Contacts of the helix formed by residues 314 - 322 (chain B) in PDB entry 2K7A
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 314 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232B ASN* 6.3 1.1 - - - +
304B TYR* 3.7 9.8 - - - +
312B PHE* 3.1 20.1 + - - +
313B ASP* 1.3 82.4 - - - +
315B ILE* 1.3 68.6 + - - +
316B PRO* 3.3 16.6 - - - +
317B LEU* 3.2 28.6 - - - +
318B LEU* 3.8 5.2 + - - +
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Residues in contact with ILE 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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232B ASN* 6.1 2.2 - - - +
234B LEU* 4.5 1.1 - - + -
239B TRP* 4.1 16.4 - - + -
264B VAL* 4.9 5.6 - - + -
273B TYR* 3.5 34.3 - - + -
275B VAL* 5.4 1.8 - - + -
294B ILE* 3.8 30.1 - - + -
304B TYR* 3.3 40.6 - - + -
314B SER* 1.3 70.7 - - - +
316B PRO* 1.3 74.9 - - + +
317B LEU 2.9 2.9 + - - -
318B LEU* 3.0 6.2 + - + +
319B ILE* 2.9 42.9 + - + +
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Residues in contact with PRO 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B LEU* 5.0 3.6 - - + -
237B TYR* 3.4 44.2 - - + +
239B TRP* 4.0 14.6 - - + -
314B SER* 3.3 15.7 - - - +
315B ILE* 1.3 97.7 - - + +
317B LEU* 1.3 58.7 + - + +
319B ILE* 3.7 2.2 + - + +
320B GLN* 3.1 32.2 + - - +
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Residues in contact with LEU 317 (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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312B PHE* 3.9 24.2 - - + -
313B ASP* 4.7 5.4 - - + +
314B SER* 3.2 31.3 + - - +
315B ILE 3.0 0.8 - - - -
316B PRO* 1.3 76.3 - - + +
318B LEU* 1.3 57.9 + - - +
319B ILE 3.1 1.3 - - - -
320B GLN* 3.0 4.6 + - + -
321B TYR* 2.6 41.0 + - + +
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Residues in contact with LEU 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B VAL* 5.8 3.1 - - + -
294B ILE* 4.0 14.6 - - + -
304B TYR* 4.6 2.7 - - + -
305B TYR* 3.7 14.8 - - - +
306B VAL* 3.4 42.4 - - + +
312B PHE* 3.5 28.1 - - + -
314B SER 3.8 6.8 + - - +
315B ILE* 3.0 11.5 + - + +
317B LEU* 1.3 79.6 - - - +
319B ILE* 1.3 67.2 + - + +
321B TYR* 4.5 0.9 - - - -
322B HIS* 2.9 46.7 + - + +
333B LEU* 4.9 1.5 - - + +
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Residues in contact with ILE 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B TRP* 3.8 31.6 - - + +
262B PHE* 3.6 25.1 - - + -
264B VAL* 3.7 23.6 - - + -
275B VAL* 3.9 22.9 - - + -
315B ILE* 2.9 32.6 + - + +
316B PRO 4.0 4.9 - - - +
318B LEU* 1.3 85.1 - - + +
320B GLN* 1.3 63.4 + - - +
322B HIS 4.0 0.2 + - - -
323B GLN* 3.2 21.9 + - - +
333B LEU* 4.0 17.1 - - + +
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Residues in contact with GLN 320 (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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239B TRP* 5.5 4.2 - - - +
316B PRO* 3.1 19.8 + - - +
317B LEU* 3.0 6.8 + - + +
319B ILE* 1.3 82.1 - - - +
321B TYR* 1.3 56.8 + - - +
322B HIS 2.9 5.4 - - - -
323B GLN* 2.7 50.4 + - + +
324B TYR* 3.4 16.4 - - + -
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Residues in contact with TYR 321 (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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310B TYR* 2.6 47.9 + + - -
312B PHE* 3.3 35.0 - + + -
317B LEU* 2.6 22.8 + - + +
318B LEU 4.4 0.9 - - - -
320B GLN* 1.3 72.7 - - - +
322B HIS* 1.3 85.7 + + - +
324B TYR* 4.4 6.5 - - - -
325B ASN* 2.3 61.7 + - - +
326B GLY 2.6 21.4 + - - -
327B GLY* 2.8 6.2 - - - -
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Residues in contact with HIS 322 (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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306B VAL* 4.2 10.8 - - + -
307B ALA* 4.9 2.0 - - + +
312B PHE* 5.4 0.7 - + - -
318B LEU* 2.9 41.3 + - + +
319B ILE 4.3 0.9 - - - +
320B GLN 2.9 1.0 - - - -
321B TYR* 1.3 106.2 - + - +
323B GLN* 1.3 65.6 + - - +
324B TYR 3.0 12.0 + - - +
325B ASN* 4.4 0.2 - - - +
327B GLY* 3.6 17.7 - - - -
328B GLY 3.3 19.8 + - - -
329B LEU* 4.0 29.9 - - + +
332B ARG* 3.8 7.0 - - + +
333B LEU* 2.8 37.5 + - + +
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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