Contacts of the helix formed by residues 338 - 348 (chain K) in PDB entry 3FKS
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 ALA 338 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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294K GLU* 4.1 9.6 - - - +
331K THR* 6.4 0.2 - - - -
332K GLN 6.3 0.9 - - - +
335K ASP* 3.8 20.5 + - + +
336K VAL 3.2 2.6 - - - -
337K SER* 1.3 79.6 - - - +
339K TYR* 1.3 58.0 + - - +
341K PRO* 3.5 25.1 - - + -
342K THR* 2.6 35.9 + - - +
314O ALA* 4.0 1.3 - - - -
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Residues in contact with TYR 339 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293K ARG* 3.5 54.1 - - + +
294K GLU* 3.0 27.2 + - + +
296K TYR* 3.7 24.9 + + + -
297K PRO 4.1 4.7 + - - -
298K GLY* 4.1 9.2 + - - -
300K VAL* 3.1 31.4 - - + +
301K PHE* 4.8 3.1 + - - +
338K ALA* 1.3 71.6 - - - +
340K ILE* 1.3 61.7 + - + +
342K THR* 2.7 19.3 + - - -
343K ASN* 3.0 42.2 + - - -
263O GLN* 5.2 4.2 + - - -
313O PRO* 5.1 10.8 - - + -
314O ALA* 4.1 6.7 - - + +
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Residues in contact with ILE 340 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274K SER* 4.4 17.5 - - - +
277K ALA* 3.6 15.3 - - + -
294K GLU* 4.6 2.5 + - - +
296K TYR* 3.5 56.1 - - + +
300K VAL* 3.7 15.0 - - + -
304K HIS* 4.8 7.0 - - + -
329K ILE* 4.4 20.0 - - + -
339K TYR* 1.3 77.1 - - + +
341K PRO* 1.3 74.1 - - + +
343K ASN* 3.2 20.6 + - + +
344K VAL* 3.2 14.6 + - + +
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Residues in contact with PRO 341 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168K LEU* 4.8 0.2 - - - +
170K ILE* 3.9 21.8 - - + -
329K ILE* 4.0 19.5 - - + -
330K GLU 5.4 1.1 - - - +
331K THR* 3.9 21.1 - - + -
335K ASP 4.4 0.2 - - - +
336K VAL 4.2 10.3 - - - +
338K ALA* 3.5 28.5 - - + -
339K TYR 3.7 0.9 - - - -
340K ILE* 1.3 94.8 - - + +
342K THR* 1.3 64.2 + - - +
344K VAL* 3.1 6.5 + - + +
345K ILE* 2.9 27.2 + - - +
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Residues in contact with THR 342 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336K VAL 3.1 20.0 - - - +
337K SER* 3.9 4.5 - - - -
338K ALA 2.6 26.7 + - - +
339K TYR* 2.7 17.2 + - - -
341K PRO* 1.3 77.0 - - - +
343K ASN* 1.3 66.2 + - - +
345K ILE* 3.1 8.7 + - - -
346K SER 3.0 19.2 + - - -
159O ALA* 3.3 12.7 - - + +
311O TYR* 3.5 13.4 + - - -
314O ALA* 3.7 25.2 + - - -
315O ASP* 3.9 10.5 - - - +
337O ARG* 4.4 6.5 - - - +
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Residues in contact with ASN 343 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300K VAL* 4.0 10.9 + - - +
301K PHE* 4.0 26.0 - - + +
304K HIS* 5.4 5.8 + - - +
339K TYR* 3.0 61.5 + - - +
340K ILE* 3.2 13.5 + - + +
342K THR* 1.3 83.5 + - - +
344K VAL* 1.3 63.7 + - + +
346K SER* 2.6 24.4 + - - -
347K ILE* 3.4 12.1 + - + +
263O GLN* 5.3 1.6 + - - -
311O TYR* 3.9 15.2 + - - -
313O PRO* 5.7 0.5 - - - +
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Residues in contact with VAL 344 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168K LEU* 3.7 22.0 - - + -
273K LEU* 4.6 2.9 - - + -
304K HIS* 4.3 24.7 - - + +
308K LEU* 4.0 9.4 - - + -
327K PRO* 4.5 4.9 - - + -
329K ILE* 3.7 32.1 - - + -
340K ILE* 3.2 14.8 + - + +
341K PRO 3.1 6.4 + - - +
343K ASN* 1.3 75.3 - - - +
345K ILE* 1.3 64.3 + - - +
347K ILE* 3.0 11.7 + - - +
348K THR* 3.0 35.7 + - + -
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Residues in contact with ILE 345 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168K LEU* 3.7 17.3 - - + -
170K ILE* 4.1 18.2 - - + -
336K VAL* 4.3 16.8 - - + +
341K PRO 2.9 26.2 + - - +
342K THR* 3.1 12.3 + - + +
344K VAL* 1.3 75.5 - - - +
346K SER* 1.3 57.2 + - - +
348K THR* 2.8 30.2 + - - +
351K GLN* 3.2 32.0 + - + +
159O ALA* 3.9 27.1 - - + +
160O GLY* 4.2 1.1 - - - +
190O ARG* 3.7 4.3 + - - -
337O ARG* 5.2 4.5 - - - +
611O PO4 5.0 0.3 + - - -
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Residues in contact with SER 346 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301K PHE* 3.4 19.9 - - - -
342K THR 3.0 7.8 + - - -
343K ASN* 2.6 20.8 + - - -
345K ILE* 1.3 77.9 - - - +
347K ILE* 1.3 57.3 + - - +
159O ALA* 3.8 7.8 - - - +
189O GLU* 5.2 2.8 - - - +
190O ARG* 2.8 33.2 + - - +
222O MET* 4.6 3.7 - - - +
260O ARG* 3.5 7.6 + - - -
311O TYR* 3.5 31.8 - - - -
611O PO4 4.7 5.0 + - - -
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Residues in contact with ILE 347 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166K ARG* 3.9 13.3 - - - +
301K PHE* 3.9 16.8 - - + +
304K HIS* 3.5 19.3 - - + +
305K SER* 3.3 33.4 - - - +
308K LEU* 3.7 29.6 - - + -
343K ASN 3.4 16.8 - - - +
344K VAL* 3.0 7.1 + - - +
346K SER* 1.3 79.8 - - - +
348K THR* 1.3 66.0 + - - +
349K ASP 3.5 0.9 + - - -
190O ARG* 3.0 20.6 + - - +
222O MET* 3.7 27.4 - - - -
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Residues in contact with THR 348 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166K ARG* 3.5 22.9 - - + +
168K LEU* 3.5 13.5 - - + +
308K LEU* 3.5 26.0 - - + -
327K PRO* 3.9 19.7 - - + -
344K VAL* 3.0 19.6 + - + +
345K ILE* 2.8 25.3 + - - +
347K ILE* 1.3 75.2 - - - +
349K ASP* 1.3 58.9 + - - +
350K GLY 3.1 20.9 + - - -
351K GLN* 4.1 1.0 + - - -
190O ARG* 3.6 5.8 + - - -
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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