Contacts of the helix formed by residues 391 - 406 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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390L GLY* 1.3 70.4 - - - -
392L LEU* 1.3 58.6 + - - +
393L LYS* 3.1 3.6 - - - +
394L LEU* 2.9 19.4 + - - +
395L PHE* 2.8 28.1 + - - +
425M THR 3.2 19.9 + - - -
426M GLY 4.3 3.1 + - - -
427M ILE* 3.4 23.3 - - - +
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Residues in contact with LEU 392 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157L ALA* 5.1 2.9 - - + -
158L LEU* 3.7 24.0 - - + -
389L ALA* 5.0 7.4 - - + -
390L GLY* 3.2 11.6 + - - +
391L SER* 1.3 77.6 - - - +
393L LYS* 1.3 56.2 + - - +
395L PHE* 4.1 9.2 - - + -
396L LEU* 2.9 52.3 + - + +
426L LEU* 3.6 38.1 - - + -
430L LEU* 5.3 6.7 - - + -
447L ILE* 4.6 23.1 - - + -
451L VAL* 4.7 20.2 - - + +
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Residues in contact with LYS 393 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157L ALA 5.8 0.2 - - - +
158L LEU* 3.4 38.0 + - + +
159L VAL* 4.7 0.4 - - + -
369L VAL* 3.5 31.3 - - + +
372L SER 3.6 20.0 - - - -
373L VAL* 3.2 38.1 - - - +
374L SER* 3.3 13.9 + - - +
390L GLY 5.1 0.6 + - - +
391L SER* 3.1 2.3 - - - -
392L LEU* 1.3 78.6 - - - +
394L LEU* 1.3 68.7 + - + +
397L ALA* 3.5 11.6 + - - +
345M TYR* 5.1 3.9 + - - -
424M PHE* 4.7 24.1 + - - +
425M THR* 6.1 0.7 - - - +
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Residues in contact with LEU 394 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391L SER* 2.9 16.3 + - - +
393L LYS* 1.3 85.2 - - + +
395L PHE* 1.3 60.4 + - - +
396L LEU 3.3 0.4 - - - -
397L ALA* 3.6 4.9 - - + +
398L GLN* 3.1 35.3 + - - +
343M GLY* 3.9 14.6 - - - +
345M TYR* 4.2 18.4 - - + -
424M PHE 5.7 0.7 - - - +
425M THR* 3.5 41.5 - - + +
427M ILE* 4.2 16.4 - - + -
458M TYR* 3.8 27.0 + - + +
459M MET* 4.4 8.5 - - + -
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Residues in contact with PHE 395 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391L SER* 2.8 15.6 + - - +
392L LEU* 3.2 12.3 + - + +
394L LEU* 1.3 78.0 - - - +
396L LEU* 1.3 61.9 + - + +
398L GLN* 3.3 10.1 + - + +
399L TYR* 2.8 27.8 + - + +
419L THR* 4.0 40.6 - - + -
422L ARG* 3.9 20.0 - - - -
423L GLY* 3.8 25.1 - - - -
426L LEU* 4.1 21.5 - - + -
455M HIS* 4.9 17.0 - + + -
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Residues in contact with LEU 396 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158L LEU* 3.5 31.2 - - + -
369L VAL* 4.3 20.6 - - + +
392L LEU* 2.9 38.3 + - + +
395L PHE* 1.3 80.0 - - + +
397L ALA* 1.3 64.8 + - - +
399L TYR* 3.8 11.9 - - + +
400L ARG* 3.3 21.7 + - - +
423L GLY* 4.3 4.7 - - - +
426L LEU* 4.2 21.5 - - + -
427L THR* 4.2 20.9 - - - +
430L LEU* 4.0 13.7 - - + -
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Residues in contact with ALA 397 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369L VAL* 4.6 7.6 - - + +
370L GLY* 5.0 8.7 - - - -
393L LYS 3.5 17.8 + - - +
394L LEU* 3.6 9.0 - - + +
395L PHE 3.3 0.4 - - - -
396L LEU* 1.3 79.6 - - - +
398L GLN* 1.3 59.8 - - - +
400L ARG* 3.9 5.3 + - - +
401L GLU* 3.8 15.1 + - - +
340M SER 5.5 0.2 - - - +
341M GLU 4.0 18.5 - - - +
342M LEU 4.5 4.0 - - - +
343M GLY* 4.1 22.2 - - - -
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Residues in contact with GLN 398 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394L LEU* 3.1 20.1 + - - +
395L PHE* 3.7 8.5 - - + +
397L ALA* 1.3 75.2 - - - +
399L TYR* 1.3 66.3 + - - +
400L ARG 3.1 2.6 + - - -
401L GLU* 3.1 5.2 + - - +
402L VAL* 2.9 31.2 + - + +
342M LEU 4.7 4.0 - - - +
412M ARG* 3.0 31.0 + - - +
455M HIS* 3.6 31.7 + - - +
