Contacts of the helix formed by residues 292 - 303 (chain B) in PDB entry 5D9K
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 292 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167B GLU* 2.7 35.6 + - - -
290B PHE 3.6 3.8 + - - -
291B LEU* 1.3 74.8 - - - +
293B PRO* 1.4 75.3 - - - +
294B GLU* 3.6 11.9 + - - +
295B ALA* 3.1 14.5 + - - +
296B GLN* 3.1 19.1 + - - +
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Residues in contact with PRO 293 (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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291B LEU 3.8 1.3 - - - +
292B SER* 1.4 85.3 - - - +
294B GLU* 1.3 72.0 + - - +
296B GLN* 3.6 11.7 + - + +
297B SER* 3.1 26.9 + - - -
300B ARG* 5.3 0.5 + - - -
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Residues in contact with GLU 294 (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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167B GLU* 4.8 4.8 - - - +
292B SER* 3.6 15.8 + - - +
293B PRO* 1.3 92.6 - - - +
295B ALA* 1.4 63.1 + - - +
297B SER* 3.4 2.9 + - - -
298B LEU* 3.2 19.6 + - - +
324B HIS* 3.2 11.8 - - - -
325B SER* 3.6 36.6 - - - +
326B PHE* 3.9 19.4 - - + +
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Residues in contact with ALA 295 (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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167B GLU* 3.5 12.3 - - - +
258B MET* 3.4 31.2 - - + +
262B LEU* 4.3 11.2 - - + -
291B LEU* 4.5 7.4 - - + -
292B SER* 3.1 27.4 + - - +
294B GLU* 1.4 71.2 - - - +
296B GLN* 1.3 64.3 + - - +
298B LEU 3.5 0.7 + - - -
299B LEU* 3.2 24.2 + - + +
326B PHE* 3.6 6.8 - - + -
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Residues in contact with GLN 296 (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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287B MET* 3.4 26.2 - - + +
288B PRO 4.1 4.0 + - - -
289B GLN* 3.3 35.6 + - - +
291B LEU* 3.0 31.7 + - + +
292B SER 3.1 11.8 + - - +
293B PRO* 3.6 12.0 - - + +
295B ALA* 1.3 77.4 - - - +
297B SER* 1.4 55.9 + - - +
299B LEU* 3.5 1.0 + - - -
300B ARG* 2.9 66.8 + - - +
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Residues in contact with SER 297 (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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293B PRO 3.1 14.3 + - - -
294B GLU* 3.4 10.5 + - - -
296B GLN* 1.4 71.9 - - - +
298B LEU* 1.3 65.6 + - - +
300B ARG* 3.5 10.8 + - - +
301B MET* 3.2 42.5 + - - +
324B HIS* 3.1 17.3 + - - -
325B SER* 5.3 1.6 - - - -
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Residues in contact with LEU 298 (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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254B PHE* 4.9 2.0 - - + -
258B MET* 3.7 15.7 - - + -
294B GLU 3.2 8.8 + - - +
295B ALA 3.9 4.0 - - - +
296B GLN 3.4 0.2 - - - -
297B SER* 1.3 77.9 - - - +
299B LEU* 1.4 56.9 + - - +
301B MET* 3.1 5.2 + - - +
302B LEU* 2.8 51.3 + - + +
311B LEU* 3.3 29.8 - - + -
321B ILE* 4.9 7.0 - - + -
324B HIS* 3.3 25.9 + - + +
326B PHE* 3.6 33.4 - - + -
327B PHE* 3.7 19.5 - - + -
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Residues in contact with LEU 299 (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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255B GLY* 3.4 29.6 - - - +
258B MET* 3.8 25.8 - - + -
259B PHE* 3.9 15.5 - - + -
262B LEU* 5.2 0.7 - - + -
287B MET* 3.9 16.6 - - + -
291B LEU* 3.8 31.0 - - + -
295B ALA* 3.2 21.8 + - + +
296B GLN 3.9 3.4 - - - +
297B SER 3.4 0.2 - - - -
298B LEU* 1.4 74.7 - - - +
300B ARG* 1.3 56.7 + - - +
302B LEU* 3.1 5.3 + - - +
303B PHE* 2.9 56.0 + - + -
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Residues in contact with ARG 300 (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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287B MET* 3.6 27.2 - - + +
289B GLN* 4.6 3.6 - - - +
293B PRO 5.3 0.6 + - - -
296B GLN* 2.9 62.9 + - - +
297B SER* 3.9 9.2 - - - +
299B LEU* 1.3 75.8 - - - +
301B MET* 1.3 62.0 + - + +
303B PHE* 3.7 13.5 + - - +
304B LYS* 3.5 23.3 + - - +
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Residues in contact with MET 301 (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 SER* 3.2 32.6 + - - +
298B LEU 3.1 5.2 + - - +
300B ARG* 1.3 76.6 - - + +
302B LEU* 1.3 64.1 + - - +
304B LYS* 3.6 23.6 - - - +
309B ASN 4.5 0.5 - - - +
310B ARG* 3.7 0.5 - - - -
311B LEU* 3.2 45.7 + - + +
324B HIS* 3.8 22.7 - - + +
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Residues in contact with LEU 302 (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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251B TRP* 3.4 28.5 - - + +
252B TRP* 3.7 7.8 - - - -
254B PHE* 3.7 20.4 - - + -
255B GLY* 3.7 29.2 - - - +
258B MET* 4.8 2.9 - - - -
298B LEU* 2.8 41.6 + - + +
299B LEU* 3.1 4.2 + - - +
301B MET* 1.3 76.7 - - - +
303B PHE* 1.4 61.4 + - + +
304B LYS 3.4 2.2 + - - -
310B ARG* 3.1 27.3 + - - +
311B LEU* 3.8 32.1 - - + +
321B ILE* 4.6 8.3 - - + -
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Residues in contact with PHE 303 (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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252B TRP* 3.6 55.4 - + + -
255B GLY* 3.4 25.1 - - - -
256B VAL* 3.6 17.0 - - + -
259B PHE* 4.4 4.0 - + + -
267B PRO* 4.1 11.9 - - + -
268B PHE* 4.3 8.1 - + + -
283B ALA* 4.4 11.7 - - - +
285B LEU* 3.5 33.7 - - + -
299B LEU* 2.9 41.6 + - + +
300B ARG* 3.7 9.8 + - - +
301B MET 3.4 1.0 - - - -
302B LEU* 1.4 77.2 - - - +
304B LYS* 1.3 60.3 + - - +
305B ARG* 3.7 4.5 + - - -
402B GOL 4.9 1.6 + - - -
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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