Contacts of the helix formed by residues 304 - 312 (chain B) in PDB entry 4BVH
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 304 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224B ARG* 4.3 19.1 - - - +
226B TYR* 3.2 11.2 - - - +
245B VAL* 4.4 2.5 - - + -
300B GLN 4.4 0.9 + - - +
301B ARG* 3.3 57.0 - - + +
302B PHE 3.1 0.4 + - - -
303B LEU* 1.3 74.9 - - - +
305B HIS* 1.3 64.9 + - - +
306B VAL 2.9 1.7 + - - -
307B VAL* 3.0 8.2 + - + +
308B ASP* 2.9 28.6 + - - +
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Residues in contact with HIS 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B TYR* 2.9 20.2 + - + +
302B PHE* 3.1 50.0 + + - +
303B LEU* 2.9 11.7 - - - +
304B LEU* 1.3 79.1 - - - +
306B VAL* 1.3 85.7 + - + +
308B ASP 4.3 0.2 - - - +
309B PHE* 3.1 46.9 + - + +
310B PRO* 3.8 0.2 - - - +
326B PRO* 6.1 0.6 - - + +
330B LEU* 3.4 24.3 - - + +
333B ALA* 5.7 0.2 - - - +
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Residues in contact with VAL 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B LEU* 3.6 16.2 - - + +
304B LEU 2.9 1.6 + - - -
305B HIS* 1.3 102.4 - - + +
307B VAL* 1.3 66.5 + - + +
310B PRO* 3.1 21.8 - - - +
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Residues in contact with VAL 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B LEU* 3.0 8.3 + - + +
306B VAL* 1.3 92.2 - - + +
308B ASP* 1.3 67.2 + - - +
309B PHE 3.3 0.4 - - - -
310B PRO* 3.4 11.6 - - + +
311B MET* 3.3 27.3 + - + +
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Residues in contact with ASP 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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141B VAL* 4.0 8.9 - - + +
223B LEU* 3.6 17.2 - - + +
224B ARG* 2.8 51.3 + - - +
226B TYR* 2.5 32.9 + - + +
304B LEU* 2.9 15.0 + - - +
307B VAL* 1.3 80.4 - - - +
309B PHE* 1.4 69.9 + - + +
311B MET* 3.0 15.4 + - - +
312B ALA* 3.1 11.3 + - - +
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Residues in contact with PHE 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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141B VAL* 3.6 15.9 - - + -
143B MET* 3.9 19.5 - - + -
226B TYR* 3.8 25.4 - + - -
305B HIS* 3.1 33.8 + - + +
308B ASP* 1.4 78.5 - - + +
310B PRO* 1.3 73.9 - - + +
312B ALA* 3.3 19.4 + - - +
315B LEU* 3.9 12.3 - - + -
330B LEU* 3.3 50.3 - - + -
333B ALA* 3.8 24.0 - - + +
334B VAL* 3.7 29.7 - - + +
335B ARG 4.6 0.7 + - - -
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Residues in contact with PRO 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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305B HIS 3.8 0.7 - - - +
306B VAL 3.1 28.0 - - - +
307B VAL* 3.4 9.0 - - - +
309B PHE* 1.3 98.2 - - + +
311B MET* 1.3 61.9 + - + +
312B ALA 3.7 0.2 + - - -
333B ALA* 4.6 9.2 - - + +
335B ARG 5.6 1.6 - - - +
1394B EDO 3.1 29.1 + - - +
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Residues in contact with MET 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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139B ARG* 2.6 65.3 + - - +
223B LEU* 3.8 16.2 - - + -
307B VAL* 3.3 25.4 - - + +
308B ASP* 3.0 10.0 + - - +
310B PRO* 1.3 82.5 - - + +
312B ALA* 1.3 64.7 + - - +
313B ASP* 3.5 0.9 + - - +
1394B EDO 4.0 5.2 + - - -
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Residues in contact with ALA 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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139B ARG 3.4 9.6 - - - +
141B VAL* 3.6 28.5 - - + -
223B LEU* 4.2 2.9 - - - -
308B ASP 3.1 4.7 + - - +
309B PHE 3.3 16.2 + - - +
310B PRO 4.5 0.5 - - - +
311B MET* 1.3 77.5 - - - +
313B ASP* 1.3 60.0 + - - +
314B LEU 4.1 7.0 - - - +
334B VAL* 3.9 17.3 - - + -
338B VAL* 3.5 12.9 - - - +
1394B EDO 3.0 15.2 + - - -
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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
------------------------------------------------------------
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