Contacts of the helix formed by residues 414 - 431 (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 ALA 414 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413S ASP* 1.3 85.3 - - + +
415S SER* 1.3 66.7 + - - +
416S THR 3.4 0.9 - - - -
417S LYS* 3.7 10.5 + - - +
418S GLN* 3.7 14.6 + - - +
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Residues in contact with SER 415 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413S ASP* 3.6 6.7 + - - -
414S ALA* 1.3 79.6 - - - +
416S THR* 1.3 59.1 + - - +
417S LYS 3.8 0.3 + - - -
418S GLN* 4.9 1.4 - - - +
419S THR* 2.7 27.9 + - - -
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Residues in contact with THR 416 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402S VAL* 5.1 22.6 - - + +
405S PHE* 5.3 7.5 - - - -
412S LEU* 3.4 16.5 - - - +
413S ASP* 2.9 29.3 + - - +
415S SER* 1.3 80.9 - - - +
417S LYS* 1.3 65.0 + - - +
418S GLN 3.5 0.7 - - - -
419S THR* 3.8 11.6 - - + +
420S LEU* 3.6 13.3 + - - +
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Residues in contact with LYS 417 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412S LEU* 3.6 35.0 - - + +
413S ASP 3.1 33.2 - - - +
414S ALA* 3.8 7.2 - - - +
415S SER 3.4 0.6 - - - -
416S THR* 1.3 82.6 + - - +
418S GLN* 1.3 62.3 + - - +
420S LEU* 3.6 4.9 + - - +
421S VAL* 3.1 27.1 + - + +
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Residues in contact with GLN 418 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414S ALA 3.7 12.0 + - - +
415S SER 4.9 1.3 - - - +
417S LYS* 1.3 78.2 - - + +
419S THR* 1.3 66.3 + - - +
420S LEU 3.2 0.4 - - - -
421S VAL* 2.8 36.6 + - - +
422S ARG* 3.0 24.0 + - + +
456S ASP* 4.0 18.0 + - - +
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Residues in contact with THR 419 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395S PHE* 3.5 32.8 - - + -
398S GLN* 5.1 19.7 - - + +
399S TYR* 4.6 6.5 - - + -
402S VAL* 5.7 8.5 - - + -
415S SER 2.7 24.9 + - - -
416S THR* 3.8 12.5 - - + +
417S LYS 3.4 0.4 - - - -
418S GLN* 1.3 80.3 - - - +
420S LEU* 1.3 61.9 + - - +
421S VAL 3.3 0.3 + - - -
422S ARG* 5.1 0.4 - - - -
423S GLY* 3.5 18.9 + - - -
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Residues in contact with LEU 420 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399S TYR* 4.4 12.9 - - + -
402S VAL* 4.8 18.8 - - + +
403S ALA* 6.1 0.7 - - - +
405S PHE* 5.9 0.9 - - + -
406S ALA* 3.7 31.2 - - + +
412S LEU* 4.0 30.7 - - + -
416S THR 3.6 14.7 + - - +
417S LYS 3.9 4.5 - - - +
418S GLN 3.2 0.8 - - - -
419S THR* 1.3 78.9 - - - +
421S VAL* 1.3 65.4 + - + +
424S GLU* 3.2 38.0 + - - +
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Residues in contact with VAL 421 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412S LEU* 5.7 1.8 - - + -
417S LYS* 3.1 25.6 - - + +
418S GLN* 2.8 29.7 + - - +
420S LEU* 1.3 84.8 - - + +
422S ARG* 1.3 67.8 + - - +
424S GLU* 3.7 6.3 + - - +
425S ARG* 3.1 43.9 + - - +
456S ASP* 4.2 14.4 - - + +
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Residues in contact with ARG 422 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395S PHE* 3.8 26.6 - - + -
418S GLN* 3.0 22.2 + - + +
419S THR* 5.6 0.2 - - - -
420S LEU 3.6 0.2 - - - -
421S VAL* 1.3 76.4 - - - +
423S GLY* 1.3 64.6 + - - +
425S ARG* 3.1 18.8 + - - +
426S LEU* 3.2 20.8 + - + +
450S GLY 3.6 12.8 - - - -
451S VAL* 3.3 19.9 + - - +
452S ASN 3.1 24.2 + - - -
453S GLY* 3.6 4.0 - - - -
456S ASP* 3.0 41.8 + - - +
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Residues in contact with GLY 423 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395S PHE* 3.5 19.6 - - - -
396S LEU* 5.2 2.0 - - - -
399S TYR* 3.7 20.0 - - - -
419S THR 3.5 7.3 + - - -
422S ARG* 1.3 79.5 - - - +
424S GLU* 1.3 62.8 + - - +
426S LEU* 3.0 17.6 + - - +
427S THR* 3.1 19.8 + - - -
