Contacts of the helix formed by residues 304 - 312 (chain A) in PDB entry 4BN4
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A ARG* 3.9 27.8 - - - +
226A TYR* 3.1 11.0 - - - +
245A VAL* 4.1 3.6 - - + -
301A ARG* 3.1 59.2 + - + +
302A PHE 3.0 0.8 + - - -
303A LEU* 1.3 78.9 - - + +
305A HIS* 1.3 63.7 + - - +
306A VAL 3.1 0.9 + - - -
307A VAL* 3.1 15.5 + - + +
308A ASP* 3.0 27.2 + - - +
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Residues in contact with HIS 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A TYR* 3.0 25.3 + - + +
302A PHE* 3.0 52.7 + + + +
303A LEU* 4.8 1.1 - - - -
304A LEU* 1.3 77.7 - - - +
306A VAL* 1.3 82.3 + - + +
309A PHE* 3.1 44.0 + + + +
310A PRO* 3.8 0.3 - - - +
330A LEU* 3.4 25.9 - - + +
333A ALA* 5.7 2.2 - - + -
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Residues in contact with VAL 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A LEU* 3.6 19.3 - - + +
304A LEU 3.1 0.2 - - - -
305A HIS* 1.3 99.1 - - + +
307A VAL* 1.3 61.4 + - + +
310A PRO* 3.1 23.6 - - - +
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Residues in contact with VAL 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A ARG* 6.0 0.4 - - - +
303A LEU 5.1 1.6 - - - +
304A LEU* 3.1 17.2 + - + +
306A VAL* 1.3 84.5 - - + +
308A ASP* 1.3 70.8 + - - +
309A PHE 3.4 0.2 - - - -
310A PRO* 3.4 3.8 - - - +
311A MET* 3.3 32.1 + - + +
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Residues in contact with ASP 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A VAL* 3.9 4.7 - - + +
223A LEU* 3.6 22.7 - - + +
224A ARG* 2.7 53.4 + - - +
226A TYR* 2.6 30.9 + - + +
304A LEU* 3.0 16.8 + - - +
305A HIS 4.3 0.7 - - - +
307A VAL* 1.3 83.9 - - - +
309A PHE* 1.3 65.4 + - + +
311A MET* 3.2 2.7 + - - -
312A ALA* 3.0 22.3 + - - +
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Residues in contact with PHE 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A VAL* 3.8 15.7 - - + -
143A MET* 3.8 27.6 - - + -
226A TYR* 3.7 29.6 - + - -
305A HIS* 3.1 35.2 + - + +
308A ASP* 1.3 81.6 - - + +
310A PRO* 1.3 65.7 - - + +
311A MET 3.3 0.5 + - - -
312A ALA* 3.4 15.9 + - - +
315A LEU* 4.1 9.6 - - + -
330A LEU* 3.3 43.7 - - + -
333A ALA* 3.8 24.0 - - + +
334A VAL* 3.7 28.0 - - + +
335A ARG 4.5 0.3 + - - -
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Residues in contact with PRO 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A HIS 3.8 0.9 - - - +
306A VAL 3.1 27.1 - - - +
307A VAL* 3.4 6.7 - - - +
309A PHE* 1.3 93.9 - - + +
311A MET* 1.3 66.2 + - + +
333A ALA 4.5 8.1 - - - +
335A ARG* 3.0 37.9 + - + -
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Residues in contact with MET 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A ARG* 3.5 49.8 + - - +
223A LEU* 4.1 14.4 - - + -
307A VAL* 3.3 28.9 + - + +
308A ASP* 3.2 4.7 + - - +
310A PRO* 1.3 84.6 - - + +
312A ALA* 1.3 66.3 + - - +
313A ASP* 3.3 2.9 + - - +
335A ARG* 4.1 6.6 + - - +
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Residues in contact with ALA 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A ARG 3.3 10.1 - - - +
141A VAL* 3.5 29.6 - - + -
223A LEU* 4.3 1.1 - - - -
308A ASP 3.0 5.7 + - - +
309A PHE* 3.4 15.5 + - - +
311A MET* 1.3 75.9 - - - +
313A ASP* 1.3 60.4 - - - +
314A LEU 4.0 7.4 - - - +
334A VAL* 4.0 16.8 - - + -
335A ARG* 2.9 19.6 + - - -
338A VAL* 3.5 10.4 - - - +
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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