Contacts of the helix formed by residues 309 - 315 (chain B) in PDB entry 2HD1
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 THR 309 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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303B TYR* 4.1 11.2 - - + -
304B GLN* 2.6 51.7 + - - +
307B ALA* 3.9 17.3 - - + +
308B ARG* 1.3 80.6 - - - +
310B GLU* 1.3 66.1 + - - +
311B LEU 3.6 1.2 + - - -
312B ALA 3.1 13.0 + - - -
313B VAL* 2.9 22.4 + - - +
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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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331A GLN* 5.9 0.3 + - - -
309B THR* 1.3 73.9 - - - +
311B LEU* 1.3 53.5 + - - +
313B VAL* 3.3 7.0 + - - +
314B ARG* 2.6 54.8 + - - +
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Residues in contact with LEU 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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297B PRO* 4.8 7.0 - - + -
304B GLN* 3.8 20.0 - - - +
309B THR* 3.2 1.4 + - - -
310B GLU* 1.3 78.3 - - + +
312B ALA* 1.3 56.9 + - - +
314B ARG* 3.2 27.3 + - - +
315B TYR* 2.9 44.8 + - + +
320B PRO* 4.0 10.3 - - + +
321B LEU* 4.0 26.9 - - + -
324B HIS* 3.7 40.6 - - + +
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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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353A ARG* 3.2 4.8 + - - +
304B GLN* 3.1 37.7 - - + +
305B ILE* 3.9 4.9 - - + +
308B ARG* 4.5 3.8 - - - -
309B THR* 3.1 10.3 + - - +
311B LEU* 1.3 78.9 - - - +
313B VAL* 1.3 57.3 + - + +
316B ASN 2.9 23.7 + - - -
317B ASP* 3.0 25.2 + - - +
320B PRO* 4.1 11.1 - - - +
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Residues in contact with VAL 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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327A ALA* 3.6 18.5 - - - +
330A PHE* 4.5 11.0 - - + +
331A GLN* 3.6 39.9 - - + +
334A ALA* 6.0 4.5 - - + -
353A ARG* 4.0 16.2 + - - +
308B ARG* 4.1 18.4 - - + +
309B THR 2.9 20.2 + - - +
310B GLU* 3.6 7.0 - - - +
312B ALA* 1.3 73.6 - - + +
314B ARG* 1.3 68.9 + - - +
315B TYR 3.3 0.3 + - - -
316B ASN* 3.4 9.9 + - - +
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Residues in contact with ARG 314 (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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314A ARG* 3.7 31.6 - - - +
315A TYR* 2.7 37.6 + - - +
327A ALA* 3.8 10.9 - - - +
331A GLN* 5.2 6.0 - - - +
310B GLU* 2.6 39.5 + - - +
311B LEU* 3.6 27.3 - - - +
313B VAL* 1.3 75.7 - - - +
315B TYR* 1.3 81.0 + - + +
316B ASN* 3.7 2.3 + - - -
324B HIS* 4.1 15.6 + - - -
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Residues in contact with TYR 315 (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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314A ARG* 2.6 35.4 + - - +
315A TYR* 3.6 25.1 - + - -
323A ASN* 4.5 2.8 - - - +
311B LEU* 2.9 36.1 + - + +
314B ARG* 1.3 98.1 + - + +
316B ASN* 1.3 73.6 + - - +
317B ASP 3.2 0.9 - - - -
318B ILE* 3.1 30.9 + - - +
320B PRO* 3.6 30.1 - - + -
323B ASN* 3.5 31.0 + - + -
324B HIS* 3.9 7.9 + - - -
327B ALA* 3.6 17.3 - - - +
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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