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Residues in contact with GLU 424 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399S TYR* 3.5 24.1 + - + +
420S LEU* 3.2 39.4 + - - +
421S VAL* 3.9 6.7 - - - +
422S ARG 3.1 1.0 + - - -
423S GLY* 1.3 75.7 - - - +
425S ARG* 1.3 61.2 + - + +
427S THR* 4.4 3.6 + - - -
428S GLN* 4.2 10.9 + - - +
460S LEU* 3.2 39.7 - - + +
399V GLN* 5.2 8.1 - - - +
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Residues in contact with ARG 425 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421S VAL* 3.1 36.1 + - - +
422S ARG* 3.2 16.2 - - - +
424S GLU* 1.3 78.2 + - - +
426S LEU* 1.3 64.4 + - + +
427S THR 3.3 1.8 - - - -
428S GLN* 3.7 9.3 + - + +
429S LEU* 3.2 22.2 + - - +
455S LEU* 3.1 30.1 - - + +
456S ASP* 2.9 22.9 + - - +
458S ILE 2.8 30.2 + - - +
459S GLU* 4.4 1.2 - - - +
460S LEU* 3.3 33.5 - - + +
463S ILE* 4.3 21.1 - - + +
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Residues in contact with LEU 426 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392S LEU* 4.3 23.1 - - + -
395S PHE* 3.8 34.5 - - + -
396S LEU* 4.8 8.5 - - + -
422S ARG* 3.2 22.9 + - + +
423S GLY* 3.0 8.0 + - - +
425S ARG* 1.3 77.6 - - + +
427S THR* 1.3 64.2 + - - +
429S LEU* 3.4 13.6 + - + +
430S LEU* 3.2 28.6 + - - +
447S ILE* 5.1 1.8 - - - +
450S GLY* 3.6 39.7 - - - +
451S VAL* 3.9 7.9 - - + +
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Residues in contact with THR 427 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363S ILE* 3.8 36.0 - - + +
396S LEU* 4.3 11.0 - - + +
399S TYR* 3.9 20.6 - - + -
423S GLY 3.1 15.6 + - - -
424S GLU 4.4 4.7 - - - -
426S LEU* 1.3 76.0 - - - +
428S GLN* 1.3 65.1 + - - +
430S LEU* 2.9 21.7 + - + +
431S LYS* 3.1 14.8 + - - +
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Residues in contact with GLN 428 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424S GLU 4.2 4.8 + - - +
425S ARG* 3.7 15.8 + - - +
427S THR* 1.3 79.2 - - - +
429S LEU* 1.3 62.3 + - - +
431S LYS* 2.9 60.1 + - - +
460S LEU* 4.2 16.5 + - + +
461S SER 5.8 0.6 + - - -
463S ILE* 3.9 25.1 - - + +
464S GLY* 4.6 16.3 - - - +
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Residues in contact with LEU 429 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153S LYS* 3.1 30.8 + - + +
425S ARG 3.2 13.8 + - - +
426S LEU* 3.5 17.5 - - + +
427S THR 3.1 0.4 - - - -
428S GLN* 1.3 81.4 - - - +
430S LEU* 1.3 61.4 + - + +
431S LYS 3.4 1.0 + - - +
446S LEU* 3.8 43.5 - - + +
447S ILE* 4.6 10.3 - - + +
450S GLY* 4.5 12.8 - - - -
455S LEU* 3.8 29.6 - - + -
463S ILE* 4.4 10.1 - - + +
467S GLU* 4.6 3.3 - - + +
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Residues in contact with LEU 430 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153S LYS* 4.0 16.4 - - + +
154S ALA* 3.8 45.5 + - + +
158S LEU* 3.9 14.4 - - + -
363S ILE* 6.2 3.1 - - + -
364S ARG 3.9 3.3 - - - +
365S PRO* 4.3 1.7 - - - +
392S LEU* 4.4 21.3 - - + -
396S LEU* 3.7 31.2 - - + -
426S LEU 3.2 14.0 + - - +
427S THR* 2.9 12.2 + - + +
429S LEU* 1.3 80.0 - - + +
431S LYS* 1.3 67.6 + - - +
432S GLN* 3.5 7.3 + - - +
447S ILE* 5.2 6.5 - - + -
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Residues in contact with LYS 431 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153S LYS* 3.1 20.6 + - - -
361S LYS 4.7 3.6 + - - -
362S GLY* 3.3 41.1 + - - +
363S ILE* 3.8 17.8 - - + +
364S ARG* 3.2 15.5 - - + +
427S THR* 3.1 12.4 + - - +
428S GLN* 2.9 54.4 + - - +
429S LEU 3.2 2.5 - - - +
430S LEU* 1.3 77.4 - - - +
432S GLN* 1.3 58.4 + - - +
467S GLU* 4.4 2.3 - - - +
376V GLU* 4.8 7.7 + - - -
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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
------------------------------------------------------------
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