Contacts of the helix formed by residues 514 - 531 (chain A) in PDB entry 2XOA
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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438A ILE* 3.4 35.3 - - - +
442A ILE* 4.0 14.2 - - - +
510A GLU 4.8 2.2 + - - -
511A ALA 3.0 10.1 + - - -
513A GLU* 1.3 82.3 - - - +
515A TRP* 1.3 66.3 + - - +
516A LYS 3.5 1.8 - - - -
517A GLU* 3.2 13.1 + - - +
518A ILE* 2.9 27.1 + - - +
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Residues in contact with TRP 515 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494A LEU* 3.1 48.6 + - + +
495A ASN* 4.4 9.9 - - - -
497A TYR* 3.3 42.2 - + + +
498A THR 4.0 4.9 - - - -
499A THR* 3.4 36.3 - - - +
511A ALA 3.6 4.4 + - - +
512A ALA* 3.6 21.9 + - + +
514A SER* 1.3 75.0 - - - +
516A LYS* 1.3 87.5 + - + +
518A ILE* 3.2 8.5 + - - +
519A VAL* 3.0 35.9 + - + +
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Residues in contact with LYS 516 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512A ALA 5.0 1.0 + - - -
513A GLU 5.4 1.0 + - - -
514A SER 3.5 0.6 - - - -
515A TRP* 1.3 98.0 - - + +
517A GLU* 1.3 63.3 + - - +
519A VAL* 4.2 3.9 - - + +
520A ASN* 3.0 56.0 + - - +
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Residues in contact with GLU 517 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A ILE* 3.8 34.6 - - + +
446A GLN* 4.2 9.5 + - - -
513A GLU 5.5 2.2 + - - +
514A SER* 3.2 16.8 + - - +
516A LYS* 1.3 78.7 - - - +
518A ILE* 1.3 59.1 + - - +
520A ASN* 3.4 4.5 + - - +
521A LEU* 3.0 40.3 + - + +
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Residues in contact with ILE 518 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A PHE* 4.4 13.2 - - + -
438A ILE* 4.0 27.1 - - + -
441A VAL* 4.0 29.2 - - + -
442A ILE* 3.7 26.5 - - + -
445A LEU* 4.2 3.4 - - + -
494A LEU* 3.9 14.1 - - + -
514A SER* 2.9 23.0 + - - +
515A TRP* 3.8 4.7 - - - +
517A GLU* 1.3 73.9 - - - +
519A VAL* 1.3 60.7 + - - +
521A LEU* 3.2 6.7 + - - +
522A LEU* 2.8 46.5 + - + +
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Residues in contact with VAL 519 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A ILE* 5.0 4.0 - - + +
494A LEU* 4.4 18.8 - - + -
495A ASN* 4.2 15.3 - - - +
515A TRP* 3.0 45.8 + - + +
516A LYS* 4.2 7.4 - - + -
518A ILE* 1.3 75.9 - - - +
520A ASN* 1.3 68.3 + - - +
522A LEU* 3.4 9.3 + - + +
523A TYR* 3.0 52.7 + - + -
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Residues in contact with ASN 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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516A LYS* 3.0 58.4 + - - +
517A GLU* 3.8 5.1 - - - +
519A VAL* 1.3 84.6 - - - +
521A LEU* 1.3 57.9 + - + +
523A TYR* 3.5 13.7 + - - +
524A GLU* 3.0 30.9 + - - +
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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
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442A ILE* 3.8 36.1 - - + +
445A LEU* 3.8 18.4 - - + -
446A GLN* 4.2 17.5 - - + +
449A ILE* 3.6 26.2 - - + +
517A GLU* 3.0 41.7 + - + +
518A ILE* 3.7 5.2 - - - +
520A ASN* 1.3 74.9 - - + +
522A LEU* 1.3 59.6 + - - +
524A GLU* 3.2 15.5 + - - +
525A LEU* 2.8 26.2 + - - +
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Residues in contact with LEU 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A TYR* 5.2 3.1 - - + -
414A PHE* 5.2 0.4 - - + -
441A VAL* 6.1 0.7 - - + -
445A LEU* 4.1 23.3 - - + +
487A VAL* 3.7 24.4 - - + +
490A CYS* 3.6 33.4 - - + -
491A ILE* 3.6 22.0 - - + +
494A LEU* 3.7 20.4 - - + -
518A ILE* 2.8 39.5 + - + +
519A VAL* 3.6 5.4 - - - +
521A LEU* 1.3 72.0 - - - +
523A TYR* 1.3 56.6 + - - +
525A LEU* 3.0 6.6 + - - +
526A LEU* 2.8 30.1 + - - +
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Residues in contact with TYR 523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A ILE* 3.6 27.2 - - + +
