Contacts of the helix formed by residues 433 - 446 (chain X) 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 ARG 433 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28K ASN* 5.6 6.7 - - - +
48K ASN* 5.2 9.4 - - - -
12O LYS* 4.5 17.2 - - - +
135X GLU* 3.3 35.3 + - - +
137X GLY* 5.3 0.2 - - - -
142X ASP* 5.0 1.1 - - - -
431X LEU* 4.8 12.0 - - + +
432X VAL* 1.3 77.7 - - - +
434X LEU* 1.3 57.0 + - - +
435X LYS* 3.6 5.2 - - + +
436X ASP* 3.4 11.8 + - + +
437X THR* 2.7 34.1 + - - -
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Residues in contact with LEU 434 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133X ILE* 4.1 25.8 - - + -
135X GLU* 3.4 25.9 + - + +
142X ASP* 4.3 31.9 + - + +
146X PRO* 5.5 1.1 - - + -
363X VAL* 5.4 3.8 - - + -
367X HIS* 3.7 21.1 - - + +
433X ARG* 1.3 69.9 - - - +
435X LYS* 1.3 75.6 + - + +
436X ASP 3.0 2.1 + - - -
437X THR* 3.1 6.3 + - - -
438X VAL* 3.0 48.0 + - + +
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Residues in contact with LYS 435 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25K ALA* 3.3 19.7 - - + +
135X GLU* 4.9 1.9 + - - +
433X ARG* 3.6 3.5 - - + +
434X LEU* 1.3 87.7 - - + +
436X ASP* 1.3 59.6 + - - +
438X VAL* 4.4 3.3 - - - +
439X ALA* 3.3 22.3 + - - +
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Residues in contact with ASP 436 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25K ALA* 3.5 15.2 - - - +
26K ASN* 3.3 16.2 - - - +
28K ASN* 3.0 27.2 + - - +
432X VAL* 3.6 17.7 - - + +
433X ARG* 3.4 20.0 + - + +
434X LEU 3.0 0.6 - - - -
435X LYS* 1.3 78.8 - - - +
437X THR* 1.3 53.0 + - - +
439X ALA* 3.2 1.7 + - - +
440X SER* 2.8 45.3 + - - -
462X GLY* 3.8 12.8 + - - -
463X ILE* 4.5 1.0 + - - +
464X GLU* 5.7 0.5 - - - +
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Residues in contact with THR 437 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139X LYS* 3.6 42.7 - - + +
142X ASP* 5.1 5.7 + - + +
143X LEU* 4.1 11.9 - - + +
432X VAL* 3.1 19.4 + - - +
433X ARG 2.7 23.0 + - - -
434X LEU* 3.1 6.8 + - - -
436X ASP* 1.3 76.9 - - - +
438X VAL* 1.3 62.9 + - - +
440X SER* 3.3 5.0 + - - -
441X PHE* 3.0 45.7 + - + -
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Residues in contact with VAL 438 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142X ASP 6.0 0.2 - - - -
143X LEU* 4.6 11.9 - - + -
366X GLU* 5.0 11.4 - - + +
367X HIS* 3.3 60.1 - - + +
370X VAL* 4.5 13.8 - - + +
434X LEU* 3.0 24.3 + - + +
435X LYS* 4.4 4.7 - - - +
437X THR* 1.3 78.5 - - - +
439X ALA* 1.3 62.5 + - - +
441X PHE* 3.7 1.6 + - - +
442X LYS* 3.2 22.5 + - + +
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Residues in contact with ALA 439 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23K ASP* 4.8 8.5 - - + -
25K ALA* 4.4 7.6 - - + -
26K ASN* 3.3 27.8 + - - +
435X LYS 3.3 19.3 + - - +
436X ASP 3.2 1.7 + - - +
437X THR 3.2 0.4 - - - -
438X VAL* 1.3 78.5 - - - +
440X SER* 1.3 64.0 + - - +
441X PHE 3.3 0.5 + - - -
442X LYS* 3.4 14.5 + - - +
443X ALA* 3.4 13.7 + - - +
