Contacts of the helix formed by residues 311 - 321 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201A THR* 4.3 4.3 - - - -
309A GLN 4.7 1.4 + - - -
310A LEU* 1.3 82.7 - - - +
312A VAL* 1.3 65.9 + - - +
313A ASP* 3.8 6.3 + - - +
314A ALA* 3.1 22.1 + - - +
315A VAL* 3.0 26.9 + - - +
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Residues in contact with VAL 312 (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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201A THR* 4.0 19.4 - - + +
204A GLN* 3.6 62.6 - - + +
205A VAL* 3.6 8.9 - - + +
208A LYS* 4.2 17.7 - - + -
311A SER* 1.3 74.2 - - - +
313A ASP* 1.3 63.8 + - - +
315A VAL 3.3 0.2 + - - -
316A ALA* 2.9 30.4 + - + +
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Residues in contact with ASP 313 (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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208A LYS* 4.8 14.9 - - - +
311A SER* 3.4 5.6 + - - +
312A VAL* 1.3 81.3 - - - +
314A ALA* 1.3 56.6 + - - +
316A ALA* 4.4 5.3 - - - +
317A ASN* 2.6 50.7 + - - +
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Residues in contact with ALA 314 (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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305A ILE* 4.2 9.4 - - + +
309A GLN 3.6 21.8 - - - +
310A LEU* 4.5 1.3 - - - -
311A SER* 3.1 25.6 + - - +
313A ASP* 1.3 80.0 - - - +
315A VAL* 1.3 60.4 + - + +
317A ASN* 4.0 4.7 - - - +
318A THR* 3.0 28.2 + - - -
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Residues in contact with VAL 315 (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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198A LEU* 6.5 1.6 - - + -
201A THR* 4.1 13.2 - - + -
202A MET* 4.1 17.5 - - - -
205A VAL* 3.9 14.8 - - + -
259A VAL* 5.2 2.5 - - + -
278A LEU* 3.6 27.6 - - + -
280A VAL* 5.7 2.2 - - + -
305A ILE* 4.7 1.1 - - + -
310A LEU* 3.5 26.7 - - + -
311A SER 3.0 16.2 + - - +
312A VAL 3.8 2.5 - - - +
314A ALA* 1.3 73.3 - - - +
316A ALA* 1.3 68.9 + - - +
318A THR* 3.0 12.2 + - - -
319A LEU* 3.0 23.3 + - + +
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Residues in contact with ALA 316 (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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205A VAL* 3.9 24.8 - - + +
208A LYS* 4.4 17.5 - - + -
209A LEU* 3.9 16.8 - - + +
312A VAL 2.9 19.2 + - - +
313A ASP* 4.1 4.9 - - - +
315A VAL* 1.3 76.0 - - - +
317A ASN* 1.3 61.5 + - - +
319A LEU* 3.3 1.0 + - - +
320A ALA* 2.9 33.4 + - - +
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Residues in contact with ASN 317 (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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313A ASP* 2.6 41.1 + - - +
314A ALA* 4.0 5.6 - - - +
316A ALA* 1.3 77.5 - - - +
318A THR* 1.3 61.5 + - - +
320A ALA* 3.6 6.4 + - - +
321A GLY* 3.2 18.5 + - - -
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Residues in contact with THR 318 (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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278A LEU* 3.4 31.6 - - + -
303A LYS* 4.0 11.7 - - + +
305A ILE* 3.6 12.6 - - - +
314A ALA 3.0 14.9 + - - -
315A VAL 3.0 8.8 + - - -
317A ASN* 1.3 78.1 - - - +
319A LEU* 1.3 64.6 + - - +
321A GLY* 3.1 11.3 + - - -
322A TRP* 3.5 38.4 + - + +
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Residues in contact with LEU 319 (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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184A VAL* 6.0 2.1 - - + +
186A VAL* 4.4 15.3 - - + -
202A MET* 4.3 17.3 - - + -
205A VAL* 4.3 2.0 - - + -
209A LEU* 4.0 23.8 - - + -
213A VAL* 5.4 3.6 - - + -
257A VAL* 4.3 22.4 - - + -
259A VAL* 4.7 5.6 - - + -
278A LEU* 4.3 13.2 - - + -
315A VAL* 3.0 32.7 + - + +
316A ALA 3.9 2.9 - - - +
318A THR* 1.3 76.6 - - - +
320A ALA* 1.3 64.3 + - - +
321A GLY 3.0 1.4 + - - -
322A TRP* 3.0 45.6 + - + +
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Residues in contact with ALA 320 (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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209A LEU* 3.9 19.0 - - + +
316A ALA 2.9 19.7 + - - +
317A ASN* 4.0 7.2 - - - +
319A LEU* 1.3 75.1 - - - +
321A GLY* 1.3 58.6 - - - +
322A TRP 3.3 3.7 + - - +
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Residues in contact with GLY 321 (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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317A ASN 3.2 9.9 + - - -
318A THR 3.1 7.9 + - - -
319A LEU 3.0 1.8 - - - -
320A ALA* 1.3 78.3 - - - +
322A TRP* 1.3 69.1 + - - +
323A SER* 3.9 1.7 + - - -
326A THR* 5.1 2.8 + - - +
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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