Contacts of the helix formed by residues 302 - 308 (chain A) in PDB entry 6HBU
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 302 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299A ASN* 3.2 30.0 + - - -
300A GLY 3.2 2.6 - - - +
301A ASP* 1.3 83.0 + - - +
303A THR* 1.3 61.9 + - - +
304A ALA* 3.4 17.0 + - - +
305A VAL* 3.3 12.1 + - - +
306A ALA* 3.0 26.6 + - - +
169B GLY* 4.7 5.2 - - - -
193B ARG* 5.5 1.9 + - - -
220B THR* 5.3 2.6 + - - -
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Residues in contact with THR 303 (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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301A ASP 3.6 3.3 + - - -
302A SER* 1.3 70.2 + - - +
304A ALA* 1.3 66.3 + - - +
305A VAL 3.3 0.2 - - - -
306A ALA* 3.8 7.2 - - - -
307A LEU* 3.2 36.9 + - - +
166B GLN* 3.1 33.2 + - - +
169B GLY* 3.7 16.4 - - - -
171B ASP* 3.2 27.1 - - + +
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Residues in contact with ALA 304 (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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302A SER* 3.2 10.2 + - - +
303A THR* 1.3 82.9 - - - +
305A VAL* 1.3 61.5 + - + +
308A ASN* 3.0 31.8 + - - +
166B GLN 4.0 1.1 - - - -
167B GLU 3.6 22.0 - - - +
168B LEU* 3.7 20.4 - - - +
169B GLY* 3.8 1.1 - - - +
193B ARG* 5.0 0.2 - - - +
220B THR* 4.9 9.9 - - + -
223B ALA* 3.6 16.0 - - + +
224B VAL* 6.3 0.9 - - + -
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Residues in contact with VAL 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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299A ASN* 3.9 22.7 - - - +
300A GLY* 4.8 8.5 - - - +
302A SER* 3.3 14.5 + - - +
304A ALA* 1.3 78.6 - - + +
306A ALA* 1.3 61.2 + - - +
308A ASN 3.1 21.3 - - - +
310A GLU* 3.2 34.0 - - - +
219B SER* 3.6 36.8 - - - +
220B THR* 5.0 1.3 - - - +
223B ALA* 4.1 8.3 - - + -
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Residues in contact with ALA 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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300A GLY 5.1 5.8 + - - +
301A ASP 5.6 1.3 - - - +
302A SER 3.0 16.6 + - - +
303A THR* 4.2 8.5 - - - -
304A ALA 3.4 0.4 - - - -
305A VAL* 1.3 77.7 - - - +
307A LEU* 1.3 64.0 + - + +
308A ASN 3.5 0.2 - - - -
310A GLU* 3.1 32.8 - - - +
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Residues in contact with LEU 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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303A THR* 3.2 35.2 + - - +
304A ALA 4.4 1.8 - - - +
306A ALA* 1.3 86.8 - - + +
308A ASN* 1.3 65.1 + - - +
309A ARG 4.1 1.1 + - - -
310A GLU 4.5 4.8 - - - +
163B ARG* 6.0 1.3 - - + -
166B GLN* 3.8 25.8 - - + +
167B GLU* 3.7 33.4 - - + +
230B ARG* 5.6 3.3 + - - -
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Residues in contact with ASN 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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304A ALA 3.0 21.0 + - - +
305A VAL* 3.1 17.0 - - - +
306A ALA 3.5 0.6 - - - -
307A LEU* 1.3 84.2 - - - +
309A ARG* 1.3 64.0 + - - +
310A GLU* 3.1 5.9 + - - +
167B GLU* 3.2 26.3 + - - +
223B ALA* 2.9 32.5 + - - +
226B LEU* 4.2 17.4 - - + +
227B LEU* 3.9 26.9 - - - +
230B ARG* 4.5 9.1 + - - +
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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