495A ASN* 3.0 22.7 + - - -
519A VAL* 3.0 47.2 + - + +
520A ASN* 3.8 13.5 - - - +
522A LEU* 1.3 73.9 - - - +
524A GLU* 1.3 63.4 + - - +
526A LEU* 3.3 17.0 - - + +
527A ALA* 3.0 23.9 + - - +
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Residues in contact with GLU 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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449A ILE* 3.7 31.2 - - + +
520A ASN* 3.0 17.3 + - - +
521A LEU* 3.2 21.6 + - - +
523A TYR* 1.3 78.1 - - - +
525A LEU* 1.3 59.9 + - - +
527A ALA* 3.5 6.3 + - - +
528A SER* 3.1 27.6 + - - +
531A ARG* 4.6 3.5 + - - +
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Residues in contact with LEU 525 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A TYR* 4.3 2.5 - - + +
445A LEU* 4.1 22.2 - - + -
448A LEU* 3.9 42.8 - - + -
449A ILE* 4.1 11.2 - - + +
452A PHE* 3.9 21.1 - - + -
487A VAL* 3.6 28.7 - - + -
521A LEU 2.8 15.6 + - - +
522A LEU* 3.0 9.8 + - - +
524A GLU* 1.3 68.9 - - - +
526A LEU* 1.3 58.4 - - - +
528A SER* 2.7 25.1 + - - -
529A LEU* 2.9 23.4 + - + +
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Residues in contact with LEU 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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484A LEU* 3.4 27.6 - - + +
487A VAL* 4.3 13.8 - - + +
488A LEU* 3.4 37.5 - - + -
491A ILE* 4.1 11.9 - - + -
522A LEU 2.8 15.4 + - - +
523A TYR* 3.3 22.7 - - + +
525A LEU* 1.3 72.6 - - - +
527A ALA* 1.3 65.5 + - - +
528A SER 3.1 0.7 + - - -
529A LEU* 3.1 14.0 + - - +
530A ILE* 3.4 20.9 + - + +
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Residues in contact with ALA 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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523A TYR 3.0 16.9 + - - +
524A GLU* 3.8 7.9 - - + +
525A LEU 3.2 0.2 - - - -
526A LEU* 1.3 76.7 - - - +
528A SER* 1.3 56.8 + - - +
530A ILE* 3.3 6.1 + - - +
531A ARG* 2.9 48.7 + - - +
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Residues in contact with SER 528 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A ILE* 4.5 16.9 + - - +
452A PHE* 3.8 36.3 + - - +
453A GLU* 5.7 0.9 - - - -
454A PRO* 5.7 0.7 - - - +
475A GLN* 2.7 27.4 + - - -
524A GLU* 3.1 15.2 + - - +
525A LEU* 2.7 19.3 + - - -
527A ALA* 1.3 73.2 - - - +
529A LEU* 1.3 53.2 + - - +
531A ARG* 3.1 25.1 + - - +
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Residues in contact with LEU 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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452A PHE* 3.5 36.3 - - + -
475A GLN* 3.5 17.6 + - - +
478A PHE* 4.1 17.3 - - + -
479A GLN* 2.9 29.5 + - + +
483A MET* 4.5 15.3 - - + +
484A LEU* 3.9 26.5 - - + +
487A VAL* 4.2 20.6 - - + -
525A LEU* 2.9 30.2 + - + +
526A LEU* 3.1 8.3 + - - +
528A SER* 1.3 79.5 - - - +
530A ILE* 1.4 57.0 + - - +
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Residues in contact with ILE 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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475A GLN* 4.0 1.1 - - - -
479A GLN* 4.6 6.3 - - - +
484A LEU* 3.5 39.7 - - + -
526A LEU* 3.5 17.3 - - + +
527A ALA* 3.3 5.3 + - - +
528A SER 3.3 0.2 - - - -
529A LEU* 1.4 84.4 - - - +
531A ARG* 1.3 70.9 + - - +
532A GLY 2.9 11.1 + - - -
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Residues in contact with ARG 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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452A PHE 5.8 0.8 + - - +
454A PRO* 4.0 33.0 - - + +
471A LEU* 5.4 2.9 - - - +
475A GLN* 2.9 26.8 + - - +
524A GLU* 4.6 4.0 + - - +
527A ALA* 2.9 30.3 + - - +
528A SER* 3.1 39.3 + - - +
529A LEU 3.8 0.6 - - - -
530A ILE* 1.3 73.0 - - - +
532A GLY* 1.3 63.2 + - - +
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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