Contacts of the helix formed by residues 304 - 310 (chain A) in PDB entry 4BN2
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 304 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158A GLU* 3.3 10.8 - - - -
276A ARG* 3.8 3.8 - - - -
277A SER* 3.9 19.9 + - - -
280A CYS* 3.5 17.3 - - - +
301A TYR 3.2 2.8 - - - +
302A ARG 3.1 3.6 - - - -
303A ASP* 1.3 82.3 - - - +
305A LYS* 1.3 64.4 + - - +
306A LEU* 3.7 1.3 + - - +
307A THR* 2.5 41.9 + - - +
308A PHE* 3.0 23.5 + - - +
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Residues in contact with LYS 305 (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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155A ILE* 4.4 17.0 - - + -
158A GLU* 2.5 62.8 + - - +
159A GLN* 4.0 2.2 - - - +
160A ILE* 3.8 28.7 - - + -
171A LEU 5.5 2.9 - - - -
172A TYR* 5.7 3.6 - - - +
173A LEU* 3.3 24.1 - - + +
304A SER* 1.3 71.4 - - - +
306A LEU* 1.3 57.1 + - - +
308A PHE* 4.4 1.3 - - - -
309A LEU* 2.9 33.3 + - - +
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Residues in contact with LEU 306 (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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155A ILE* 4.2 18.8 - - + +
223A HIS* 3.7 41.1 - - + +
225A VAL* 5.2 4.7 - - + -
250A VAL* 4.9 4.5 - - + -
252A LEU* 4.0 20.4 - - + -
277A SER* 4.1 25.9 - - - +
278A LEU* 4.4 1.1 - - + -
281A LEU* 4.3 20.2 - - + -
304A SER* 3.0 5.7 - - - +
305A LYS* 1.3 77.6 - - - +
307A THR* 1.3 62.4 + - + +
309A LEU* 3.8 2.5 - - + +
310A LEU* 2.9 52.0 + - + +
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Residues in contact with THR 307 (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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277A SER 4.3 2.2 - - - +
280A CYS* 3.8 6.5 - - - +
281A LEU* 3.7 44.6 - - + +
284A VAL* 3.9 18.8 - - + -
300A CYS 4.0 2.8 + - - -
301A TYR* 2.7 30.4 + - - -
304A SER* 2.5 30.3 + - - +
306A LEU* 1.3 78.3 - - + +
308A PHE* 1.3 55.1 + - - +
310A LEU* 3.5 5.1 - - - -
311A ARG* 3.0 26.3 + - - -
314A LEU* 4.5 4.2 - - + +
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Residues in contact with PHE 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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173A LEU* 3.8 35.7 - - + -
174A ARG* 5.1 0.9 - - - -
175A GLU* 4.4 12.8 - - + -
181A VAL* 3.7 23.8 - - + +
301A TYR* 2.8 18.4 + - + +
302A ARG* 3.7 52.0 - - + -
304A SER 3.0 15.4 + - - +
305A LYS* 3.6 3.8 - - - +
307A THR* 1.3 75.6 - - - +
309A LEU* 1.3 65.8 + - - +
310A LEU 3.0 1.3 - - - -
311A ARG* 2.9 46.2 + - - +
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Residues in contact with LEU 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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153A ILE* 4.4 17.3 - - + -
155A ILE* 4.6 11.2 - - + -
160A ILE* 6.1 0.2 - - + -
173A LEU* 4.1 19.7 - - + +
181A VAL* 3.5 43.5 - - + +
182A PHE* 4.2 8.3 - - - -
183A VAL* 4.4 12.1 - - + -
225A VAL* 4.8 15.0 - - + -
248A ASN* 5.0 7.5 + - - +
305A LYS 2.9 16.4 + - - +
306A LEU* 3.9 4.9 - - + +
308A PHE* 1.3 77.4 - - - +
310A LEU* 1.3 68.5 + - + +
311A ARG 3.3 1.0 + - - -
312A ASP 5.2 0.9 + - - -
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Residues in contact with LEU 310 (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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90A THR* 5.0 0.4 - - + -
92A PHE* 4.0 33.4 - - + -
225A VAL* 5.5 4.3 - - + -
248A ASN* 4.5 16.6 - - + +
250A VAL* 4.5 22.0 - - + -
252A LEU* 5.5 1.8 - - + -
281A LEU* 5.7 3.8 - - + -
306A LEU* 2.9 40.6 + - + +
307A THR* 3.5 4.3 - - - +
309A LEU* 1.3 91.4 - - + +
311A ARG* 1.3 53.5 + - - +
312A ASP 3.2 2.9 - - - -
313A SER* 2.7 42.7 + - - +
314A LEU* 3.2 20.1 + - + +
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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