Contacts of the helix formed by residues 515 - 527 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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451D CYS* 3.9 1.1 - - - -
452D GLY* 3.6 26.4 - - - -
481D ARG* 3.0 20.3 + - - +
483D LYS* 3.9 9.6 - - - +
490D THR* 3.8 14.1 - - - -
513D THR 3.5 1.2 + - - -
514D MET* 1.3 78.2 - - - +
516D CYS* 1.3 60.1 + - - +
517D SER 3.6 2.1 + - - -
518D ASP* 3.0 30.7 + - - +
519D LYS* 3.0 23.6 + - - +
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Residues in contact with CYS 516 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394D HIS* 3.4 8.1 - - - -
396D GLU* 3.6 33.0 - - + +
397D ILE* 3.7 10.8 - - + -
450D PRO* 4.0 7.9 - - + -
451D CYS* 3.4 6.3 - - - -
483D LYS* 3.4 15.9 - - - +
515D SER* 1.3 71.1 - - - +
517D SER* 1.3 60.7 + - - +
519D LYS* 4.3 5.8 - - - +
520D ILE* 2.8 37.9 + - - +
802D ZN 2.3 35.7 - - - -
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Residues in contact with SER 517 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450D PRO* 3.2 4.0 + - - +
451D CYS 2.7 24.6 + - - -
453D ASP* 3.5 17.7 - - - -
454D ALA* 2.9 34.8 + - - +
515D SER* 3.3 2.4 - - - -
516D CYS* 1.3 75.6 - - - +
518D ASP* 1.3 57.3 + - - +
520D ILE 3.6 0.2 + - - -
521D ALA* 3.0 23.9 + - - +
559D ALA* 4.4 0.2 - - - -
560D MET* 3.7 16.4 - - - +
563D ARG* 3.2 18.7 + - - -
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Residues in contact with ASP 518 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453D ASP 4.9 2.3 + - - -
479D GLN 4.6 0.9 - - - +
480D LEU* 3.3 17.9 - - + +
481D ARG 2.9 33.4 + - - +
514D MET* 3.3 6.2 - - + +
515D SER* 3.0 18.9 + - - +
516D CYS 3.1 0.4 - - - -
517D SER* 1.3 77.5 - - - +
519D LYS* 1.3 65.1 + - - +
521D ALA* 3.3 4.5 + - - +
522D ARG 2.9 18.0 + - - -
563D ARG* 2.8 29.2 + - - +
679D PHE* 5.1 0.4 - - - -
687D TRP* 3.4 30.7 - - + -
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Residues in contact with LYS 519 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392D ASP* 3.2 19.4 + - - +
397D ILE* 3.5 25.7 - - + +
513D THR* 4.1 0.9 - - - -
514D MET* 3.6 32.3 - - + +
515D SER 3.0 17.0 + - - +
516D CYS 3.9 3.1 - - - +
518D ASP* 1.3 75.9 - - - +
520D ILE* 1.3 59.1 + - - +
522D ARG* 3.0 10.5 + - - +
523D TRP* 2.8 42.6 + - + +
687D TRP* 4.0 12.3 - - + -
801D IHP 2.6 66.2 + - - +
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Residues in contact with ILE 520 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396D GLU* 4.3 8.3 - - + -
444D LEU* 4.2 10.8 - - + -
446D ILE* 3.9 18.8 - - + -
450D PRO* 3.9 26.7 - - + -
516D CYS* 2.8 21.1 + - + +
517D SER 3.9 3.1 - - - +
519D LYS* 1.3 76.2 - - - +
521D ALA* 1.3 57.3 + - - +
523D TRP* 3.1 34.4 + - + +
524D ASN* 2.9 28.0 + - - +
542D PHE* 5.9 1.8 - - + -
545D ILE* 3.8 18.4 - - + -
560D MET* 3.4 23.8 - - - -
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Residues in contact with ALA 521 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517D SER 3.0 10.9 + - - +
518D ASP 3.5 8.3 - - - +
520D ILE* 1.3 75.7 - - - +
522D ARG* 1.3 54.7 + - - +
524D ASN* 2.8 23.4 + - - +
525D VAL* 3.1 14.4 + - - +
559D ALA 3.6 23.0 + - - +
560D MET* 3.8 17.4 - - - +
