Contacts of the helix formed by residues 514 - 531 (chain A) in PDB entry 1BHG
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 LEU 514 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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506A SER* 3.5 6.5 - - - -
512A GLY 3.4 6.2 + - - +
513A HIS* 1.3 71.9 - - - +
515A GLU* 1.3 60.5 + - - +
516A LEU 3.1 2.0 + - - -
517A ILE* 3.5 17.8 + - + +
518A GLN 4.5 0.3 + - - -
554A PRO* 3.9 13.0 - - + -
561A TYR* 3.2 49.1 - - + +
564A SER* 3.8 17.3 - - - -
565A LEU* 3.6 34.3 - - + +
568A GLN* 3.7 29.4 - - + +
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Residues in contact with GLU 515 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512A GLY 4.2 2.4 - - - +
513A HIS* 2.6 46.6 + - - +
514A LEU* 1.3 79.7 + - - +
516A LEU* 1.3 72.0 + - + +
518A GLN* 4.9 4.9 + - - +
519A LEU* 5.0 5.2 + - - +
568A GLN* 5.6 1.3 - - - -
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Residues in contact with LEU 516 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506A SER 6.3 0.4 - - - +
510A ASP* 4.1 18.2 - - + +
513A HIS* 3.1 41.2 + - + +
514A LEU 3.1 0.6 - - - -
515A GLU* 1.3 93.1 - - + +
517A ILE* 1.3 68.4 + - - +
518A GLN 3.3 2.2 - - - -
519A LEU* 2.8 32.4 + - + +
520A GLN* 3.0 36.4 + - - +
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Residues in contact with ILE 517 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505A TYR* 3.4 27.4 - - + +
506A SER* 2.8 30.5 - - - +
513A HIS 3.8 0.8 + - - -
514A LEU* 3.5 21.1 + - + +
516A LEU* 1.3 77.7 - - - +
518A GLN* 1.3 68.2 + - - +
520A GLN* 3.2 1.2 + - - +
521A LEU* 2.9 24.8 + - + +
565A LEU* 3.8 23.3 - - + -
568A GLN* 3.8 31.6 - - + +
569A TYR* 3.8 28.7 - - + +
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Residues in contact with GLN 518 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514A LEU 4.5 2.2 + - - -
515A GLU 5.3 4.0 - - - +
516A LEU 3.1 1.0 + - - -
517A ILE* 1.3 82.7 - - - +
519A LEU* 1.3 65.1 + - - +
521A LEU* 3.7 4.3 - - - +
522A ALA* 3.4 21.0 + - - +
568A GLN* 2.9 29.9 + - - +
571A LEU* 3.7 41.8 - - + +
572A GLY* 4.7 11.9 - - - +
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Residues in contact with LEU 519 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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515A GLU 5.0 3.9 + - - +
516A LEU* 2.8 33.7 + - + +
518A GLN* 1.3 77.1 - - - +
520A GLN* 1.3 68.8 + - + +
521A LEU 3.0 1.2 + - - -
522A ALA* 3.5 7.3 + - - +
523A THR* 3.0 19.8 + - + +
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Residues in contact with GLN 520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505A TYR* 3.6 51.4 + - + +
506A SER 4.8 0.7 + - - -
509A HIS* 4.3 3.7 - - - -
510A ASP* 3.3 27.3 + - - +
516A LEU* 3.0 35.9 + - + +
517A ILE* 4.0 0.7 - - - +
519A LEU* 1.3 80.0 - - + +
521A LEU* 1.3 60.1 + - - +
523A THR* 3.0 16.0 + - - -
524A GLN* 3.5 7.4 + - - +
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Residues in contact with LEU 521 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505A TYR* 3.4 24.0 - - + -
517A ILE* 2.9 18.2 + - + +
518A GLN* 3.7 5.4 - - - +
519A LEU 3.0 1.6 + - - -
520A GLN* 1.3 73.4 - - - +
522A ALA* 1.3 66.8 + - - +
523A THR 2.9 3.4 + - - -
524A GLN* 3.0 34.5 + - - +
525A PHE* 3.3 31.8 + - + -
538A GLN* 4.4 0.9 - - - +
569A TYR* 3.4 46.7 - - + +
572A GLY* 3.7 24.7 - - - -
573A LEU* 4.1 2.5 - - + +
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Residues in contact with ALA 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518A GLN* 3.4 12.2 + - + +
519A LEU* 3.5 3.3 + - - +
521A LEU* 1.3 79.2 - - - +
523A THR* 1.3 56.2 + - - +
525A PHE* 3.5 4.5 + - - +
526A GLU* 3.1 27.1 + - - +
572A GLY* 5.6 0.9 - - - -
575A GLN* 6.0 1.8 - - + -
576A LYS* 3.5 31.9 - - + +
580A TYR* 5.4 0.2 + - - -
