Contacts of the helix formed by residues 514 - 531 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B LEU* 5.2 4.5 - - - -
442B ILE* 4.3 18.4 - - - -
511B ALA* 3.8 18.9 + - - -
512B ALA 3.2 1.2 - - - -
513B GLU* 1.3 75.9 - - - +
515B TRP* 1.3 59.3 + - - +
516B LYS 3.3 2.0 - - - -
517B GLU* 3.3 9.1 + - - +
518B ILE* 2.9 33.9 + - - +
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Residues in contact with TRP 515 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494B LEU* 3.4 53.9 + - + +
495B ASN* 5.1 6.7 - - - -
497B TYR* 5.1 7.0 - - + +
498B THR 5.1 2.2 - - - -
499B THR* 4.5 19.7 - - - -
500B ALA* 4.1 29.2 - - + -
503B PHE* 4.3 25.0 - + + +
511B ALA* 3.3 16.0 + - - +
512B ALA 3.6 9.4 - - - +
513B GLU 3.4 1.6 - - - -
514B SER* 1.3 77.7 - - - +
516B LYS* 1.3 69.4 + - + +
518B ILE* 3.2 7.8 + - + +
519B VAL* 2.9 60.9 + - + +
553B ARG* 5.3 7.4 - - - -
555B GLU* 4.5 22.9 - - + -
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Residues in contact with LYS 516 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500B ALA* 5.5 0.4 - - - +
512B ALA 4.9 0.4 + - - -
513B GLU 4.4 7.0 + - - +
514B SER 3.3 0.6 - - - -
515B TRP* 1.3 89.5 - - + +
517B GLU* 1.3 57.8 + - - +
519B VAL* 3.1 14.2 - - + +
520B ASN* 2.9 35.2 + - + +
555B GLU* 5.6 9.4 - - + +
556B ALA* 5.9 5.4 - - + +
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Residues in contact with GLU 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442B ILE* 4.7 11.9 - - + -
513B GLU 4.8 1.9 + - - +
514B SER* 3.3 15.7 + - - +
515B TRP 3.3 0.4 - - - -
516B LYS* 1.3 79.2 - - - +
518B ILE* 1.3 57.7 + - - +
520B ASN* 3.3 5.9 + - - +
521B LEU* 2.9 42.2 + - + +
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Residues in contact with ILE 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B PHE* 4.6 22.0 - - + -
436B LEU* 5.4 0.4 - - + -
438B LEU* 4.4 19.5 - - + +
441B VAL* 4.8 5.4 - - + -
442B ILE* 3.6 29.6 - - + -
445B LEU* 5.3 2.2 - - + -
494B LEU* 3.6 24.5 - - + -
511B ALA* 4.6 9.2 - - + -
514B SER* 2.9 24.6 + - - +
515B TRP* 3.6 8.3 - - + +
517B GLU* 1.3 78.1 - - - +
519B VAL* 1.3 56.8 + - - +
521B LEU* 3.3 5.1 + - - +
522B LEU* 2.9 45.6 + - + +
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Residues in contact with VAL 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494B LEU* 3.7 20.9 - - + -
495B ASN* 6.3 0.7 - - - +
515B TRP* 2.9 53.5 + - + +
516B LYS* 3.1 23.1 - - + +
518B ILE* 1.3 75.1 - - - +
520B ASN* 1.3 56.9 + - - +
522B LEU* 3.7 7.3 - - - +
523B TYR* 2.9 47.8 + - + +
555B GLU 6.0 0.2 - - - -
556B ALA* 4.3 20.6 - - + -
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Residues in contact with ASN 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516B LYS* 2.9 23.2 + - + +
517B GLU* 3.6 8.1 - - - +
519B VAL* 1.3 79.3 - - + +
521B LEU* 1.3 62.1 + - + +
523B TYR* 3.4 7.4 + - - +
524B GLU* 2.9 31.9 + - - +
556B ALA* 5.3 7.9 - - + +
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Residues in contact with LEU 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442B ILE* 5.0 8.1 - - + +
445B LEU* 3.6 29.1 - - + +
446B GLN* 3.8 40.6 - - + +
449B ILE* 3.7 26.8 - - + +
517B GLU* 2.9 31.9 + - + +
518B ILE* 3.7 2.9 - - - +
520B ASN* 1.3 82.6 - - + +
522B LEU* 1.3 57.5 + - - +
524B GLU* 3.7 4.2 - - + +
525B ILE* 2.9 32.7 + - - +
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Residues in contact with LEU 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B TYR* 5.4 9.6 - - + +
414B PHE* 6.0 3.6 - - + -
441B VAL* 5.6 3.1 - - + -
445B LEU* 3.5 22.9 - - + -
487B VAL* 4.7 16.6 - - + +
490B CYS* 4.7 12.8 - - + -
491B ILE* 3.7 33.2 - - + +
494B LEU* 5.2 5.4 - - + -
518B ILE* 2.9 42.7 + - + +
519B VAL* 3.7 7.9 - - - +
520B ASN 3.3 0.2 - - - -
521B LEU* 1.3 76.6 - - - +
523B TYR* 1.3 64.9 + - + +
525B ILE* 3.1 14.0 - - + +
526B LEU* 2.9 25.6 + - - +
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Residues in contact with TYR 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491B ILE* 4.4 29.4 + - + +
