Contacts of the helix formed by residues 515 - 527 (chain A) in PDB entry 5ED1
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 515 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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451A CYS* 3.5 19.2 + - - -
452A GLY* 3.6 14.8 - - - -
481A ARG* 2.8 22.9 + - - +
483A LYS* 3.8 10.5 - - - +
490A THR* 4.5 6.1 - - - -
513A THR 3.4 1.5 + - - -
514A MET* 1.3 78.1 - - - +
516A CYS* 1.3 66.3 + - - +
518A ASP* 3.1 32.1 + - - +
519A LYS* 3.1 18.5 + - - +
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Residues in contact with CYS 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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394A HIS* 3.4 13.2 - - - -
396A GLU* 3.3 27.1 - - + +
397A ILE* 3.7 9.9 - - + -
450A PRO* 3.8 10.5 - - + -
451A CYS* 3.4 4.6 - - - -
483A LYS* 3.3 18.4 - - - +
515A SER* 1.3 72.2 - - - +
517A SER* 1.3 66.7 + - - +
519A LYS* 3.1 7.0 + - - +
520A ILE* 2.9 29.3 + - - +
802A ZN 2.3 35.9 - - - -
12B 8AZ 3.2 4.7 - - - +
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Residues in contact with SER 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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450A PRO* 2.9 26.8 + - - +
451A CYS 2.9 12.1 + - - -
453A ASP 3.3 15.9 + - - -
454A ALA* 3.1 22.5 + - - +
515A SER* 4.0 0.4 - - - -
516A CYS* 1.3 77.1 - - - +
518A ASP* 1.3 61.3 - - - +
521A ALA* 3.0 29.5 + - - +
559A ALA* 4.4 1.6 - - - -
560A MET* 3.7 19.5 - - - +
563A ARG* 3.5 9.7 + - - -
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Residues in contact with ASP 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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453A ASP 4.8 2.1 + - - -
479A GLN 4.4 1.6 - - - +
480A LEU* 3.3 27.0 - - + +
481A ARG 2.6 37.4 + - - +
514A MET* 3.5 7.2 - - + +
515A SER* 3.1 16.0 + - - +
516A CYS 3.2 0.4 - - - -
517A SER* 1.3 79.0 - - - +
519A LYS* 1.3 57.9 + - - +
521A ALA* 3.4 3.9 + - - +
522A ARG* 3.0 22.3 + - - +
563A ARG* 3.0 28.0 + - - +
679A PHE* 5.0 0.3 - - - -
687A TRP* 3.3 21.9 - - + -
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Residues in contact with LYS 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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392A ASP* 3.0 20.7 + - - +
397A ILE* 3.6 25.2 - - + +
483A LYS* 4.7 0.2 - - - +
513A THR* 4.2 0.9 - - - -
514A MET* 3.5 32.5 - - + +
515A SER 3.1 15.3 + - - +
516A CYS 3.1 6.7 + - - +
518A ASP* 1.3 77.9 - - - +
520A ILE* 1.3 55.7 + - - +
522A ARG* 3.1 8.8 - - - +
523A TRP* 2.9 41.5 + - - +
687A TRP* 4.1 11.4 - - + -
801A IHP 2.9 63.3 + - - +
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Residues in contact with ILE 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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396A GLU* 4.6 5.4 - - + -
397A ILE* 5.6 0.2 - - + -
444A LEU* 4.2 9.2 - - + -
446A ILE* 3.9 19.1 - - + -
450A PRO* 3.8 28.9 - - + -
516A CYS* 2.9 22.1 + - - +
517A SER 3.9 2.5 - - - +
519A LYS* 1.3 72.6 - - + +
521A ALA* 1.3 67.4 + - - +
523A TRP* 2.9 38.1 + - + +
524A ASN* 2.9 23.8 + - - +
542A PHE* 5.6 1.6 - - + -
545A ILE* 3.8 16.2 - - + -
560A MET* 3.5 24.2 - - - -
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Residues in contact with ALA 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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517A SER 3.0 18.3 + - - +
518A ASP 3.5 5.8 - - - +
520A ILE* 1.3 74.6 - - - +
522A ARG* 1.3 59.6 + - - +
524A ASN* 2.8 21.5 + - - +
