Contacts of the helix formed by residues 391 - 402 (chain S) 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 SER 391 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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390S GLY* 1.3 76.5 - - - +
392S LEU* 1.3 67.2 + - - +
393S LYS 3.1 3.8 + - - -
394S LEU* 3.3 13.2 + - - +
395S PHE* 3.0 29.6 + - - +
451S VAL* 3.7 19.6 - - - +
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Residues in contact with LEU 392 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157S ALA* 4.2 19.1 - - + +
158S LEU* 3.6 25.6 - - + -
389S ALA* 3.8 22.4 + - + +
390S GLY 3.8 0.6 - - - -
391S SER* 1.3 79.0 + - - +
393S LYS* 1.3 63.8 + - - +
395S PHE* 3.9 4.1 - - + +
396S LEU* 3.3 38.0 + - + +
426S LEU* 4.3 25.6 - - + -
430S LEU* 4.4 20.6 - - + -
447S ILE* 4.7 8.7 - - + -
451S VAL* 4.2 21.8 - - + +
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Residues in contact with LYS 393 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157S ALA 5.6 1.8 - - - +
158S LEU* 3.6 39.1 - - + +
159S VAL* 5.1 2.7 - - - -
369S VAL* 3.3 49.7 + - + +
370S GLY* 4.9 3.0 + - - -
372S SER 3.8 12.6 - - - -
373S VAL* 4.0 17.7 - - - +
389S ALA 4.9 3.3 + - - +
391S SER 3.1 1.0 + - - -
392S LEU* 1.3 82.1 - - - +
394S LEU* 1.3 75.4 + - + +
395S PHE 3.3 0.2 + - - -
396S LEU 3.6 5.5 + - - -
397S ALA* 3.7 3.6 + - - +
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Residues in contact with LEU 394 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390S GLY 4.4 6.7 - - - +
391S SER* 3.3 19.9 + - - +
393S LYS* 1.3 87.9 - - + +
395S PHE* 1.3 62.8 + - - +
397S ALA* 3.4 9.6 + - - +
398S GLN* 3.3 28.4 + - - +
341W GLU* 6.1 1.3 - - - +
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Residues in contact with PHE 395 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391S SER* 3.0 24.1 + - - +
392S LEU* 3.9 5.6 - - + +
394S LEU* 1.3 76.2 - - - +
396S LEU* 1.3 66.7 + - + +
398S GLN* 3.0 23.2 + - - +
399S TYR* 2.9 28.4 + - + +
419S THR* 3.5 46.2 - - + -
422S ARG* 3.8 18.6 - - + -
423S GLY* 3.5 28.3 - - - -
426S LEU* 3.8 20.2 - - + -
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Residues in contact with LEU 396 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158S LEU* 3.7 11.2 - - + -
369S VAL* 3.6 41.0 - - + +
392S LEU* 3.3 22.0 + - + +
394S LEU 3.4 0.2 - - - -
395S PHE* 1.3 85.8 - - + +
397S ALA* 1.3 56.6 + - - +
399S TYR* 3.5 17.5 - - + +
400S ARG* 2.9 27.7 + - - +
423S GLY* 5.0 1.8 - - - +
426S LEU* 4.8 16.8 - - + -
427S THR* 4.3 20.4 - - + +
430S LEU* 3.7 28.0 - - + -
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Residues in contact with ALA 397 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369S VAL* 4.2 9.1 - - + +
370S GLY* 5.1 11.9 - - - +
393S LYS* 3.7 11.6 + - - +
394S LEU* 3.4 12.9 + - - +
395S PHE 3.1 0.6 - - - -
396S LEU* 1.3 77.2 - - - +
398S GLN* 1.3 63.8 + - + +
399S TYR 3.1 0.4 + - - -
400S ARG* 3.4 7.3 + - - +
401S GLU* 3.4 22.0 + - - +
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Residues in contact with GLN 398 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394S LEU* 3.3 18.1 + - - +
395S PHE* 3.0 29.7 + - + +
397S ALA* 1.3 77.6 - - + +
399S TYR* 1.3 57.8 + - - +
401S GLU* 3.8 8.9 + - - +
402S VAL* 3.1 31.6 + - + +
419S THR* 5.1 10.9 - - + +
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Residues in contact with TYR 399 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395S PHE* 2.9 15.7 + - + +
396S LEU* 3.5 20.2 - - + +
397S ALA 3.1 0.2 - - - -
398S GLN* 1.3 78.6 - - - +
400S ARG* 1.3 62.8 + - - +
401S GLU 3.2 0.2 - - - -
402S VAL* 3.3 4.3 + - + +
403S ALA* 2.8 43.7 + - + +
419S THR* 4.6 13.4 - - + +
420S LEU* 4.4 15.0 - - + -
423S GLY* 3.9 17.5 - - - -
424S GLU* 3.5 39.0 + - + +
427S THR* 3.9 18.8 + - + -
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Residues in contact with ARG 400 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355S GLU* 3.2 25.1 + - - -
358S LEU* 3.5 22.5 - - - +
367S ILE 3.7 2.4 + - - -
368S ASN* 3.1 32.6 + - - +
369S VAL* 3.5 22.4 - - - +
370S GLY* 4.3 11.6 - - - +
396S LEU 2.9 15.7 + - - +
397S ALA* 3.4 8.2 + - - +
399S TYR* 1.3 80.9 - - + +
401S GLU* 1.3 61.6 + - - +
403S ALA* 3.6 17.0 + - + +
404S ALA* 4.5 3.3 + - - +
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Residues in contact with GLU 401 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397S ALA 3.4 14.0 + - - +
398S GLN* 4.1 8.6 - - - +
399S TYR 3.2 0.6 - - - -
400S ARG* 1.3 79.3 - - - +
402S VAL* 1.3 65.5 + - + +
403S ALA 3.3 1.2 + - - -
404S ALA* 4.4 8.8 + - - +
405S PHE* 5.2 0.7 - - - +
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Residues in contact with VAL 402 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398S GLN* 3.1 20.6 + - + +
399S TYR* 3.3 7.4 + - - +
401S GLU* 1.3 86.6 - - + +
403S ALA* 1.3 62.4 + - - +
404S ALA 3.3 2.2 - - - -
405S PHE* 3.6 35.4 + - + +
406S ALA 4.5 2.4 + - - -
412S LEU* 6.4 0.9 - - + -
416S THR* 5.1 24.0 - - + +
419S THR* 5.7 8.7 - - + -
420S LEU* 4.8 15.5 - - + +
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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