563D ARG* 4.1 6.5 - - - +
564D ILE* 4.4 17.0 - - + +
675D LEU* 4.9 2.7 - - - -
679D PHE* 4.4 6.5 - - + -
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Residues in contact with ARG 522 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518D ASP 2.9 13.6 + - - +
519D LYS* 3.0 14.8 + - - +
521D ALA* 1.3 75.9 - - - +
523D TRP* 1.3 66.8 + - - +
525D VAL* 3.0 3.1 + - - +
526D VAL* 2.8 41.1 + - + +
668D TYR* 3.8 7.2 + - - -
672D LYS* 3.6 14.0 - - - +
675D LEU* 3.6 31.3 - - + +
676D PHE* 4.0 17.2 - - - -
687D TRP* 3.8 40.0 - - + +
801D IHP 2.7 66.2 + - - -
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Residues in contact with TRP 523 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396D GLU* 3.6 25.8 - - + -
397D ILE* 3.9 29.2 - - + -
400D ARG* 3.4 44.9 - - + +
444D LEU* 4.2 13.0 - - + -
519D LYS* 2.8 33.1 + - + +
520D ILE* 3.1 35.2 + - + +
522D ARG* 1.3 86.2 - - + +
524D ASN* 1.3 61.6 + - - +
525D VAL 3.0 0.2 - - - -
526D VAL* 5.2 0.4 - - + -
527D GLY* 3.0 40.4 + - - +
528D ILE* 3.8 15.8 + - + +
541D TYR* 3.5 7.1 - - - -
542D PHE* 4.1 18.5 + + + -
668D TYR* 6.1 0.2 - - - -
801D IHP 5.2 3.9 + - - -
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Residues in contact with ASN 524 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520D ILE* 2.9 16.0 + - - +
521D ALA 2.8 12.5 + - - +
523D TRP* 1.3 78.5 - - - +
525D VAL* 1.3 59.4 + - - +
541D TYR* 3.9 3.1 - - - -
542D PHE* 4.7 7.4 + - - +
545D ILE* 4.1 14.8 - - - +
560D MET* 3.0 39.2 + - - +
575D THR 3.3 1.2 - - - +
576D LEU* 3.7 3.0 - - + +
577D ASN* 2.8 72.2 + - - +
579D PRO* 3.8 6.2 - - - +
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Residues in contact with VAL 525 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521D ALA 3.1 7.4 + - - +
522D ARG 3.0 5.8 + - - +
524D ASN* 1.3 85.2 - - - +
526D VAL* 1.3 71.4 + - + +
527D GLY 3.3 1.3 - - - -
541D TYR* 2.9 21.3 + - - -
564D ILE* 4.2 4.0 - - + -
567D ILE* 3.8 28.5 - - + -
570D LEU* 3.8 19.3 - - + -
574D TYR* 3.6 8.8 - - - +
575D THR 3.6 4.8 - - - +
576D LEU* 3.6 25.1 - - + -
671D ALA* 4.5 4.3 - - + +
675D LEU* 4.1 19.7 - - + -
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Residues in contact with VAL 526 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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522D ARG* 2.8 36.5 + - + +
523D TRP* 4.5 1.1 - - + -
525D VAL* 1.3 77.6 - - + +
527D GLY* 1.3 64.5 + - - +
529D GLN* 3.3 21.3 + - - -
539D PRO* 4.5 0.7 - - - +
541D TYR* 4.6 0.7 - - - -
574D TYR* 3.6 15.8 - - - -
668D TYR* 3.3 36.9 - - + +
671D ALA* 3.8 10.8 - - + -
672D LYS* 3.8 37.2 - - + +
675D LEU* 4.7 7.4 - - + -
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Residues in contact with GLY 527 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400D ARG* 5.4 0.2 + - - -
523D TRP* 3.0 35.2 + - - +
525D VAL 3.3 2.6 + - - -
526D VAL* 1.3 88.5 - - - +
528D ILE* 1.3 61.7 + - - -
529D GLN* 3.4 8.0 + - - -
530D GLY 4.5 2.9 + - - -
539D PRO* 5.0 0.7 - - - -
540D ILE 3.1 15.5 - - - -
541D TYR* 3.8 8.6 - - - -
668D TYR* 4.7 0.9 + - - -
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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