Contacts of the helix formed by residues 508 - 520 (chain A) in PDB entry 5X61
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 THR 508 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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506A THR* 5.6 1.3 - - - +
507A VAL* 1.3 76.9 - - - +
509A ARG* 1.3 58.7 + - - +
510A GLU* 3.4 11.4 + - - +
511A GLU* 3.0 41.3 + - - +
512A PHE* 2.8 26.2 + - - +
542A ASP 5.4 2.0 - - - -
544A PRO* 5.3 4.7 - - + -
547A ASN* 3.9 2.7 - - - +
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Residues in contact with ARG 509 (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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508A THR* 1.3 72.2 - - - +
510A GLU* 1.3 65.0 + - - +
512A PHE* 3.7 17.0 - - - -
513A LEU* 3.1 46.0 + - + +
532A VAL* 3.8 12.3 + - - +
536A THR* 2.8 45.2 + - - +
538A TRP* 4.7 9.7 - - - -
541A PRO* 3.3 22.3 + - - +
542A ASP* 4.0 26.7 + - + +
547A ASN* 2.8 39.3 + - - +
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Residues in contact with GLU 510 (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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508A THR* 3.2 10.6 + - - +
509A ARG* 1.3 80.4 - - - +
511A GLU* 1.3 62.9 + - + +
513A LEU* 3.5 6.1 + - - +
514A GLN* 3.2 24.3 + - - +
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Residues in contact with GLU 511 (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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498A LEU* 3.9 29.0 - - + +
506A THR 4.0 3.1 - - - +
507A VAL* 3.6 20.0 - - + +
508A THR* 3.0 41.9 + - - +
510A GLU* 1.3 76.1 - - + +
512A PHE* 1.3 60.0 + - - +
514A GLN* 3.3 7.5 + - - +
515A ALA* 2.9 29.3 + - - +
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Residues in contact with PHE 512 (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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507A VAL* 3.5 6.9 - - + +
508A THR 2.8 18.7 + - - +
509A ARG* 3.7 29.2 - - - +
510A GLU 3.4 0.2 - - - -
511A GLU* 1.3 76.4 - - - +
513A LEU* 1.3 72.2 + - + +
515A ALA* 3.2 5.1 + - - +
516A VAL* 3.2 48.6 + - + +
532A VAL* 4.1 24.5 - - + -
535A TYR* 3.2 31.0 - - + -
547A ASN* 3.5 34.8 - - + +
550A ALA* 3.6 15.5 - - + -
551A LEU* 3.6 13.7 - - + -
554A MET* 4.8 1.8 - - - -
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Residues in contact with LEU 513 (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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509A ARG* 3.1 53.2 + - + +
510A GLU* 3.7 7.0 - - - +
511A GLU 3.3 0.2 - - - -
512A PHE* 1.3 88.9 - - + +
514A GLN* 1.3 61.2 + - - +
516A VAL* 3.3 19.1 - - - +
517A ARG* 3.8 7.4 + - - +
532A VAL* 4.0 17.9 - - + -
807A SO4 3.8 27.5 + - - +
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Residues in contact with GLN 514 (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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510A GLU* 3.2 15.4 + - - +
511A GLU* 3.7 10.3 - - - +
512A PHE 3.2 0.2 - - - -
513A LEU* 1.3 77.5 + - - +
515A ALA* 1.3 62.9 + - - +
517A ARG* 3.4 19.0 - - - +
518A GLU* 3.1 48.0 + - - +
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Residues in contact with ALA 515 (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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495A LEU* 4.6 14.4 - - + -
498A LEU* 4.8 3.1 - - + -
511A GLU 2.9 17.1 + - - +
512A PHE 3.2 2.0 + - - +
514A GLN* 1.3 73.1 - - - +
516A VAL* 1.3 53.7 + - - +
517A ARG 3.0 4.3 - - - -
518A GLU* 2.8 10.0 + - - +
519A LEU* 2.6 44.9 + - + +
551A LEU* 3.6 35.2 - - + -
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Residues in contact with VAL 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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512A PHE* 3.2 35.4 + - + +
513A LEU* 3.3 17.0 - - + +
515A ALA* 1.3 74.9 - - - +
517A ARG* 1.3 63.9 + - + +
519A LEU* 4.6 0.2 - - - -
520A ASN* 3.0 33.7 + - - +
528A ARG* 4.4 16.3 - - + +
531A ILE* 4.4 9.2 - - + -
532A VAL* 3.6 26.7 - - + -
551A LEU* 4.5 1.1 - - + -
554A MET* 3.6 30.7 - - + -
807A SO4 5.2 1.6 - - - +
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Residues in contact with ARG 517 (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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513A LEU 4.0 8.5 - - - +
514A GLN* 3.4 26.6 + - - +
515A ALA 3.0 0.4 - - - -
516A VAL* 1.3 82.2 - - - +
518A GLU* 1.3 62.6 + - + +
520A ASN 3.5 11.8 - - - +
521A PRO* 3.6 25.8 + - - +
528A ARG* 3.7 47.9 - - - +
804A SO4 4.6 8.7 + - - -
807A SO4 4.8 3.6 - - - +
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Residues in contact with GLU 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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446A ILE* 5.1 1.4 + - - +
494A TYR* 3.9 21.7 + - + +
495A LEU* 3.3 29.9 - - + +
497A GLU* 4.6 5.9 - - - +
514A GLN* 3.1 35.7 + - - +
515A ALA 2.8 6.0 + - - +
517A ARG* 1.3 81.7 - - + +
519A LEU* 1.3 62.9 - - - +
520A ASN 3.3 0.6 + - - -
521A PRO* 3.7 17.7 - - - +
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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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446A ILE* 3.6 47.7 - - + +
491A ILE* 4.3 17.0 - - + -
494A TYR* 4.1 14.6 - - + -
495A LEU* 4.2 13.0 - - + -
515A ALA* 2.6 25.8 + - + +
516A VAL* 4.6 0.4 - - - -
518A GLU* 1.3 72.3 - - - +
520A ASN* 1.3 70.9 + - - +
521A PRO* 3.8 4.8 - - - +
551A LEU* 4.0 30.1 - - + +
554A MET* 4.6 5.2 - - + -
555A VAL* 3.7 24.0 - - + +
558A TYR* 6.1 0.3 - - - -
559A HIS* 4.9 4.5 + - - -
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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 VAL 3.0 17.8 + - - +
517A ARG* 3.5 11.0 + - - +
519A LEU* 1.3 83.0 + - - +
521A PRO* 1.3 60.1 - - - +
522A TYR* 3.2 10.7 + - - -
523A VAL* 3.4 30.0 + - + +
528A ARG* 4.8 1.9 - - - +
531A ILE* 3.8 8.6 - - + +
554A MET* 2.8 30.3 + - - +
558A TYR* 5.2 8.1 - - - -
686A TRP* 3.4 33.3 - - - -
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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
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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