525A VAL* 3.2 15.5 + - - +
559A ALA 3.5 19.5 - - - +
560A MET* 3.7 18.4 - - - +
563A ARG* 3.9 6.3 - - - +
564A ILE* 4.7 6.0 - - + +
675A LEU* 5.0 1.6 - - - -
679A PHE* 4.2 14.4 - - + -
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Residues in contact with ARG 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 ASP 3.0 13.9 + - - +
519A LYS* 3.1 17.3 - - - +
521A ALA* 1.3 75.9 - - - +
523A TRP* 1.3 64.9 + - + +
525A VAL* 2.9 4.2 + - - +
526A VAL* 2.9 41.5 + - + +
668A TYR* 4.2 6.8 + - - -
672A LYS* 3.6 15.8 - - + +
675A LEU* 3.6 30.5 - - + +
676A PHE* 4.3 13.3 - - - -
679A PHE* 5.5 0.2 - - - -
687A TRP* 3.4 40.7 - - + +
801A IHP 2.8 63.8 + - - -
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Residues in contact with TRP 523 (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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396A GLU* 3.7 26.5 - - + -
397A ILE* 4.0 22.0 - - + -
400A ARG* 3.3 43.2 - - + +
444A LEU* 3.6 24.9 - - + -
519A LYS* 2.9 33.5 + - + +
520A ILE* 2.9 34.6 + - + +
522A ARG* 1.3 87.8 - - - +
524A ASN* 1.3 60.6 + - - +
525A VAL 3.1 0.7 + - - -
526A VAL* 5.6 0.4 - - + -
527A GLY* 3.0 40.7 + - - -
528A ILE* 3.8 17.4 + - + +
541A TYR* 3.4 5.9 - - - -
542A PHE* 3.8 23.6 - + + -
801A IHP 5.2 3.8 + - - -
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Residues in contact with ASN 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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520A ILE* 2.9 16.9 + - - +
521A ALA 2.8 11.9 + - - +
523A TRP* 1.3 77.9 - - - +
525A VAL* 1.3 60.6 + - - +
541A TYR* 3.8 3.7 - - - -
542A PHE* 4.6 8.0 + - - +
545A ILE* 4.0 15.4 - - - +
560A MET* 3.1 37.3 + - - +
575A THR 3.2 1.7 - - - +
576A LEU* 3.7 3.0 - - + +
577A ASN* 2.8 70.8 + - - +
579A PRO* 3.9 8.0 - - - +
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Residues in contact with VAL 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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521A ALA 3.2 8.2 + - - +
522A ARG 2.9 8.0 + - - +
523A TRP 3.0 0.2 - - - -
524A ASN* 1.3 85.4 - - - +
526A VAL* 1.3 61.6 + - + +
527A GLY 3.3 1.6 - - - -
541A TYR* 2.8 21.8 + - - -
564A ILE* 4.0 4.7 - - + -
567A ILE* 3.7 25.6 - - + -
570A LEU* 3.8 20.4 - - + -
574A TYR* 3.5 7.1 - - - +
575A THR 3.5 6.8 + - - +
576A LEU* 3.7 22.2 - - + -
671A ALA* 4.4 10.3 - - + +
675A LEU* 3.8 24.7 - - + -
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Residues in contact with VAL 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 ARG* 2.9 37.7 + - + +
523A TRP* 5.6 0.4 - - + -
525A VAL* 1.3 77.9 - - + +
527A GLY* 1.3 65.4 - - - +
529A GLN* 3.1 20.4 + - - -
539A PRO* 4.6 0.9 - - - +
541A TYR* 4.5 0.7 - - - -
574A TYR* 3.3 19.4 - - - -
668A TYR* 3.3 35.6 - - + +
671A ALA* 3.7 10.5 - - + +
672A LYS* 3.5 41.5 - - + +
675A LEU* 5.0 2.5 - - + -
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Residues in contact with GLY 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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400A ARG* 5.6 0.3 + - - -
523A TRP* 3.0 33.7 + - - +
525A VAL 3.3 2.0 + - - -
526A VAL* 1.3 89.5 - - - +
528A ILE* 1.3 62.0 + - - -
529A GLN* 3.3 8.5 - - - -
530A GLY 4.5 2.6 + - - -
539A PRO* 5.0 0.7 - - - -
540A ILE 3.3 13.5 - - - -
541A TYR* 3.7 9.8 - - - -
668A TYR* 4.9 0.2 + - - -
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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
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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