Contacts of the helix formed by residues 510 - 528 (chain D) in PDB entry 6FQS
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 ASP 510 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C ASP* 4.6 2.9 - - - -
435D GLU* 4.7 1.4 - - - +
508D ASP* 2.8 36.0 + - - +
509D ALA* 1.3 77.5 - - - +
511D VAL* 1.3 64.8 + - + +
512D ASP* 3.6 10.1 + - - +
513D GLY* 2.8 32.1 + - - -
514D ALA* 2.9 27.4 + - - +
582D GLY* 5.2 2.8 - - - -
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Residues in contact with VAL 511 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C ASP* 3.5 36.5 + - - +
25C TYR* 3.2 18.4 - - + +
28C SER* 3.4 40.6 - - - +
29C VAL* 6.2 0.2 - - + -
33C ARG* 4.5 7.6 - - - +
81C HIS* 6.1 1.3 - - + -
510D ASP* 1.3 75.6 - - + +
512D ASP* 1.3 71.6 + - - +
514D ALA* 3.4 4.9 - - - +
515D HIS 3.2 18.2 + - - -
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Residues in contact with ASP 512 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C TYR* 3.4 15.6 - - - -
33C ARG* 2.6 42.6 + - - -
81C HIS* 4.1 12.5 + - - -
435D GLU* 4.7 7.4 - - - +
460D LYS* 3.9 17.3 + - - -
510D ASP* 3.1 9.0 + - - +
511D VAL* 1.3 80.8 - - - +
513D GLY* 1.3 61.8 + - - +
515D HIS* 3.1 4.8 + - - +
516D ILE* 3.1 30.9 + - + +
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Residues in contact with GLY 513 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435D GLU* 3.6 19.2 + - - -
507D THR* 3.1 19.8 + - - -
508D ASP 3.5 13.9 - - - -
510D ASP* 2.8 19.3 + - - -
512D ASP* 1.3 75.2 - - - +
514D ALA* 1.3 64.0 + - - +
516D ILE* 3.6 0.8 + - - -
517D ARG* 3.2 18.0 + - - +
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Residues in contact with ALA 514 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C SER* 3.7 20.2 - - - +
24C ASP* 3.7 21.5 - - - +
510D ASP 2.9 8.8 + - - +
511D VAL 3.4 10.8 - - - +
513D GLY* 1.3 77.5 - - - +
515D HIS* 1.3 62.0 + - - +
517D ARG* 3.4 29.0 + - - +
518D THR* 3.1 26.7 + - - +
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Residues in contact with HIS 515 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C PHE* 5.3 9.3 - + - -
25C TYR* 3.3 58.2 - + + +
460D LYS* 3.2 28.8 + - + +
511D VAL 3.2 4.6 + - - -
512D ASP 3.1 10.7 + - - +
514D ALA* 1.3 74.3 - - - +
516D ILE* 1.3 66.2 + - - +
518D THR* 2.4 34.5 + - - -
519D LEU* 3.1 30.2 + - + +
622D MET* 5.5 1.6 - - + +
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Residues in contact with ILE 516 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435D GLU* 3.1 43.3 - - + +
457D LEU* 5.2 8.1 - - + -
459D GLY 5.3 9.0 - - - +
460D LYS* 3.8 29.8 - - + +
461D ILE* 5.2 5.8 - - + -
507D THR* 4.0 17.3 - - + -
512D ASP* 3.1 15.1 + - + +
513D GLY 4.0 3.8 - - - +
515D HIS* 1.3 74.0 - - - +
517D ARG* 1.3 57.7 + - - +
519D LEU* 3.1 12.4 + - - +
520D LEU* 2.9 42.2 + - + +
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Residues in contact with ARG 517 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C GLU* 3.1 23.7 + - + -
