.9 + - - -
298B ARG* 5.6 5.3 - - - +
309B TRP* 3.5 24.1 + - + +
310B ALA* 4.1 25.0 - - - +
311B ARG 3.0 1.4 - - - -
312B ARG* 1.3 81.6 - - + +
314B THR* 1.3 62.2 + - + +
315B LEU 3.5 0.9 - - - -
413B ASP* 2.6 32.3 + - - -
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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