Contacts of the helix formed by residues 303 - 310 (chain B) in PDB entry 3D7T
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 SER 303 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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297B LEU* 4.1 1.8 - - - -
302B MET* 1.3 76.1 - - - +
304B PRO* 1.3 74.7 - - - +
305B GLU* 2.8 9.4 + - - +
306B ALA* 2.9 24.9 + - - +
307B PHE* 2.8 23.2 + - - +
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Residues in contact with PRO 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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297B LEU* 3.8 12.3 - - + -
302B MET 4.1 4.7 - - - +
303B SER* 1.3 84.5 - - - +
305B GLU* 1.3 59.4 + - + +
307B PHE 3.9 0.2 - - - -
308B LEU* 2.8 39.2 + - + +
330B SER 5.2 0.4 - - - +
334B ILE* 3.2 34.8 - - + -
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Residues in contact with GLU 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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303B SER* 2.8 9.6 + - - +
304B PRO* 1.3 76.9 - - + +
306B ALA* 1.3 55.9 + - - +
307B PHE 3.1 1.1 - - - -
308B LEU* 3.6 2.5 - - - -
309B GLN* 2.8 39.2 + - - +
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Residues in contact with ALA 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 MET* 3.4 24.3 - - + +
303B SER* 2.9 22.5 + - - +
305B GLU* 1.3 80.1 - - - +
307B PHE* 1.3 64.7 + - - +
309B GLN* 3.5 13.4 - - - +
310B GLU* 3.8 7.8 + - - +
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Residues in contact with PHE 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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278B PHE* 4.2 15.3 - + + -
295B LYS* 3.8 24.0 - - + -
296B THR 3.6 11.7 - - - -
297B LEU* 3.5 55.0 - - + -
302B MET* 3.5 16.6 - - + +
303B SER 2.8 16.2 + - - +
304B PRO 3.5 3.8 - - - +
306B ALA* 1.3 73.4 - - - +
308B LEU* 1.3 60.3 + - + +
309B GLN 2.7 3.3 + - - -
310B GLU* 2.6 53.7 + - - +
311B ALA 4.2 0.3 + - - -
334B ILE* 3.8 24.2 - - + -
336B ILE* 3.7 21.7 - - + +
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Residues in contact with LEU 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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304B PRO* 2.8 21.8 + - + +
305B GLU* 3.6 2.9 - - - +
307B PHE* 1.3 75.5 - - + +
309B GLN* 1.3 59.4 + - - +
310B GLU 3.2 0.4 - - - -
311B ALA* 3.6 11.7 + - + +
312B GLN* 3.1 24.2 + - - +
328B VAL* 4.1 26.0 - - + -
329B VAL 4.8 0.4 - - - +
330B SER* 3.9 23.8 - - - +
334B ILE* 3.4 39.9 - - + -
335B TYR 4.1 1.1 - - - +
336B ILE* 4.0 24.0 - - + -
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Residues in contact with GLN 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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305B GLU 2.8 21.3 + - - +
306B ALA* 3.5 11.7 - - - +
307B PHE 2.7 3.0 + - - -
308B LEU* 1.3 69.4 - - - +
310B GLU* 1.3 57.8 + - - +
311B ALA 3.0 5.4 - - - -
312B GLN* 2.9 50.6 + - - +
313B VAL* 4.3 6.4 + - - +
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Residues in contact with GLU 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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278B PHE* 6.0 0.2 - - - +
295B LYS* 2.6 34.3 + - - +
302B MET* 3.9 18.3 - - + +
306B ALA 3.9 10.3 - - - +
307B PHE* 2.6 27.4 + - - +
309B GLN* 1.3 79.4 - - - +
311B ALA* 1.3 57.4 + - - +
313B VAL* 4.9 7.5 + - - +
314B MET* 5.3 2.4 + - - +
336B ILE* 4.6 4.3 - - + +
404B ASP* 2.8 34.7 - - - +
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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