Contacts of the helix formed by residues 514 - 531 (chain D) in PDB entry 6X34
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 514 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438D LEU* 5.2 4.3 - - - -
442D ILE* 4.3 19.1 - - - -
510D GLU 5.7 0.2 - - - -
511D ALA* 3.8 19.4 + - - -
512D ALA 3.2 0.8 - - - -
513D GLU* 1.3 77.0 - - - +
515D TRP* 1.3 58.6 + - - +
516D LYS 3.3 1.8 - - - -
517D GLU* 3.3 9.9 + - - +
518D ILE* 2.9 33.5 + - - +
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Residues in contact with TRP 515 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494D LEU* 3.4 54.4 + - + +
495D ASN* 5.1 7.9 - - - -
497D TYR* 5.1 6.3 - - + +
498D THR 5.1 2.5 - - - -
499D THR* 4.5 20.2 - - - -
500D ALA* 4.1 27.4 - - + -
503D PHE* 4.3 24.4 - + + +
511D ALA 3.3 16.9 + - - +
512D ALA 3.6 9.0 - - - +
513D GLU 3.4 1.6 - - - -
514D SER* 1.3 77.8 - - - +
516D LYS* 1.3 72.0 + - + +
518D ILE* 3.2 8.5 + - + +
519D VAL* 2.9 60.1 + - + +
553D ARG* 5.3 6.7 - - - -
555D GLU* 4.5 23.1 - - + -
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Residues in contact with LYS 516 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500D ALA* 5.5 0.4 - - - +
512D ALA 4.9 0.2 + - - -
513D GLU 4.4 7.2 + - - +
514D SER 3.3 0.4 - - - -
515D TRP* 1.3 89.4 - - + +
517D GLU* 1.3 58.1 + - - +
519D VAL* 3.1 13.0 - - + +
520D ASN* 2.9 36.5 + - + +
555D GLU* 5.6 9.8 - - + +
556D ALA* 5.9 5.4 - - + +
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Residues in contact with GLU 517 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442D ILE* 4.7 12.8 - - + -
513D GLU 4.8 2.1 + - - +
514D SER* 3.3 15.9 + - - +
515D TRP 3.3 0.4 - - - -
516D LYS* 1.3 79.5 - - - +
518D ILE* 1.3 58.2 + - - +
520D ASN* 3.3 4.8 + - - +
521D LEU* 2.9 42.9 + - + +
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Residues in contact with ILE 518 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414D PHE* 4.6 22.0 - - + -
436D LEU* 5.4 0.4 - - + -
438D LEU* 4.4 20.2 - - + +
441D VAL* 4.8 4.9 - - + -
442D ILE* 3.6 29.2 - - + -
445D LEU* 5.3 2.5 - - + -
494D LEU* 3.6 25.1 - - + -
511D ALA* 4.6 8.7 - - + -
514D SER* 2.9 25.4 + - - +
515D TRP* 3.2 8.5 + - + +
517D GLU* 1.3 76.4 - - - +
519D VAL* 1.3 57.1 + - - +
521D LEU* 3.3 5.4 + - - +
522D LEU* 2.9 46.4 + - + +
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Residues in contact with VAL 519 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494D LEU* 3.7 21.1 - - + -
495D ASN* 6.3 0.9 - - - +
515D TRP* 2.9 52.7 + - + +
516D LYS* 3.1 22.7 - - + +
518D ILE* 1.3 76.2 - - - +
520D ASN* 1.3 56.6 + - - +
522D LEU* 3.4 6.4 + - - +
523D TYR* 2.9 48.7 + - + +
555D GLU* 6.0 0.4 - - + -
556D ALA* 4.3 20.0 - - + -
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Residues in contact with ASN 520 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516D LYS* 2.9 22.6 + - + +
517D GLU* 3.6 7.4 - - - +
519D VAL* 1.3 77.2 - - + +
521D LEU* 1.3 63.1 + - + +
523D TYR* 3.4 8.1 + - - +
524D GLU* 2.9 32.2 + - - +
556D ALA* 5.3 8.1 - - + +
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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
----------------------------------------------------------
442D ILE* 5.0 7.6 - - + +
445D LEU* 3.6 28.0 - - + +
446D GLN* 3.8 39.0 - - + +
449D ILE* 3.7 26.8 - - + +
517D GLU* 2.9 32.9 + - + +
518D ILE* 3.7 2.7 - - - +
520D ASN* 1.3 82.8 - - + +
522D LEU* 1.3 58.1 + - - +
524D GLU* 3.3 4.0 + - + +
525D ILE* 2.9 33.3 + - - +
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Residues in contact with LEU 522 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411D TYR* 5.4 10.3 - - + +
414D PHE* 6.0 3.6 - - + -
441D VAL* 5.6 2.5 - - + -
445D LEU* 3.5 22.4 - - + -
487D VAL* 4.7 17.0 - - + +
490D CYS* 4.7 12.3 - - + -
491D ILE* 3.7 33.6 - - + +
494D LEU* 5.2 6.3 - - + -
518D ILE* 2.9 42.4 + - + +
519D VAL* 3.7 7.9 - - - +
521D LEU* 1.3 76.6 - - - +
523D TYR* 1.3 64.1 + - + +
525D ILE* 3.1 14.1 - - + +
526D LEU* 2.9 25.3 + - - +
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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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491D ILE* 4.4 28.8 + - + -
495D ASN* 3.3 29.3 + - - +