458M TYR* 3.0 55.9 - - + +
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Residues in contact with TYR 399 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395L PHE* 2.8 22.4 + - + +
396L LEU* 3.8 15.3 - - + +
397L ALA 3.5 0.2 - - - -
398L GLN* 1.3 76.7 - - - +
400L ARG* 1.3 68.4 + - + +
402L VAL* 3.5 8.2 + - + +
403L ALA* 3.1 32.7 + - + +
419L THR* 4.1 12.6 - - - +
420L LEU* 3.9 19.7 - - + -
423L GLY* 3.5 24.7 - - - -
424L GLU* 3.1 41.2 - - + +
427L THR* 3.5 22.9 + - + -
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Residues in contact with ARG 400 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368L ASN* 4.6 16.3 + - - +
370L GLY* 6.1 3.1 - - - -
396L LEU 3.3 14.0 + - - +
397L ALA* 4.0 7.0 - - - +
398L GLN 3.1 0.2 - - - -
399L TYR* 1.3 86.0 - - + +
401L GLU* 1.3 67.0 + - - +
403L ALA* 3.1 7.9 + - - +
404L ALA* 3.0 34.1 + - + +
341M GLU* 3.8 29.3 + - - +
342M LEU* 5.4 9.8 - - - +
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Residues in contact with GLU 401 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397L ALA 3.8 7.2 + - - +
398L GLN* 3.1 7.4 + - - +
400L ARG* 1.3 86.0 - - - +
402L VAL* 1.3 62.8 + - - +
404L ALA* 3.3 6.4 + - - +
405L PHE* 3.0 23.0 + - + +
341M GLU 6.0 0.2 - - - +
342M LEU* 3.8 45.3 - - + +
344M ILE* 4.9 0.5 - - - +
381M TYR* 4.8 2.4 + - - -
408M ARG* 3.8 22.2 + - - +
411M GLN* 5.1 5.4 - - - +
412M ARG* 2.8 38.2 + - - +
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Residues in contact with VAL 402 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398L GLN* 2.9 26.4 + - + +
399L TYR* 3.7 8.1 - - + +
401L GLU* 1.3 76.1 - - - +
403L ALA* 1.3 64.3 + - - +
405L PHE* 3.3 16.0 + - - +
406L ALA* 3.5 12.1 + - - +
412L LEU* 5.5 3.8 - - + -
416L THR* 4.3 29.8 - - + +
419L THR* 4.3 14.4 - - - +
420L LEU* 4.9 13.0 - - + -
408M ARG* 5.1 5.8 - - - +
412M ARG* 4.7 10.8 - - - +
454M GLU* 5.1 9.9 - - - +
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Residues in contact with ALA 403 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399L TYR* 3.1 31.7 + - + +
400L ARG* 3.5 6.1 - - - +
402L VAL* 1.3 81.6 - - - +
404L ALA* 1.3 61.5 + - - +
405L PHE 3.4 0.2 + - - -
406L ALA* 3.5 18.5 + - - +
407L GLN* 5.1 1.9 - - - +
420L LEU* 4.8 14.6 - - + -
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Residues in contact with ALA 404 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400L ARG* 3.0 25.8 + - - +
401L GLU* 3.8 6.7 - - - +
403L ALA* 1.3 75.7 - - - +
405L PHE* 1.3 64.7 + - - +
407L GLN* 3.1 27.3 - - - +
389M ALA* 5.7 2.9 - - - +
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Residues in contact with PHE 405 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401L GLU* 3.0 17.1 + - + +
402L VAL* 3.3 6.9 + - - +
404L ALA* 1.3 78.3 - - - +
406L ALA* 1.3 58.5 + - + +
407L GLN* 2.8 11.3 + - - +
408L PHE* 3.5 16.2 - + - -
412L LEU* 5.9 3.4 - - + -
381M TYR* 4.7 7.4 - + - -
388M ILE* 4.2 22.1 - - + +
389M ALA* 5.7 2.4 - - - +
393M MET* 3.7 44.4 - - + -
404M VAL* 4.9 4.7 - - + -
408M ARG* 3.1 56.1 - - - +
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Residues in contact with ALA 406 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402L VAL 3.5 6.3 + - - +
403L ALA* 3.5 15.7 + - - +
404L ALA 3.3 0.6 - - - -
405L PHE* 1.3 76.1 - - + +
407L GLN* 1.3 64.3 + - - +
408L PHE* 3.4 23.3 - - + -
409L GLY* 4.7 4.6 + - - +
412L LEU* 4.0 28.9 - - + -
420L LEU* 5.4 2.7 - - + -
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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
------------------------------------------------------------
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