21C SER* 3.0 22.3 + - - +
505D ILE* 4.1 29.1 + - + -
507D THR* 3.2 25.4 + - - +
508D ASP 4.8 3.8 + - - -
509D ALA* 5.9 1.4 - - - +
510D ASP 5.6 0.2 + - - -
513D GLY 3.2 13.5 + - - +
514D ALA* 3.4 26.1 - - - +
515D HIS 3.1 0.2 - - - -
516D ILE* 1.3 79.7 - - - +
518D THR* 1.3 63.3 + - - +
520D LEU* 3.1 1.8 + - - +
521D LEU* 2.9 37.5 + - + +
539D ILE* 3.7 28.3 - - + +
540D ALA 5.9 0.2 + - - -
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Residues in contact with THR 518 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C MET* 3.9 24.2 - - - +
21C SER* 3.6 23.6 - - - -
22C PHE* 3.8 21.8 - - + +
514D ALA 3.1 13.9 + - - +
515D HIS* 2.4 35.8 + - - -
517D ARG* 1.3 75.8 - - - +
519D LEU* 1.3 56.9 + - - +
521D LEU* 3.5 4.0 + - + +
522D THR* 2.8 33.5 + - - -
622D MET* 4.1 14.5 - - - +
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Residues in contact with LEU 519 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460D LYS* 4.7 7.4 - - + -
461D ILE* 2.9 49.6 - - + +
462D LEU 4.5 2.9 - - - +
463D ASN* 3.7 26.0 - - + +
464D VAL* 5.4 0.7 + - - +
515D HIS* 3.1 39.9 + - + +
516D ILE* 3.4 11.7 - - - +
518D THR* 1.3 82.4 + - - +
520D LEU* 1.3 61.9 + - - +
522D THR* 3.2 4.2 + - - -
523D PHE* 3.0 19.1 + - - +
622D MET* 3.3 25.8 - - + -
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Residues in contact with LEU 520 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433D LEU* 3.9 13.9 - - + -
457D LEU* 3.5 33.9 - - + -
461D ILE* 3.2 23.3 - - + -
481D MET* 3.7 21.5 - - + -
505D ILE* 3.9 26.5 - - + -
507D THR* 5.3 1.3 - - + -
516D ILE* 2.9 29.6 + - + +
517D ARG 3.7 3.6 - - - +
519D LEU* 1.3 75.3 - - - +
521D LEU* 1.3 64.1 + - - +
523D PHE* 3.0 5.9 + - + +
524D PHE* 3.0 39.5 + - + -
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Residues in contact with LEU 521 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C ILE* 4.8 10.6 - - + +
17C GLU* 3.8 32.5 - - + -
18C MET* 4.2 21.8 - - + -
505D ILE* 3.8 24.0 - - + -
517D ARG* 2.9 26.6 + - + +
518D THR* 3.8 5.4 - - + +
520D LEU* 1.3 76.4 - - - +
522D THR* 1.3 56.3 + - - +
524D PHE* 3.3 8.2 + - + +
525D TYR* 2.9 31.5 + - - +
532D ILE* 5.1 3.1 - - + +
537D VAL* 4.5 6.1 - - + -
539D ILE* 5.0 3.1 - - + -
606D VAL* 4.5 26.7 - - + -
618D PHE* 3.9 6.3 - - + -
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Residues in contact with THR 522 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C MET* 3.9 0.2 - - - +
463D ASN* 4.1 5.6 - - - +
464D VAL* 3.7 16.3 - - + +
465D GLU* 3.9 32.5 - - + +
518D THR 2.8 20.3 + - - -
519D LEU* 3.2 9.2 + - - -
521D LEU* 1.3 76.2 - - - +
523D PHE* 1.3 62.8 + - - +
525D TYR 3.4 0.5 + - - -
526D ARG* 3.2 26.3 + - + +
618D PHE* 3.6 19.0 - - + -
622D MET* 3.2 24.9 - - + +
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Residues in contact with PHE 523 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461D ILE* 5.0 4.9 - - + -