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Residues in contact with THR 523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519A LEU* 3.0 22.7 + - + +
520A GLN* 3.0 14.6 + - - -
521A LEU 2.9 0.6 + - - -
522A ALA* 1.3 73.5 - - + +
524A GLN* 1.3 65.0 + - - -
525A PHE 3.0 1.6 - - - -
526A GLU* 2.9 7.1 + - + +
527A ASN* 2.8 41.3 + - - +
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Residues in contact with GLN 524 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487A TYR* 6.5 0.2 - - - -
501A LEU* 3.9 21.6 - - - +
502A ASN 4.8 1.2 - - - +
503A SER* 3.0 27.7 + - - -
505A TYR* 3.3 23.6 + - - +
520A GLN 3.5 5.3 + - - +
521A LEU* 3.0 26.2 + - - +
523A THR* 1.3 76.6 - - - +
525A PHE* 1.3 73.8 + - + +
527A ASN* 4.0 6.1 - - - +
528A TRP* 2.7 45.7 + - + +
538A GLN* 3.3 16.2 + - - -
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Residues in contact with PHE 525 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501A LEU* 5.3 2.7 - - + -
521A LEU* 3.3 36.1 + - + -
522A ALA 3.5 6.3 - - - +
523A THR 3.0 0.4 - - - -
524A GLN* 1.3 100.2 - - + +
526A GLU* 1.3 59.4 + - - +
528A TRP* 3.2 2.1 + - - +
529A TYR* 2.9 33.1 + - - +
536A ILE* 3.7 37.1 - - + +
538A GLN* 3.5 22.4 - - + -
572A GLY 4.2 3.8 - - - -
573A LEU* 4.1 17.5 - - + -
576A LYS* 3.4 31.0 - - - -
580A TYR* 4.2 11.9 - - + +
581A VAL* 4.0 16.6 - - + -
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Residues in contact with GLU 526 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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522A ALA 3.1 14.6 + - - +
523A THR* 2.9 15.4 + - + +
525A PHE* 1.3 71.7 - - - +
527A ASN* 1.3 61.5 + - - +
529A TYR* 5.9 2.1 - - - +
530A LYS* 2.9 49.9 + - - +
580A TYR* 3.9 19.2 + - - +
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Residues in contact with ASN 527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487A TYR* 3.9 41.6 + - + -
523A THR* 2.8 46.5 + - - +
524A GLN* 4.0 5.7 - - - +
526A GLU* 1.3 74.6 - - - +
528A TRP* 1.3 62.9 + - + +
530A LYS* 3.2 31.1 + - - +
531A LYS* 3.3 14.0 + - - +
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Residues in contact with TRP 528 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483A SER* 4.3 1.1 - - - -
485A SER 2.9 27.2 + - - -
487A TYR* 3.8 20.9 - + + +
490A ASP* 3.1 28.9 - - + -
493A ALA* 3.7 8.1 - - + -
499A ILE* 3.4 19.7 - - + -
501A LEU* 3.6 41.5 - - + +
524A GLN* 2.7 42.0 + - - +
525A PHE 3.2 4.0 + - - +
527A ASN* 1.3 75.0 - - + +
529A TYR* 1.3 60.5 + - - +
531A LYS* 3.7 7.3 + - - +
532A TYR* 2.8 75.2 + + - +
536A ILE* 4.2 12.8 - - + -
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Residues in contact with TYR 529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333A LYS* 2.8 42.6 + - - +
334A SER* 3.9 8.4 - - - -
525A PHE 2.9 10.2 + - - +
526A GLU* 4.4 3.1 - - - +
528A TRP* 1.3 71.7 - - - +
530A LYS* 1.3 58.1 + - - +
532A TYR 2.9 14.8 - - - +
533A GLN* 2.6 45.2 + - + +
534A LYS 3.0 34.8 - - - -
536A ILE* 4.3 3.1 - - + +
580A TYR* 3.5 58.1 - + + -
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Residues in contact with LYS 530 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487A TYR* 3.1 37.0 + - - -
526A GLU* 2.9 33.5 + - - +
527A ASN* 3.2 21.2 + - - +
529A TYR* 1.3 79.1 - - - +
531A LYS* 1.3 82.8 + - - +
533A GLN* 3.2 10.6 + - - +
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Residues in contact with LYS 531 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487A TYR* 3.4 29.4 - - + +
488A ALA* 3.3 31.9 - - + +
527A ASN 3.3 12.8 + - - +
528A TRP* 3.7 6.1 + - - +
529A TYR 3.2 0.2 - - - -
530A LYS* 1.3 95.4 - - + +
532A TYR* 1.3 111.5 + - + +
533A GLN* 3.4 10.2 + - - +
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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