Contacts of the helix formed by residues 505 - 520 (chain A) in PDB entry 7REQ
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 PRO 505 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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500A ARG 5.4 5.6 - - - +
503A ARG* 3.3 13.9 - - + +
504A ASP* 1.3 86.2 - - - +
506A GLU* 1.3 62.1 + - - +
508A VAL* 3.5 8.8 + - + +
509A LYS* 3.1 24.8 + - - +
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Residues in contact with GLU 506 (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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504A ASP* 3.0 11.2 + - - +
505A PRO* 1.3 76.1 - - - +
507A LYS* 1.3 62.9 + - + +
509A LYS* 3.5 6.3 + - - +
510A ALA* 3.1 23.8 + - - +
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Residues in contact with LYS 507 (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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504A ASP* 3.2 36.9 + - + +
506A GLU* 1.3 76.9 - - + +
508A VAL* 1.3 62.2 + - - +
510A ALA* 3.6 5.5 + - - +
511A ALA* 3.1 25.5 + - - +
541A ALA* 4.3 14.2 - - + +
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Residues in contact with VAL 508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A ARG* 3.5 50.9 - - + +
504A ASP 3.2 16.7 + - - +
505A PRO* 3.6 8.3 - - + +
506A GLU 3.4 0.2 - - - -
507A LYS* 1.3 74.0 - - - +
509A LYS* 1.3 59.2 + - - +
511A ALA* 3.3 3.8 + - - +
512A LEU* 2.9 51.8 + - + +
541A ALA* 3.4 27.8 - - - +
542A MET 4.7 0.2 - - - -
543A ALA* 4.4 7.2 - - + -
547A GLU* 4.3 1.3 - - - +
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Residues in contact with LYS 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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505A PRO 3.1 14.5 + - - +
506A GLU* 3.8 6.1 - - - +
508A VAL* 1.3 79.7 - - - +
510A ALA* 1.3 55.3 + - - +
512A LEU* 3.3 8.6 + - + +
513A ASP* 2.9 54.1 + - - +
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Residues in contact with ALA 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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506A GLU 3.1 17.4 + - - +
507A LYS* 4.1 6.1 - - - +
509A LYS* 1.3 74.3 - - - +
511A ALA* 1.4 56.6 + - - +
513A ASP* 3.5 5.9 + - - +
514A LYS* 3.0 30.3 + - - +
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Residues in contact with ALA 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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507A LYS 3.1 18.4 + - - +
508A VAL 3.9 3.1 - - - +
510A ALA* 1.4 72.4 - - - +
512A LEU* 1.3 64.0 + - - +
514A LYS* 3.6 8.3 + - - +
515A ILE* 3.4 25.5 + - - +
534A LEU* 4.9 1.5 - - - +
537A ASP* 4.5 8.3 - - + +
538A ALA* 3.7 31.9 - - - +
541A ALA* 4.6 6.1 - - + -
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Residues in contact with LEU 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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508A VAL* 2.9 37.7 + - + +
509A LYS* 3.8 6.7 - - - +
511A ALA* 1.3 75.6 - - - +
513A ASP* 1.4 64.7 + - - +
515A ILE* 3.2 19.2 + - + +
516A THR* 3.3 15.9 + - - -
538A ALA* 4.5 1.1 - - + -
543A ALA* 3.7 24.0 - - + -
547A GLU* 3.8 44.6 - - + +
548A MET* 4.0 11.9 - - + +
551A ALA* 3.7 7.5 - - + +
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Residues in contact with ASP 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 LYS* 2.9 47.2 + - - +
510A ALA* 4.0 6.8 - - - +
512A LEU* 1.4 77.1 - - - +
514A LYS* 1.3 60.0 + - - +
516A THR* 3.4 9.1 + - - -
517A TRP* 3.0 26.2 + - - +
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Residues in contact with LYS 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 ALA 3.0 18.0 + - - +
511A ALA* 3.7 9.2 - - - +
512A LEU 3.3 0.2 - - - -
513A ASP* 1.3 74.6 - - - +
515A ILE* 1.3 60.9 + - - +
517A TRP* 3.4 21.8 + - + +
518A ALA* 2.9 24.9 + - - +
528A ASP* 4.7 6.9 + - - +
533A LYS* 5.9 2.4 - - - +
534A LEU* 3.8 36.1 - - + +
537A ASP* 5.2 3.4 + - - -
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Residues in contact with ILE 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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511A ALA 3.4 9.4 + - - +
512A LEU* 3.2 14.8 + - + +
514A LYS* 1.3 75.8 - - - +
516A THR* 1.3 55.6 + - - +
518A ALA* 3.4 1.8 + - - +
519A ALA* 2.9 27.7 + - - +
531A LEU* 4.0 5.5 - - + +
534A LEU* 3.9 30.1 - - + +
535A CYS* 4.0 18.8 - - - -
538A ALA* 3.6 31.0 - - + -
548A MET* 4.1 12.6 - - + +
551A ALA* 3.9 10.8 - - + -
552A LEU* 3.5 34.1 - - + +
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Residues in contact with THR 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 LEU 3.3 12.7 + - - -
513A ASP* 3.8 12.0 + - - -
515A ILE* 1.3 71.1 - - - +
517A TRP* 1.3 65.0 + - - +
519A ALA* 3.3 5.7 + - - +
520A GLY* 3.0 19.6 + - - -
551A ALA* 2.9 32.5 + - - +
554A LYS* 4.0 22.2 + - + +
555A VAL* 3.8 14.4 - - + +
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Residues in contact with TRP 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 ASP 3.0 19.0 + - - +
514A LYS* 3.7 28.3 - - + +
516A THR* 1.3 74.6 - - - +
518A ALA* 1.4 74.1 + - + +
520A GLY* 3.1 2.3 + - - -
521A ASN* 2.9 63.0 + - + +
526A ASP* 5.1 1.3 - - - -
528A ASP 5.7 0.4 - - - -
529A ARG* 3.7 60.3 - - + -
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Residues in contact with ALA 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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219A ARG* 3.0 16.7 + - - -
514A LYS 2.9 9.2 + - - +
515A ILE 4.0 2.2 - - - +
517A TRP* 1.4 85.6 - - + +
519A ALA* 1.4 61.4 + - - +
521A ASN 3.2 19.6 + - - +
522A PRO* 4.1 0.2 - - - +
529A ARG* 3.4 32.3 - - + +
531A LEU* 4.0 4.0 - - + -
534A LEU* 3.5 22.0 - - + -
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Residues in contact with ALA 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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219A ARG* 2.8 29.8 + - - +
515A ILE 2.9 13.7 + - - +
516A THR* 3.3 10.7 + - - +
518A ALA* 1.4 74.7 - - - +
520A GLY* 1.4 59.3 + - - +
522A PRO* 4.1 0.9 - - - +
531A LEU* 3.9 3.9 - - - +
552A LEU* 4.2 15.5 - - + -
555A VAL* 3.6 20.0 - - + +
556A PHE* 3.8 24.5 - - + -
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Residues in contact with GLY 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 THR 3.0 14.2 + - - -
517A TRP 3.6 2.5 - - - -
519A ALA* 1.4 74.9 - - - +
521A ASN* 1.4 67.2 + - - +
522A PRO* 3.7 6.2 - - - +
555A VAL* 3.8 19.0 - - - +
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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