Contacts of the helix formed by residues 514 - 531 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438H LEU* 5.2 4.5 - - - -
442H ILE* 4.3 18.4 - - - -
511H ALA* 3.8 18.1 + - - -
512H ALA 3.2 1.2 - - - -
513H GLU* 1.3 76.8 - - - +
515H TRP* 1.3 58.9 + - - +
516H LYS 3.3 1.6 - - - -
517H GLU* 3.3 9.4 + - - +
518H ILE* 2.9 33.6 + - - +
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Residues in contact with TRP 515 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494H LEU* 3.4 53.5 + - + +
495H ASN* 5.1 7.2 - - - -
497H TYR* 5.1 6.3 - - + +
498H THR 5.1 2.5 - - - -
499H THR* 4.5 20.0 - - - -
500H ALA* 4.1 28.3 - - + -
503H PHE* 4.3 24.6 - + + +
511H ALA 3.3 16.8 + - - +
512H ALA 3.6 9.4 - - - +
513H GLU 3.4 1.8 - - - -
514H SER* 1.3 78.9 - - - +
516H LYS* 1.3 69.8 + - + +
518H ILE* 3.2 8.5 + - + +
519H VAL* 2.9 61.6 + - + +
553H ARG* 5.3 7.4 - - - -
555H GLU* 4.5 23.1 - - + -
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Residues in contact with LYS 516 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500H ALA* 5.5 0.6 - - - +
512H ALA 4.9 0.4 + - - -
513H GLU 4.4 7.0 + - - +
514H SER 3.3 0.4 - - - -
515H TRP* 1.3 88.7 - - + +
517H GLU* 1.3 58.9 + - - +
519H VAL* 3.1 13.6 - - + +
520H ASN* 2.9 35.1 + - + +
555H GLU* 5.6 10.0 - - + +
556H ALA* 5.9 5.2 - - + +
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Residues in contact with GLU 517 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442H ILE* 4.7 12.8 - - + -
513H GLU 4.8 1.7 + - - +
514H SER* 3.3 15.5 + - - +
515H TRP 3.3 0.4 - - - -
516H LYS* 1.3 78.6 - - - +
518H ILE* 1.3 57.0 + - - +
520H ASN* 3.3 5.6 + - - +
521H LEU* 2.9 43.3 + - + +
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Residues in contact with ILE 518 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414H PHE* 4.6 22.2 - - + -
436H LEU* 5.4 0.7 - - + -
438H LEU* 4.4 20.2 - - + +
441H VAL* 4.8 5.4 - - + -
442H ILE* 3.6 30.1 - - + -
445H LEU* 5.3 3.1 - - + -
494H LEU* 3.6 24.7 - - + -
511H ALA* 4.6 9.4 - - + -
514H SER* 2.9 25.7 + - - +
515H TRP* 3.2 8.5 + - + +
517H GLU* 1.3 77.7 - - - +
519H VAL* 1.3 58.1 + - - +
521H LEU* 3.3 5.3 + - - +
522H LEU* 2.9 46.3 + - + +
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Residues in contact with VAL 519 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494H LEU* 3.7 21.1 - - + -
495H ASN* 6.3 0.7 - - - +
515H TRP* 2.9 53.6 + - + +
516H LYS* 3.1 22.0 - - + +
518H ILE* 1.3 75.8 - - - +
520H ASN* 1.3 57.7 + - - +
522H LEU* 3.4 7.3 + - - +
523H TYR* 2.9 47.9 + - + +
555H GLU* 6.0 0.4 - - + -
556H ALA* 4.3 19.7 - - + -
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Residues in contact with ASN 520 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516H LYS* 2.9 24.0 + - + +
517H GLU* 3.6 7.9 - - - +
519H VAL* 1.3 79.2 - - + +
521H LEU* 1.3 61.9 + - + +
523H TYR* 3.4 8.3 + - - +
524H GLU* 2.9 32.1 + - - +
556H ALA* 5.3 7.0 - - + +
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Residues in contact with LEU 521 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442H ILE* 5.0 7.0 - - + +
445H LEU* 3.6 28.7 - - + +
446H GLN* 3.8 39.5 - - + +
449H ILE* 3.7 27.7 - - + +
517H GLU* 2.9 32.8 + - + +
518H ILE* 3.7 2.2 - - - +
520H ASN* 1.3 82.4 - - + +
522H LEU* 1.3 58.0 + - - +
524H GLU* 3.7 3.8 - - + +
525H ILE* 2.9 32.7 + - - +
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Residues in contact with LEU 522 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411H TYR* 5.4 10.1 - - + +
414H PHE* 6.0 4.3 - - + -
441H VAL* 5.6 3.4 - - + -
445H LEU* 3.5 22.7 - - + -
487H VAL* 4.7 16.4 - - + +
490H CYS* 4.7 11.9 - - + -
491H ILE* 3.7 34.0 - - + +
494H LEU* 5.2 5.6 - - + -
518H ILE* 2.9 41.4 + - + +
519H VAL* 3.7 8.1 - - - +
521H LEU* 1.3 76.6 - - - +
523H TYR* 1.3 64.8 + - + +
525H ILE* 3.1 13.5 - - + +
526H LEU* 2.9 25.2 + - - +
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Residues in contact with TYR 523 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491H ILE* 4.4 29.6 + - + +