495B ASN* 3.3 28.2 + - - +
519B VAL* 2.9 33.3 + - + +
520B ASN* 3.8 4.9 - - - +
522B LEU* 1.3 78.1 - - + +
524B GLU* 1.3 57.5 + - - +
526B LEU* 3.4 8.3 + - + +
527B ALA* 2.9 30.7 + - - +
546B TRP* 5.9 3.6 - + - -
550B LYS* 5.0 6.2 + - + +
555B GLU 4.7 2.8 + - - -
556B ALA* 3.6 36.6 - - + -
559B GLY* 4.4 20.4 - - - +
560B ILE* 3.6 33.6 - - + +
563B VAL* 4.3 5.3 - - + +
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Residues in contact with GLU 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449B ILE* 3.8 16.6 - - + -
520B ASN* 2.9 23.7 + - - +
521B LEU* 3.7 6.7 - - + +
523B TYR* 1.3 77.3 - - - +
525B ILE* 1.3 57.8 + - - +
527B ALA* 3.3 6.4 + - - +
528B SER* 2.9 30.1 + - - -
562B GLU* 6.2 0.2 - - - -
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Residues in contact with ILE 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B TYR* 3.7 22.4 - - - +
445B LEU* 4.6 11.9 - - + -
448B LEU* 4.4 22.4 - - + -
449B ILE* 3.7 19.0 - - + +
452B PHE* 6.4 0.2 - - + -
478B PHE* 5.5 8.1 - - + -
483B MET* 6.5 0.2 - - + -
487B VAL* 6.3 5.4 - - + -
521B LEU 2.9 16.7 + - - +
522B LEU* 3.1 29.6 - - + +
524B GLU* 1.3 76.5 - - - +
526B LEU* 1.3 58.1 + - + +
528B SER* 2.8 17.7 + - - -
529B LEU* 2.9 37.7 + - + +
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Residues in contact with LEU 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487B VAL* 4.8 12.6 - - + -
488B LEU* 4.1 17.3 - - + -
491B ILE* 3.7 32.1 - - + -
522B LEU 2.9 18.5 + - - +
523B TYR* 3.8 8.1 - - + +
525B ILE* 1.3 78.5 - - + +
527B ALA* 1.3 55.8 + - - +
529B LEU* 3.8 3.4 - - - +
530B ILE* 2.9 48.2 + - + +
540B PHE* 5.4 9.0 - - + -
546B TRP* 5.4 2.9 - - + -
563B VAL* 3.6 37.7 - - + -
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Residues in contact with ALA 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523B TYR 2.9 18.3 + - - +
524B GLU* 3.7 6.1 - - - +
526B LEU* 1.3 78.2 - - - +
528B SER* 1.3 58.2 + - - +
530B ILE* 4.1 3.8 - - - +
531B ARG* 3.1 46.5 + - - +
559B GLY* 5.0 1.3 - - - +
562B GLU* 4.5 15.0 - - + +
563B VAL* 3.6 24.9 - - + +
566B CYS* 4.7 3.9 - - + -
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Residues in contact with SER 528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449B ILE* 4.6 11.9 - - - +
452B PHE* 4.4 19.8 - - - +
454B PRO* 6.4 1.1 - - - -
475B GLN* 3.9 5.2 + - - -
524B GLU 2.9 15.5 + - - -
525B ILE* 2.8 21.7 + - - +
527B ALA* 1.3 78.2 - - - +
529B LEU* 1.3 66.8 + - - +
531B ARG* 3.4 33.7 + - - +
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Residues in contact with LEU 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448B LEU 5.6 0.9 - - - +
449B ILE* 6.1 0.7 - - - -
452B PHE* 4.3 36.1 - - + -
475B GLN* 4.1 16.7 + - + +
478B PHE* 3.5 46.4 - - + -
484B LEU* 6.3 2.7 - - + -
525B ILE* 2.9 40.0 + - + +
526B LEU* 4.2 3.8 - - - +
528B SER* 1.3 84.7 - - - +
530B ILE* 1.3 65.5 + - + +
531B ARG 4.0 4.0 - - - +
533B ASN* 4.4 0.2 - - - +
536B ASN* 3.2 24.6 + - - +
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Residues in contact with ILE 530 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484B LEU* 4.7 10.1 - - + -
526B LEU* 2.9 38.0 + - + +
527B ALA* 4.1 5.6 - - - +
529B LEU* 1.3 78.0 - - + +
531B ARG* 1.3 65.1 + - - +
532B GLY 3.4 2.1 + - - -
533B ASN* 3.5 18.7 + - - +
536B ASN* 3.7 34.5 - - + +
537B CYS* 4.6 16.5 - - + -
539B LEU* 6.1 0.2 - - + -
540B PHE* 5.1 15.3 - - + -
563B VAL* 5.4 6.1 - - + +
566B CYS* 4.9 14.7 - - + +
567B VAL* 5.0 13.0 - - + -
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Residues in contact with ARG 531 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454B PRO* 4.9 21.0 - - - +
471B LEU* 5.5 0.5 - - - +
475B GLN* 2.7 31.7 + - - -
527B ALA* 3.1 33.2 + - - +
528B SER* 3.4 20.9 - - - +
529B LEU 3.3 0.4 - - - -
530B ILE* 1.3 76.6 - - - +
532B GLY* 1.3 56.0 + - - +
533B ASN 3.3 0.7 + - - -
562B GLU* 2.5 41.6 + - - +
566B CYS* 3.5 29.3 - - - +
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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