Contacts of the helix formed by residues 508 - 526 (chain D) in PDB entry 4KPE
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 508 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76B HIS* 5.8 5.3 - - + -
433D GLU* 4.1 3.9 - - - +
506D ASP* 3.2 29.5 - - - +
507D ALA* 1.3 83.8 - - - +
509D THR* 1.3 63.4 + - - +
510D ASP* 3.7 13.9 + - - +
511D GLY* 3.0 25.8 + - - -
512D ALA* 3.0 23.2 + - - +
581D LYS 4.5 11.7 - - - +
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Residues in contact with THR 509 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ARG* 3.8 18.2 - - + +
20B TYR* 3.7 15.8 - - - +
23B TYR* 3.0 58.1 - - + -
28B ARG* 4.3 0.2 + - - -
508D ASP* 1.3 72.2 - - - +
510D ASP* 1.3 65.8 + - - +
511D GLY 3.0 1.8 - - - -
512D ALA* 3.0 11.6 + - - +
513D HIS* 2.8 25.3 + - - +
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Residues in contact with ASP 510 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B TYR* 3.7 4.3 - - - -
28B ARG* 2.9 45.5 + - - -
76B HIS* 4.3 9.4 + - - -
433D GLU* 4.4 7.6 - - - +
458D LYS* 3.4 21.1 + - - +
508D ASP* 3.4 12.5 + - - +
509D THR* 1.3 78.9 + - - +
511D GLY* 1.3 55.6 + - - +
513D HIS* 3.5 8.5 - - - +
514D ILE* 3.1 36.4 + - + +
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Residues in contact with GLY 511 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433D GLU* 3.7 21.5 + - - -
505D THR* 3.7 6.3 - - - +
506D ASP 3.7 9.9 - - - -
508D ASP* 3.0 17.2 + - - -
509D THR 3.0 0.6 - - - -
510D ASP* 1.3 73.4 - - - +
512D ALA* 1.3 64.1 + - - +
513D HIS 3.0 1.6 + - - -
514D ILE 3.2 1.2 + - - -
515D GLN* 3.1 32.3 + - - +
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Residues in contact with ALA 512 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ARG* 3.6 44.5 - - + +
19B ARG* 4.6 8.5 - - + -
20B TYR 4.9 0.7 - - - +
506D ASP 4.7 0.2 + - - -
508D ASP 3.0 11.2 + - - +
509D THR* 3.0 14.8 + - - +
511D GLY* 1.3 74.6 - - - +
513D HIS* 1.3 59.5 + - - +
515D GLN* 4.0 11.1 - - - +
516D THR* 3.3 20.8 + - - -
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Residues in contact with HIS 513 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B PHE* 4.8 8.0 - + - -
20B TYR* 3.2 59.5 - + + +
458D LYS* 2.7 30.4 + - + +
509D THR 2.8 5.8 + - - +
510D ASP 3.5 9.0 - - - +
511D GLY 3.0 0.6 - - - -
512D ALA* 1.3 74.9 - - - +
514D ILE* 1.3 67.8 + - - +
516D THR* 2.9 37.1 - - + +
517D LEU* 3.0 35.8 + - + +
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Residues in contact with ILE 514 (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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433D GLU* 4.3 25.4 - - + +
455D LEU* 5.1 5.8 - - + -
457D GLY 4.4 13.5 - - - +
458D LYS* 4.1 27.6 - - + +
459D VAL* 4.7 15.4 - - + +
505D THR* 3.6 22.7 - - + -
510D ASP* 3.1 29.2 + - + +
511D GLY* 3.2 5.8 + - - +
513D HIS* 1.3 77.0 - - - +
515D GLN* 1.3 58.0 + - - +
517D LEU* 3.1 8.8 + - + +
518D LEU* 2.9 47.4 + - + +
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Residues in contact with GLN 515 (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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16B ARG* 3.1 37.2 + - + +
503D ILE* 4.0 14.1 - - + -
505D THR* 2.7 35.5 + - + -
506D ASP 4.5 1.6 + - - -
511D GLY 3.1 16.5 + - - +
512D ALA* 3.8 9.8 - - - +
513D HIS 3.1 0.6 - - - -
514D ILE* 1.3 76.5 - - - +
516D THR* 1.3 64.4 + - - +
518D LEU* 3.3 5.1 + - - +
519D LEU* 2.9 36.3 + - + +
537D ILE* 3.7 35.4 - - + +
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Residues in contact with THR 516 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B MET* 3.4 23.3 + - + +
16B ARG* 4.2 4.7 - - - +
17B PHE* 3.7 39.5 + - + +
512D ALA 3.3 9.1 + - - -
513D HIS* 2.9 28.2 + - + +
515D GLN* 1.3 78.8 - - - +
517D LEU* 1.3 65.8 + - + +
519D LEU* 5.5 0.2 - - - -
520D THR* 2.7 40.4 + - + +
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Residues in contact with LEU 517 (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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458D LYS* 5.0 4.0 - - + -
459D VAL* 3.4 44.1 - - + +
460D ILE 4.7 4.4 - - - +
461D ASN* 4.3 31.1 - - + +
462D THR* 4.5 2.1 + - - -
513D HIS* 3.0 56.0 + - + +
514D ILE* 3.1 10.7 + - + +
516D THR* 1.3 86.5 - - + +
518D LEU* 1.3 65.7 + - - +
520D THR* 3.4 9.5 + - - -
521D PHE* 3.2 19.9 + - - +
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Residues in contact with LEU 518 (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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431D LEU* 4.2 9.0 - - + +