519D VAL* 2.9 34.4 + - + +
520D ASN* 3.8 5.2 - - - +
522D LEU* 1.3 77.1 - - + +
524D GLU* 1.3 57.9 + - - +
526D LEU* 3.8 8.8 - - + +
527D ALA* 2.9 30.9 + - - +
546D TRP* 5.9 3.6 - + - -
550D LYS* 5.0 6.0 + - + +
553D ARG* 5.5 0.2 - - - -
555D GLU 4.7 2.5 + - - -
556D ALA* 3.6 36.1 - - + -
559D GLY* 4.4 20.0 - - - -
560D ILE* 3.6 33.6 - - + +
563D VAL* 4.3 4.7 - - + +
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Residues in contact with GLU 524 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449D ILE* 3.8 17.0 - - + -
520D ASN* 2.9 23.7 + - - +
521D LEU* 3.7 6.5 - - + +
522D LEU 3.2 0.2 - - - -
523D TYR* 1.3 77.2 - - - +
525D ILE* 1.3 57.3 + - - +
527D ALA* 3.3 6.0 + - - +
528D SER* 2.9 30.2 + - - -
559D GLY* 6.4 0.2 - - - -
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Residues in contact with ILE 525 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411D TYR* 3.7 23.6 - - + +
445D LEU* 4.6 11.7 - - + -
448D LEU* 4.4 22.2 - - + -
449D ILE* 3.7 19.0 - - + +
452D PHE* 6.4 0.2 - - + -
478D PHE* 5.5 9.0 - - + -
487D VAL* 6.3 5.4 - - + -
521D LEU 2.9 18.2 + - - +
522D LEU* 3.1 29.2 - - + +
524D GLU* 1.3 76.3 - - - +
526D LEU* 1.3 57.5 + - + +
528D SER* 2.8 17.9 + - - -
529D LEU* 2.9 36.3 + - + +
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Residues in contact with LEU 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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487D VAL* 4.8 13.0 - - + -
488D LEU* 4.1 17.7 - - + -
491D ILE* 3.7 31.9 - - + -
522D LEU 2.9 17.9 + - - +
523D TYR* 3.8 8.1 - - + +
525D ILE* 1.3 80.1 - - + +
527D ALA* 1.3 56.3 + - - +
529D LEU* 3.8 3.0 - - - +
530D ILE* 2.9 47.9 + - + +
540D PHE* 5.4 9.2 - - + -
546D TRP* 5.4 3.1 - - + -
563D VAL* 3.6 37.7 - - + -
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Residues in contact with ALA 527 (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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523D TYR 2.9 18.0 + - - +
524D GLU* 3.3 6.5 + - - +
526D LEU* 1.3 76.9 - - - +
528D SER* 1.3 57.4 + - - +
530D ILE* 4.0 4.4 - - - +
531D ARG* 3.1 46.2 + - - +
559D GLY* 5.0 1.8 - - - +
562D GLU* 4.5 14.6 - - + +
563D VAL* 3.6 24.7 - - + +
566D CYS* 4.7 3.2 - - + -
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Residues in contact with SER 528 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449D ILE* 4.6 12.4 - - - +
452D PHE* 4.4 20.2 - - - +
454D PRO* 6.4 1.3 - - - -
475D GLN* 3.9 5.2 + - - -
524D GLU 2.9 14.9 + - - -
525D ILE* 2.8 22.9 + - - +
527D ALA* 1.3 78.1 - - - +
529D LEU* 1.3 67.4 + - - +
531D ARG* 3.4 33.2 + - - +
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Residues in contact with LEU 529 (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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448D LEU 5.6 0.4 - - - +
449D ILE* 6.1 0.7 - - - -
452D PHE* 4.3 35.7 - - + -
475D GLN* 4.1 16.8 + - + +
478D PHE* 3.5 47.8 - - + -
484D LEU* 6.3 2.7 - - + -
525D ILE* 2.9 39.4 + - + +
526D LEU* 4.2 3.4 - - - +
528D SER* 1.3 84.5 - - - +
530D ILE* 1.3 66.6 + - + +
531D ARG 4.0 3.6 - - - +
533D ASN* 4.4 0.2 - - - +
536D ASN* 3.2 23.9 + - - +
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Residues in contact with ILE 530 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484D LEU* 4.7 11.4 - - + -
526D LEU* 2.9 37.9 + - + +
527D ALA* 4.1 5.4 - - - +
529D LEU* 1.3 77.9 - - + +
531D ARG* 1.3 65.3 + - - +
532D GLY 3.4 2.1 + - - -
533D ASN* 3.5 19.2 + - - +
536D ASN* 3.7 34.9 - - + +
537D CYS* 4.6 17.1 - - + -
540D PHE* 5.1 15.7 - - + -
563D VAL* 5.4 6.7 - - + +
566D CYS* 4.9 14.9 - - + +
567D VAL* 5.0 12.8 - - + -
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Residues in contact with ARG 531 (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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454D PRO* 4.9 20.3 - - - +
471D LEU* 5.5 0.5 - - - +
475D GLN* 2.7 31.5 + - - -
527D ALA* 3.1 31.8 + - - +
528D SER* 3.4 22.1 - - - +
529D LEU 3.3 0.4 - - - -
530D ILE* 1.3 77.7 - - - +
532D GLY* 1.3 55.7 + - - +
533D ASN 3.3 0.9 + - - -
562D GLU* 2.5 42.4 + - - +
566D CYS* 3.5 30.3 - - - +
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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