Contacts of the helix formed by residues 514 - 531 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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438F LEU* 5.2 4.3 - - - -
442F ILE* 4.3 18.4 - - - -
510F GLU 5.7 0.2 - - - -
511F ALA* 3.8 18.7 + - - +
512F ALA 3.2 1.2 - - - -
513F GLU* 1.3 76.6 - - - +
515F TRP* 1.3 59.0 + - - +
516F LYS 3.3 1.3 - - - -
517F GLU* 3.3 9.5 + - - +
518F ILE* 2.9 33.5 + - - +
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Residues in contact with TRP 515 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494F LEU* 3.4 53.4 + - + +
495F ASN* 5.1 7.2 - - - -
497F TYR* 5.1 6.5 - - + +
498F THR 5.1 2.5 - - - -
499F THR* 4.5 20.4 - - - -
500F ALA* 4.1 27.8 - - + -
503F PHE* 4.3 23.8 - + + +
511F ALA* 3.3 16.2 + - - +
512F ALA 3.6 9.2 - - - +
513F GLU 3.4 1.4 - - - -
514F SER* 1.3 79.1 - - - +
516F LYS* 1.3 69.5 + - + +
518F ILE* 3.2 8.3 + - + +
519F VAL* 2.9 60.8 + - + +
553F ARG* 5.3 7.9 - - - -
555F GLU* 4.5 22.4 - - + -
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Residues in contact with LYS 516 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500F ALA* 5.5 0.8 - - - +
512F ALA 4.9 0.4 + - - -
513F GLU 4.4 6.3 + - - +
514F SER 3.3 0.2 - - - -
515F TRP* 1.3 90.8 - - + +
517F GLU* 1.3 58.0 + - - +
519F VAL* 3.1 14.7 - - + +
520F ASN* 2.9 34.7 + - + +
555F GLU* 5.6 10.0 - - + +
556F ALA* 5.9 4.7 - - + +
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Residues in contact with GLU 517 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442F ILE* 4.7 13.2 - - + -
513F GLU 4.8 1.9 + - - +
514F SER* 3.3 15.9 + - - +
515F TRP 3.3 0.4 - - - -
516F LYS* 1.3 78.2 - - - +
518F ILE* 1.3 58.3 + - - +
520F ASN* 3.3 5.4 + - - +
521F LEU* 2.9 42.8 + - + +
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Residues in contact with ILE 518 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414F PHE* 4.6 21.3 - - + -
436F LEU* 5.4 0.9 - - + -
438F LEU* 4.4 19.7 - - + +
441F VAL* 4.8 5.8 - - + -
442F ILE* 3.6 29.4 - - + -
445F LEU* 5.3 2.2 - - + -
494F LEU* 3.6 23.8 - - + -
511F ALA* 4.6 9.2 - - + -
514F SER* 2.9 25.0 + - - +
515F TRP* 3.2 8.0 + - + +
517F GLU* 1.3 77.0 - - - +
519F VAL* 1.3 57.3 + - - +
521F LEU* 3.3 6.1 + - - +
522F LEU* 2.9 47.0 + - + +
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Residues in contact with VAL 519 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494F LEU* 3.7 22.0 - - + -
495F ASN* 6.3 0.9 - - - +
515F TRP* 2.9 53.1 + - + +
516F LYS* 3.1 22.4 - - + +
518F ILE* 1.3 77.0 - - - +
520F ASN* 1.3 57.4 + - - +
522F LEU* 3.4 6.6 + - - +
523F TYR* 2.9 47.7 + - + +
555F GLU* 6.1 0.7 - - + -
556F ALA* 4.3 19.3 - - + -
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Residues in contact with ASN 520 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516F LYS* 2.9 23.6 + - + +
517F GLU* 3.6 7.2 - - - +
519F VAL* 1.3 79.6 - - + +
521F LEU* 1.3 61.9 + - + +
523F TYR* 3.4 7.2 + - - +
524F GLU* 2.9 32.1 + - - +
556F ALA* 5.3 7.7 - - + +
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Residues in contact with LEU 521 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442F ILE* 5.0 7.4 - - + +
445F LEU* 3.6 29.7 - - + +
446F GLN* 3.8 39.9 - - + +
449F ILE* 3.7 27.1 - - + +
517F GLU* 2.9 33.3 + - + +
518F ILE* 3.3 2.4 + - - +
520F ASN* 1.3 83.1 - - + +
522F LEU* 1.3 58.1 + - - +
524F GLU* 3.7 3.8 - - + +
525F ILE* 2.9 33.4 + - - +
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Residues in contact with LEU 522 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411F TYR* 5.4 9.9 - - + +
414F PHE* 6.0 4.0 - - + -
441F VAL* 5.6 3.1 - - + -
445F LEU* 3.5 22.7 - - + -
487F VAL* 4.7 17.0 - - + +
490F CYS* 4.7 11.2 - - + -
491F ILE* 3.7 32.8 - - + +
494F LEU* 5.2 5.8 - - + -
518F ILE* 2.9 41.9 + - + +
519F VAL* 3.7 7.6 - - - +
521F LEU* 1.3 76.3 - - - +
523F TYR* 1.3 65.6 + - + +
525F ILE* 3.1 14.4 - - + +
526F LEU* 2.9 26.3 + - - +
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Residues in contact with TYR 523 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491F ILE* 4.4 28.5 + - + -
495F ASN* 3.3 28.4 + - - +
519F VAL* 2.9 32.2 + - + +
