Contacts of the helix formed by residues 311 - 321 (chain B) in PDB entry 1F0K
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 311 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201B THR* 4.4 0.9 - - - -
309B GLN 3.5 3.3 + - - -
310B LEU* 1.3 87.5 - - - +
312B VAL* 1.3 64.2 + - - +
313B ASP* 3.5 7.9 + - - +
314B ALA* 3.0 25.9 + - - +
315B VAL* 3.1 25.6 + - - +
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Residues in contact with VAL 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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201B THR* 4.0 20.6 - - + +
204B GLN* 3.6 64.4 - - + +
205B VAL* 3.8 7.4 - - + +
208B LYS* 4.2 16.2 - - + +
311B SER* 1.3 75.6 - - - +
313B ASP* 1.3 62.3 + - - +
315B VAL* 3.3 1.9 + - - +
316B ALA* 2.9 30.7 + - - +
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Residues in contact with ASP 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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208B LYS* 5.2 8.7 - - - +
311B SER* 3.3 6.8 + - - +
312B VAL* 1.3 83.8 - - - +
314B ALA* 1.3 56.5 + - - +
316B ALA* 4.4 5.4 - - - +
317B ASN* 2.8 48.2 + - - +
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Residues in contact with ALA 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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305B ILE* 4.2 13.5 - - + -
309B GLN 3.5 20.6 - - - +
311B SER* 3.0 24.1 + - - +
313B ASP* 1.3 75.8 - - - +
315B VAL* 1.3 55.2 + - - +
317B ASN* 4.0 4.4 - - - +
318B THR* 2.7 38.3 + - - -
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Residues in contact with VAL 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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198B LEU* 6.4 1.8 - - + -
201B THR* 4.2 11.0 - - + -
202B MET* 3.9 14.6 - - - -
205B VAL* 3.8 19.3 - - + -
259B VAL* 5.4 3.4 - - + -
278B LEU* 4.0 20.2 - - + -
280B VAL* 5.7 1.6 - - + -
305B ILE* 4.5 5.2 - - + -
310B LEU* 3.8 24.9 - - + -
311B SER 3.1 14.0 + - - +
312B VAL 3.8 4.5 - - - +
314B ALA* 1.3 74.1 - - - +
316B ALA* 1.3 67.1 + - - +
318B THR* 3.2 3.5 + - - -
319B LEU* 3.0 40.5 + - + +
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Residues in contact with ALA 316 (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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205B VAL* 4.0 21.3 - - + +
208B LYS* 4.3 18.4 - - + -
209B LEU* 3.6 19.4 - - + +
312B VAL 2.9 18.6 + - - +
313B ASP* 4.0 5.8 - - - +
315B VAL* 1.3 78.7 - - - +
317B ASN* 1.3 59.2 + - - +
319B LEU* 3.9 0.3 - - - -
320B ALA* 2.9 30.9 + - - +
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Residues in contact with ASN 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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313B ASP* 2.8 44.3 + - - +
314B ALA* 4.1 4.1 - - - +
316B ALA* 1.3 75.1 - - - +
318B THR* 1.3 63.2 + - - +
320B ALA* 3.4 6.6 + - - +
321B GLY* 3.1 19.6 + - - -
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Residues in contact with THR 318 (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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278B LEU* 3.7 17.9 - - + -
303B LYS* 2.7 52.8 + - + +
305B ILE* 3.6 4.7 - - - +
314B ALA 2.7 22.4 + - - -
315B VAL 3.5 4.0 - - - -
317B ASN* 1.3 76.3 - - - +
319B LEU* 1.3 63.9 + - - +
321B GLY* 3.2 10.7 + - - -
322B TRP* 3.6 38.0 + - + +
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Residues in contact with LEU 319 (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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184B VAL* 5.8 6.1 - - + +
186B VAL* 4.6 14.4 - - + -
202B MET* 4.4 10.5 - - + -
205B VAL* 4.3 5.6 - - + -
209B LEU* 4.1 23.1 - - + -
213B VAL* 5.3 4.5 - - + -
257B VAL* 4.1 27.8 - - + -
259B VAL* 4.7 7.0 - - + -
278B LEU* 4.4 11.4 - - + -
315B VAL* 3.0 35.1 + - + +
316B ALA 4.0 2.2 - - - +
318B THR* 1.3 76.8 - - - +
320B ALA* 1.3 63.1 + - - +
322B TRP* 3.1 42.8 + - + +
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Residues in contact with ALA 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B LEU* 3.9 17.2 - - + +
316B ALA 2.9 19.2 + - - +
317B ASN* 3.8 7.6 - - - +
318B THR 3.3 0.2 - - - -
319B LEU* 1.3 77.2 - - - +
321B GLY* 1.3 60.2 + - - +
322B TRP 3.2 3.4 + - - +
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Residues in contact with GLY 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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317B ASN 3.1 12.5 + - - -
318B THR 3.2 4.2 + - - -
319B LEU 3.1 1.8 - - - -
320B ALA* 1.3 77.1 - - - +
322B TRP* 1.3 68.9 + - - +
323B SER 3.7 3.0 + - - -
326B THR* 4.8 4.2 + - - +
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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