464D VAL* 3.6 31.4 - - + +
472D ILE* 5.1 1.3 - - + -
478D ILE* 3.8 29.8 - - + -
481D MET* 4.0 26.5 - - + -
482D ILE* 4.2 6.3 - - + -
489D ILE* 4.6 3.1 - - + -
519D LEU 3.0 12.9 + - - +
520D LEU* 3.0 8.7 + - + +
522D THR* 1.3 77.8 - - - +
524D PHE* 1.3 88.1 + + - +
526D ARG 3.3 1.2 + - - -
527D PHE* 3.0 45.2 + + + +
528D MET* 3.5 39.5 - - + -
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Residues in contact with PHE 524 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433D LEU* 3.9 15.0 - - + -
481D MET* 4.3 3.8 - - - -
485D PHE* 3.3 41.7 - + - -
503D ILE* 4.6 8.7 - - + -
505D ILE* 3.9 28.0 - - + -
520D LEU* 3.0 24.4 + - + -
521D LEU* 3.8 13.0 - - + +
523D PHE* 1.3 97.8 - + - +
525D TYR* 1.3 57.8 + - - +
528D MET* 2.9 48.0 + - + +
529D ARG 2.9 0.7 + - - -
531D LEU* 6.2 1.3 - - + -
532D ILE* 3.6 18.8 - - + -
537D VAL* 4.7 14.6 - - + -
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Residues in contact with TYR 525 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C ILE* 4.0 10.1 - - + -
521D LEU 2.9 17.6 + - - +
522D THR 4.0 3.1 - - - +
523D PHE 3.3 0.2 - - - -
524D PHE* 1.3 76.0 - - - +
526D ARG* 1.3 91.9 + - - +
529D ARG* 3.6 39.2 + - + +
532D ILE* 3.7 12.5 - - + +
608D LEU* 4.2 21.1 - - + -
611D ALA* 3.2 7.8 + - - -
614D ALA* 3.6 21.4 - - + +
615D ASP* 2.4 37.0 + - - -
618D PHE* 3.2 36.1 - + + -
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Residues in contact with ARG 526 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464D VAL* 4.4 4.5 - - + -
465D GLU* 2.8 40.7 + - - +
490D GLY* 5.6 1.0 - - - -
522D THR* 3.2 25.8 + - + +
524D PHE 3.2 0.6 - - - -
525D TYR* 1.3 116.6 - - + +
527D PHE* 1.3 82.9 + - + +
528D MET 3.8 0.4 - - - -
529D ARG* 5.0 5.5 - - - +
615D ASP* 3.5 20.8 + - - +
618D PHE* 4.1 9.5 - - + +
619D GLU* 4.1 10.7 + - - +
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Residues in contact with PHE 527 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464D VAL* 3.9 25.6 - - + -
469D LEU* 4.2 20.0 - - + -
472D ILE* 4.0 24.7 - - + -
473D LEU* 6.3 0.7 - - + -
489D ILE* 3.9 20.6 - - + -
490D GLY* 2.9 38.3 + - - +
493D PHE* 4.8 1.4 - - - +
523D PHE* 3.0 40.0 + + + +
526D ARG* 1.3 95.6 - - + +
528D MET* 1.3 67.3 + - + +
529D ARG 3.8 1.1 - - - -
530D PRO* 5.4 1.0 - - - +
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Residues in contact with MET 528 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482D ILE* 3.8 17.7 - - + -
485D PHE* 3.3 38.4 - - + -
487D THR* 4.7 3.6 - - - +
488D GLY 4.4 6.5 - - - +
489D ILE* 3.4 25.8 - - + -
493D PHE* 3.9 24.7 - - + -
523D PHE* 3.5 23.8 - - + -
524D PHE* 2.9 22.0 + - + +
527D PHE* 1.3 85.4 - - + +
529D ARG* 1.3 66.2 + - - +
530D PRO* 3.2 8.5 - - - -
531D LEU* 3.2 21.7 + - + +
532D ILE* 3.9 5.9 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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