520F ASN* 3.8 5.4 - - - +
522F LEU* 1.3 77.7 - - + +
524F GLU* 1.3 57.4 + - - +
526F LEU* 3.4 10.3 + - + +
527F ALA* 2.9 30.8 + - - +
546F TRP* 5.9 3.8 - + - -
550F LYS* 5.0 6.4 + - + +
553F ARG* 5.5 0.2 - - - -
555F GLU 4.7 3.1 + - - -
556F ALA* 3.6 35.4 - - + -
559F GLY* 4.4 20.8 - - - +
560F ILE* 3.6 33.8 - - + +
563F VAL* 4.2 4.7 - - + +
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Residues in contact with GLU 524 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449F ILE* 3.8 16.8 - - + +
520F ASN* 2.9 23.7 + - - +
521F LEU* 3.7 6.5 - - + +
523F TYR* 1.3 77.3 - - - +
525F ILE* 1.3 58.2 + - - +
527F ALA* 3.3 5.6 + - - +
528F SER* 2.9 29.9 + - - -
562F GLU* 6.2 0.2 - - - -
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Residues in contact with ILE 525 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411F TYR* 3.7 23.3 - - - +
445F LEU* 4.6 10.1 - - + -
448F LEU* 4.4 22.2 - - + -
449F ILE* 3.7 19.4 - - + +
452F PHE* 6.4 0.2 - - + -
478F PHE* 5.5 8.5 - - + -
483F MET* 6.5 0.2 - - + -
487F VAL* 6.3 4.7 - - + -
521F LEU 2.9 17.6 + - - +
522F LEU* 3.1 29.2 - - + +
524F GLU* 1.3 75.9 - - - +
526F LEU* 1.3 58.4 + - + +
528F SER* 2.8 17.8 + - - -
529F LEU* 2.9 37.0 + - + +
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Residues in contact with LEU 526 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487F VAL* 4.8 13.9 - - + -
488F LEU* 4.1 17.3 - - + -
491F ILE* 3.7 31.6 - - + -
522F LEU 2.9 18.1 + - - +
523F TYR* 3.8 8.5 - - + +
525F ILE* 1.3 79.6 - - + +
527F ALA* 1.3 57.5 + - - +
529F LEU* 3.8 3.0 - - - +
530F ILE* 2.9 47.9 + - + +
540F PHE* 5.4 8.5 - - + -
546F TRP* 5.4 3.1 - - + -
563F VAL* 3.6 38.1 - - + -
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Residues in contact with ALA 527 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523F TYR 2.9 18.3 + - - +
524F GLU* 3.3 5.6 + - - +
526F LEU* 1.3 76.3 - - - +
528F SER* 1.3 59.3 + - - +
530F ILE* 3.6 4.0 + - - +
531F ARG* 3.1 45.7 + - - +
559F GLY* 5.0 1.6 - - - +
562F GLU* 4.5 15.0 - - + +
563F VAL* 3.6 24.2 - - + +
566F CYS* 4.7 4.2 - - + -
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Residues in contact with SER 528 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449F ILE* 4.6 12.2 - - - +
452F PHE* 4.4 20.8 - - - +
454F PRO* 6.4 1.3 - - - -
475F GLN* 3.9 5.4 + - - -
524F GLU 2.9 14.7 + - - -
525F ILE* 2.8 22.5 + - - +
527F ALA* 1.3 78.2 - - - +
529F LEU* 1.3 65.1 + - - +
531F ARG* 3.4 33.0 + - - +
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Residues in contact with LEU 529 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448F LEU 5.6 0.7 - - - +
449F ILE* 6.1 0.9 - - - -
452F PHE* 4.3 36.1 - - + -
475F GLN* 4.1 16.7 + - + +
478F PHE* 3.5 47.3 - - + -
484F LEU* 6.3 2.0 - - + -
525F ILE* 2.9 40.3 + - + +
526F LEU* 4.2 4.0 - - - +
528F SER* 1.3 85.3 - - - +
530F ILE* 1.3 64.6 + - + +
531F ARG 4.0 4.0 - - - +
533F ASN* 4.4 0.3 - - - +
536F ASN* 3.2 24.8 + - - +
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Residues in contact with ILE 530 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484F LEU* 4.7 11.0 - - + -
526F LEU* 2.9 38.1 + - + +
527F ALA* 4.1 5.2 - - - +
529F LEU* 1.3 77.2 - - + +
531F ARG* 1.3 64.1 + - - +
532F GLY 3.4 1.9 + - - -
533F ASN* 3.5 19.2 + - - +
536F ASN* 3.7 33.9 - - + +
537F CYS* 4.6 16.5 - - + -
539F LEU* 6.1 0.2 - - + -
540F PHE* 5.1 15.0 - - + -
563F VAL* 5.4 7.4 - - + +
566F CYS* 4.9 15.2 - - + +
567F VAL* 5.0 13.0 - - + -
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Residues in contact with ARG 531 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454F PRO* 4.9 21.2 - - - +
471F LEU* 5.5 0.5 - - - +
475F GLN* 2.7 31.2 + - - -
527F ALA* 3.1 32.2 + - - +
528F SER* 3.4 21.6 + - - +
529F LEU 3.3 0.6 - - - -
530F ILE* 1.3 77.2 - - - +
532F GLY* 1.3 56.8 + - - +
533F ASN 3.3 1.1 + - - -
562F GLU* 2.5 42.2 + - - +
566F CYS* 3.5 28.8 - - - +
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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
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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