495H ASN* 3.3 28.2 + - - +
519H VAL* 2.9 32.5 + - + +
520H ASN* 3.8 5.2 - - - +
522H LEU* 1.3 76.8 - - + +
524H GLU* 1.3 58.6 + - - +
526H LEU* 3.4 9.4 + - + +
527H ALA* 2.9 29.6 + - - +
546H TRP* 5.9 3.6 - + - -
550H LYS* 5.0 6.2 + - + +
555H GLU 4.7 2.8 + - - -
556H ALA* 3.6 35.4 - - + -
559H GLY* 4.4 20.4 - - - -
560H ILE* 3.6 32.4 - - + +
563H VAL* 4.2 4.6 - - + +
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Residues in contact with GLU 524 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449H ILE* 3.8 16.3 - - + +
520H ASN* 2.9 24.4 + - - +
521H LEU* 3.7 7.0 - - + +
522H LEU 3.2 0.2 - - - -
523H TYR* 1.3 76.6 - - - +
525H ILE* 1.3 56.9 + - - +
527H ALA* 3.3 5.9 + - - +
528H SER* 2.9 30.2 + - - -
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Residues in contact with ILE 525 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411H TYR* 3.7 22.4 - - - +
445H LEU* 4.6 11.4 - - + -
448H LEU* 4.4 22.7 - - + -
449H ILE* 3.7 19.6 - - + +
478H PHE* 5.5 8.7 - - + -
483H MET* 6.5 0.2 - - + -
487H VAL* 6.3 5.2 - - + -
521H LEU 2.9 18.4 + - - +
522H LEU* 3.1 29.2 - - + +
524H GLU* 1.3 76.7 - - - +
526H LEU* 1.3 58.3 + - + +
528H SER* 2.8 17.9 + - - -
529H LEU* 2.9 37.0 + - + +
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Residues in contact with LEU 526 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487H VAL* 4.8 13.9 - - + -
488H LEU* 4.1 18.2 - - + -
491H ILE* 3.7 30.7 - - + -
522H LEU 2.9 18.3 + - - +
523H TYR* 3.8 8.7 - - + +
525H ILE* 1.3 80.4 - - + +
527H ALA* 1.3 56.5 + - - +
529H LEU* 3.4 3.3 + - - +
530H ILE* 2.9 48.5 + - + +
540H PHE* 5.4 8.7 - - + -
546H TRP* 5.4 2.9 - - + -
563H VAL* 3.6 37.2 - - + -
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Residues in contact with ALA 527 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523H TYR 2.9 18.3 + - - +
524H GLU* 3.7 5.8 - - - +
526H LEU* 1.3 78.2 - - - +
528H SER* 1.3 57.7 + - - +
530H ILE* 4.0 3.7 - - - +
531H ARG* 3.1 45.3 + - - +
559H GLY* 5.0 1.6 - - - +
562H GLU* 4.5 15.5 - - + +
563H VAL* 3.6 24.9 - - + +
566H CYS* 4.7 4.4 - - + -
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Residues in contact with SER 528 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449H ILE* 4.6 12.3 - - - +
452H PHE* 4.4 20.3 - - - +
454H PRO* 6.4 1.6 - - - -
475H GLN* 3.9 5.2 + - - -
524H GLU 2.9 14.2 + - - -
525H ILE* 2.8 22.7 + - - +
527H ALA* 1.3 77.1 - - - +
529H LEU* 1.3 66.7 + - - +
531H ARG* 3.4 32.0 + - - +
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Residues in contact with LEU 529 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448H LEU 5.6 0.4 - - - +
449H ILE* 6.1 0.4 - - - -
452H PHE* 4.3 35.9 - - + -
475H GLN* 4.1 17.1 + - + +
478H PHE* 3.5 48.2 - - + -
484H LEU* 6.3 2.7 - - + -
525H ILE* 2.9 39.3 + - + +
526H LEU* 4.2 3.6 - - - +
528H SER* 1.3 85.8 - - - +
530H ILE* 1.3 65.2 + - + +
531H ARG 4.0 4.4 - - - +
533H ASN* 4.4 0.2 - - - +
536H ASN* 3.2 24.5 + - - +
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Residues in contact with ILE 530 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484H LEU* 4.7 11.2 - - + -
526H LEU* 2.9 37.7 + - + +
527H ALA* 4.1 4.9 - - - +
529H LEU* 1.3 77.6 - - + +
531H ARG* 1.3 65.0 + - - +
532H GLY 3.4 1.9 + - - -
533H ASN* 3.5 18.7 + - - +
536H ASN* 3.7 33.9 - - + +
537H CYS* 4.6 16.7 - - + -
539H LEU* 6.1 0.2 - - + -
540H PHE* 5.1 15.7 - - + -
563H VAL* 5.4 6.5 - - + +
566H CYS* 4.9 15.0 - - + +
567H VAL* 5.0 12.8 - - + -
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Residues in contact with ARG 531 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454H PRO* 4.9 20.8 - - - +
471H LEU* 5.5 0.7 - - - +
475H GLN* 2.7 31.9 + - - -
527H ALA* 3.1 33.4 + - - +
528H SER* 3.4 20.3 - - - +
529H LEU 3.3 0.8 - - - -
530H ILE* 1.3 77.6 - - - +
532H GLY* 1.3 55.6 + - - +
533H ASN 3.3 0.9 + - - -
562H GLU* 2.5 42.4 + - - +
566H CYS* 3.5 30.1 - - - +
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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