455D LEU* 3.3 36.6 - - + -
459D VAL* 3.9 17.0 - - + -
476D ILE* 6.1 0.4 - - + -
479D MET* 4.4 19.3 - - + -
503D ILE* 3.6 44.2 - - + -
514D ILE* 2.9 25.8 + - + +
515D GLN 3.8 2.9 - - - +
517D LEU* 1.3 75.9 - - - +
519D LEU* 1.3 64.0 + - - +
521D PHE* 2.9 18.9 + - + +
522D PHE* 3.1 22.3 + - + -
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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
----------------------------------------------------------
9B LEU* 4.0 22.4 - - + +
12B ILE* 3.9 27.4 - - + -
13B MET* 3.8 16.6 - - - -
16B ARG* 6.5 0.2 - - + -
503D ILE* 4.2 13.5 - - + -
515D GLN* 2.9 23.2 + - + +
518D LEU* 1.3 75.2 - - - +
520D THR* 1.3 58.3 + - - +
521D PHE 3.0 0.5 + - - -
522D PHE* 3.2 6.2 + - + +
523D TYR* 2.8 32.0 + - - +
530D VAL* 6.3 2.7 - - + -
535D VAL* 4.1 25.8 - - + +
537D ILE* 4.0 18.8 - - + -
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Residues in contact with THR 520 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B MET* 3.1 26.0 - - + -
461D ASN* 4.3 12.0 + - - -
462D THR* 3.6 11.5 + - - -
463D ALA* 4.5 9.6 + - + +
516D THR* 2.7 30.2 + - + +
517D LEU* 3.5 9.1 + - - -
518D LEU 3.3 0.6 - - - -
519D LEU* 1.3 74.8 - - - +
521D PHE* 1.3 57.2 + - - +
523D TYR* 4.2 7.4 - - - -
524D ARG* 3.0 39.0 + - - +
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Residues in contact with PHE 521 (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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459D VAL* 5.9 2.5 - - + -
460D ILE 5.9 0.4 - - - +
462D THR* 3.4 31.4 - - + +
470D ILE* 5.2 2.2 - - + -
476D ILE* 3.8 45.8 - - + -
479D MET* 4.7 14.4 - - + -
480D ILE* 5.4 7.2 - - + -
487D VAL* 5.6 4.9 - - + -
517D LEU 3.2 10.0 + - - +
518D LEU* 2.9 15.0 + - + +
520D THR* 1.3 76.3 + - - +
522D PHE* 1.3 84.0 + + - +
524D ARG 3.1 1.2 + - - -
525D TYR* 2.6 60.9 + + + +
526D MET* 4.0 15.5 - - - -
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Residues in contact with PHE 522 (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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431D LEU* 3.9 16.2 - - + -
479D MET* 3.3 29.6 - - + -
483D ILE* 4.3 6.3 - - + -
501D ILE* 4.4 10.3 - - + -
503D ILE* 4.5 8.7 - - + -
518D LEU* 3.1 24.6 + - + -
519D LEU* 3.9 7.2 - - + +
521D PHE* 1.3 101.3 - + - +
523D TYR* 1.3 58.4 + - - +
526D MET* 2.7 71.2 + - + +
527D ARG* 4.8 0.2 - - - -
529D LEU* 4.8 4.0 - - + -
530D VAL* 5.0 5.8 - - + -
535D VAL* 4.0 36.8 - - + -
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Residues in contact with TYR 523 (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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9B LEU* 4.3 30.3 - - + -
519D LEU 2.8 17.6 + - - +
520D THR* 4.0 7.2 - - - +
522D PHE* 1.3 80.9 - - - +
524D ARG* 1.3 86.5 + - + +
525D TYR 3.4 0.2 + - - -
527D ARG* 3.5 26.8 - - + +
530D VAL* 5.2 10.2 - - + +
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Residues in contact with ARG 524 (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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462D THR* 3.1 20.7 + - - +
463D ALA* 3.5 33.5 + - + +
488D GLY* 5.3 2.3 - - - -
520D THR* 3.0 26.4 + - - +
521D PHE 3.1 2.0 + - - -
523D TYR* 1.3 103.4 - - + +
525D TYR* 1.3 87.0 + - + +
526D MET 3.8 0.2 - - - -
527D ARG* 5.8 0.2 - - - -
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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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462D THR* 4.1 15.8 + - + -
467D MET* 4.0 24.2 - - + +
470D ILE* 3.8 24.4 - - + +
487D VAL* 3.9 11.2 - - + -
488D GLY* 3.0 43.4 + - - +
491D PHE* 4.5 0.5 - - - -
521D PHE* 2.6 47.8 + + + +
524D ARG* 1.3 109.9 + - + +
526D MET* 1.3 69.6 + - - +
527D ARG 4.0 0.7 - - - -
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Residues in contact with MET 526 (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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479D MET 5.7 0.4 - - - +
480D ILE* 5.6 7.6 - - - -
483D ILE* 3.5 28.3 - - + -
486D GLY 4.6 6.3 - - - +
487D VAL* 5.1 1.8 - - - -
491D PHE* 3.4 36.8 - - + -
521D PHE* 4.0 15.5 - - - -
522D PHE* 2.7 43.7 + - + +
525D TYR* 1.3 84.4 - - + +
527D ARG* 1.3 66.7 + - - +
528D PRO* 3.1 9.0 - - - -
529D LEU* 2.8 46.3 + - + +
530D VAL 3.5 2.8 + - - -
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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