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Residues in contact with SER 440 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139X LYS* 6.2 0.4 - - - -
413X PHE* 3.7 17.0 - - - -
436X ASP* 2.8 36.5 + - - -
437X THR* 3.3 6.9 + - - -
439X ALA* 1.3 75.2 - - - +
441X PHE* 1.3 60.0 + - - +
443X ALA* 3.7 4.9 + - - +
444X VAL* 3.3 24.9 + - - +
462X GLY* 3.8 2.6 - - - -
463X ILE* 2.9 48.1 + - - +
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Residues in contact with PHE 441 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139X LYS* 4.0 9.2 - - + -
143X LEU* 3.6 27.8 - - + -
370X VAL* 4.3 9.9 - - + -
374X VAL* 4.4 12.1 - - + -
410X ILE* 4.3 18.4 - - + -
413X PHE* 3.2 53.8 - + + -
414X LEU* 3.9 23.1 - - + -
437X THR* 3.0 45.2 + - + +
438X VAL 4.3 2.5 - - - +
440X SER* 1.3 74.0 - - - +
442X LYS* 1.3 66.0 + - - +
443X ALA 3.1 2.2 - - - -
444X VAL* 3.3 8.9 + - + +
445X LEU* 3.1 28.4 + - + +
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Residues in contact with LYS 442 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366X GLU* 2.8 41.1 + - + +
370X VAL* 3.9 20.3 - - + +
373X LYS* 6.2 1.8 - - - +
438X VAL* 3.2 19.5 + - + +
439X ALA* 3.4 7.8 + - - +
441X PHE* 1.3 77.0 - - - +
443X ALA* 1.3 57.1 + - - +
445X LEU* 3.5 6.0 + - + +
446X GLU* 3.0 56.2 + - + +
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Residues in contact with ALA 443 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22K SER* 6.2 4.0 - - - -
26K ASN* 5.8 2.9 - - - +
439X ALA 3.4 9.3 + - - +
440X SER* 3.7 11.7 - - - +
441X PHE 3.1 0.4 - - - -
442X LYS* 1.3 78.4 - - - +
444X VAL* 1.3 65.7 + - - +
446X GLU* 3.1 19.8 + - - +
447X GLY 3.3 8.3 + - - -
448X LYS* 3.4 19.4 + - + +
449X TYR* 3.7 25.1 - - + -
463X ILE* 5.0 2.7 - - + -
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Residues in contact with VAL 444 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406X ARG* 3.4 23.0 + - + +
409X LYS* 5.0 5.8 - - + -
410X ILE* 4.2 26.5 - - + -
413X PHE* 4.5 11.4 - - + -
440X SER 3.3 18.6 - - - +
441X PHE* 3.3 10.5 + - + +
443X ALA* 1.3 75.4 - - - +
445X LEU* 1.3 59.9 + - + +
447X GLY* 3.3 10.4 + - - -
448X LYS 4.9 1.8 - - - +
449X TYR* 4.8 10.8 - - + +
450X ASP* 4.1 4.1 - - - +
457X PHE* 4.0 35.0 - - + -
463X ILE* 4.6 7.6 - - + -
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Residues in contact with LEU 445 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370X VAL* 3.8 25.6 - - + +
373X LYS* 4.2 29.4 - - + +
374X VAL* 3.6 24.2 - - + -
377X THR* 4.2 14.8 - - - +
406X ARG* 3.3 22.8 + - - +
410X ILE* 3.9 25.6 - - + -
441X PHE 3.1 19.5 + - - +
442X LYS* 3.8 7.0 - - + +
444X VAL* 1.3 73.2 - - - +
446X GLU* 1.3 58.9 + - + +
447X GLY 2.9 9.5 + - - -
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Residues in contact with GLU 446 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373X LYS* 6.1 2.9 - - - +
406X ARG* 5.0 0.4 - - - -
442X LYS* 3.0 50.0 + - + +
443X ALA* 3.1 9.0 + - - +
445X LEU* 1.3 75.3 - - + +
447X GLY* 1.3 65.1 + - - +
448X LYS* 3.6 29.6 + - + +
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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