Contacts of the helix formed by residues 305 - 313 (chain B) in PDB entry 4BL8
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 LEU 305 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86B PHE* 6.2 0.9 - - + -
89B LYS* 3.6 30.7 - - + +
90B LEU* 3.3 22.1 - - + +
109B ILE 4.7 0.2 + - - -
286B LEU* 3.7 10.5 - - + +
287B THR* 3.4 42.6 - - - +
288B ASP* 3.9 1.8 - - - +
291B LEU* 3.4 26.6 - - + +
303B VAL* 3.3 2.5 - - + +
304B ALA* 1.3 75.4 - - - +
306B LYS* 1.3 68.1 + - - +
307B SER* 2.9 23.8 + - - +
308B TYR* 3.1 3.5 + - + +
309B GLU* 3.0 20.8 + - - +
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Residues in contact with LYS 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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88B ASP* 3.1 41.7 + - - +
89B LYS* 2.7 18.0 + - - +
90B LEU 3.4 18.6 + - - -
91B TYR* 3.7 43.3 - - + +
92B PRO* 4.4 10.6 - - - +
304B ALA 3.3 2.0 + - - -
305B LEU* 1.3 70.0 - - - +
307B SER* 1.3 61.0 + - - +
309B GLU* 3.4 1.6 + - - +
310B GLU* 3.2 37.2 + - - +
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Residues in contact with SER 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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89B LYS 4.5 0.4 + - - -
288B ASP* 2.6 33.7 + - - -
305B LEU* 2.9 17.6 + - - +
306B LYS* 1.3 80.8 - - - +
308B TYR* 1.3 61.5 + - - -
309B GLU 3.1 1.0 + - - -
310B GLU* 3.3 17.1 + - - +
311B GLU* 3.4 10.7 + - - +
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Residues in contact with TYR 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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288B ASP* 3.3 36.3 + - + +
291B LEU* 3.9 26.0 - - + -
292B GLU* 3.1 49.8 + - + +
295B ASN* 4.2 12.4 + - + +
296B LYS* 5.8 0.9 - - - +
303B VAL* 3.7 14.1 - - + -
305B LEU* 3.1 7.1 + - + +
307B SER* 1.3 79.8 + - - +
309B GLU* 1.3 61.0 + - - +
311B GLU* 3.1 34.3 + - - -
312B LEU* 3.4 57.4 + - + +
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Residues in contact with GLU 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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91B TYR* 3.3 35.3 + - + +
302B ALA* 4.5 15.1 - - + +
303B VAL* 3.4 30.9 - - + +
305B LEU 3.0 16.7 + - - +
306B LYS 3.6 0.9 - - - +
307B SER 3.0 0.2 - - - -
308B TYR* 1.3 74.3 - - - +
310B GLU* 1.3 64.0 + - - +
311B GLU 3.0 5.1 + - - -
312B LEU* 3.2 3.8 + - - +
313B ALA* 2.9 39.3 + - - +
318B ILE* 4.5 5.5 - - - +
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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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91B TYR* 4.2 9.9 - - - +
306B LYS* 3.2 26.3 + - - +
307B SER* 3.8 9.5 - - - +
309B GLU* 1.3 80.1 - - - +
311B GLU* 1.3 60.7 + - - +
312B LEU 3.4 0.2 - - - -
313B ALA* 3.9 13.0 + - - +
314B LYS* 4.7 10.6 - - - +
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Residues in contact with GLU 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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288B ASP* 5.2 5.0 - - - +
292B GLU* 5.4 0.7 - - - +
307B SER 3.4 9.4 + - - +
308B TYR* 3.1 39.0 - - + +
309B GLU 3.0 1.0 - - - -
310B GLU* 1.3 81.2 - - - +
312B LEU* 1.3 65.5 + - + +
314B LYS* 4.1 19.0 - - - +
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Residues in contact with LEU 312 (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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295B ASN* 3.9 24.7 - - - +
301B GLY 5.0 6.1 - - - +
303B VAL* 4.9 9.4 - - + -
308B TYR* 3.4 57.6 + - + +
309B GLU* 3.2 5.4 + - - +
311B GLU* 1.3 82.7 - - + +
313B ALA* 1.3 65.7 + - - +
314B LYS* 3.0 4.0 - - - -
315B ASP* 2.9 26.8 + - + +
318B ILE* 4.0 16.2 - - + +
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Residues in contact with ALA 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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309B GLU* 2.9 35.6 + - - +
310B GLU* 4.0 11.7 - - - +
311B GLU 3.5 1.4 - - - -
312B LEU* 1.3 76.4 - - - +
314B LYS* 1.3 62.0 + - + +
315B ASP 3.3 7.0 + - - +
318B ILE* 4.8 6.8 - - - +
319B ALA* 4.9 8.1 + - - +
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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