Contacts of the helix formed by residues 665 - 682 (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 ALA 665 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531A SER* 3.3 15.7 - - - +
534A SER* 3.3 26.7 - - - +
535A ILE* 3.9 12.3 - - + +
650A SER* 4.8 2.7 - - - -
661A SER 4.0 0.6 + - - -
662A LYS 2.9 15.1 + - - +
663A LEU 3.9 2.7 - - - -
664A ALA* 1.3 73.5 - - - +
666A LYS* 1.3 64.2 + - - +
667A GLU 3.3 2.7 - - - -
668A TYR* 3.1 8.4 + - + -
669A GLN* 3.0 21.4 + - - +
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Residues in contact with LYS 666 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650A SER* 4.7 3.9 + - - +
652A ILE* 5.3 14.8 - - + -
663A LEU 4.1 9.0 - - - +
664A ALA 2.9 12.3 + - - +
665A ALA* 1.3 70.4 - - - +
667A GLU* 1.3 61.2 + - + +
669A GLN* 3.2 8.5 - - - +
670A ALA* 3.0 27.1 + - - +
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Residues in contact with GLU 667 (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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571A PRO* 3.5 16.4 - - + +
572A PRO* 3.8 34.1 - - - +
574A TYR* 4.3 12.4 - - + +
649A ARG* 3.9 22.9 + - - +
665A ALA 3.3 1.0 - - - -
666A LYS* 1.3 76.2 - - + +
668A TYR* 1.3 60.1 + - - +
670A ALA* 3.0 9.9 + - - +
671A ALA* 2.9 24.8 + - - +
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Residues in contact with TYR 668 (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* 4.2 3.1 + - - -
526A VAL* 3.3 49.0 - - + +
527A GLY 4.9 0.2 + - - -
529A GLN* 3.5 17.0 - - - -
530A GLY* 3.5 20.2 - - - -
531A SER* 3.4 34.1 - - - -
534A SER* 3.6 13.0 + - - +
574A TYR* 3.4 18.6 + - - +
665A ALA* 3.1 11.0 + - + +
667A GLU* 1.3 78.1 - - - +
669A GLN* 1.3 66.3 + - - +
671A ALA* 3.1 2.9 + - - +
672A LYS* 2.9 40.5 + - + +
801A IHP 2.7 29.5 + - - -
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Residues in contact with GLN 669 (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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531A SER* 4.2 13.1 - - - -
662A LYS* 3.2 32.7 + - - +
663A LEU* 3.8 29.1 - - + +
665A ALA 3.0 10.4 + - - +
666A LYS* 3.2 13.9 - - + +
668A TYR* 1.3 77.6 - - - +
670A ALA* 1.3 57.6 + - - +
672A LYS* 2.8 47.6 + - - +
673A ALA* 3.0 26.0 + - - +
801A IHP 5.3 1.6 + - - -
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Residues in contact with ALA 670 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571A PRO* 3.9 14.6 - - + -
666A LYS 3.0 12.9 + - - +
667A GLU* 3.0 11.9 + - - +
669A GLN* 1.3 73.1 - - - +
671A ALA* 1.3 60.1 + - - +
673A ALA* 3.2 8.2 + - - +
674A ARG* 2.9 46.7 + - - +
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Residues in contact with ALA 671 (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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525A VAL* 4.4 0.7 - - - +
526A VAL* 3.7 13.0 - - + +
570A LEU* 4.3 11.3 - - + +
571A PRO* 3.8 12.7 - - + +
574A TYR* 3.5 38.6 - - + -
667A GLU 2.9 9.9 + - - +
668A TYR 3.5 7.9 - - - +
670A ALA* 1.3 74.6 - - - +
672A LYS* 1.3 64.0 + - - +
674A ARG* 3.1 5.2 + - - +
675A LEU* 2.9 22.2 + - - +
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Residues in contact with LYS 672 (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* 3.6 20.6 - - - +
526A VAL* 3.5 14.5 - - + +
663A LEU* 6.0 0.6 - - - +
668A TYR* 2.9 22.6 + - + +
669A GLN* 2.8 37.1 + - - +
670A ALA 3.3 0.2 - - - -
671A ALA* 1.3 76.5 - - - +
673A ALA* 1.3 57.1 + - - +
675A LEU* 3.2 8.8 - - + +
676A PHE* 3.0 60.9 + - + -
689A GLU* 4.2 8.2 + - - -
801A IHP 2.5 35.9 + - - +
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Residues in contact with ALA 673 (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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669A GLN 3.0 14.2 + - - +
670A ALA* 3.2 9.8 + - - +
672A LYS* 1.3 74.6 - - - +
674A ARG* 1.3 80.8 + - - +
676A PHE* 3.3 10.2 + - - +
677A THR* 3.0 28.7 + - - +
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Residues in contact with ARG 674 (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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567A ILE* 4.0 6.9 - - + +
568A GLU* 3.1 28.4 + - - +
569A ASP* 3.3 33.2 + - - +
570A LEU* 3.6 19.1 - - + -
571A PRO* 4.8 1.8 - - + +
670A ALA* 2.9 39.4 + - - +
671A ALA 3.1 7.4 + - - +
673A ALA* 1.3 88.1 - - - +
675A LEU* 1.3 58.2 + - - +
677A THR* 3.4 8.1 + - - -
678A ALA* 2.9 28.9 + - - +
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Residues in contact with LEU 675 (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* 3.6 43.3 - - + +
525A VAL* 3.8 22.2 - - + -
526A VAL* 5.0 4.3 - - + -
564A ILE* 3.7 20.0 - - + -
567A ILE* 3.9 7.6 - - + +
671A ALA 2.9 12.5 + - - +
672A LYS* 3.2 10.3 - - + +
674A ARG* 1.3 77.5 - - - +
676A PHE* 1.3 80.0 + - + +
678A ALA* 3.0 13.0 + - - +
679A PHE* 3.0 41.2 + - + -
687A TRP* 4.5 5.4 - - + -
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Residues in contact with PHE 676 (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* 4.3 6.5 - - - -
672A LYS* 3.0 46.7 + - + +
673A ALA* 3.3 8.0 + - - +
675A LEU* 1.3 88.5 - - + +
677A THR* 1.3 65.0 + - - +
679A PHE* 3.2 7.1 + + - +
680A ILE* 2.9 33.7 + - + +
685A GLY 5.0 0.2 - - - +
687A TRP* 3.3 65.5 - + + +
689A GLU* 3.7 23.6 - - - -
801A IHP 5.6 0.4 - - - -
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Residues in contact with THR 677 (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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568A GLU* 6.4 1.6 - - + -
673A ALA* 3.0 17.5 + - - +
674A ARG* 3.8 8.6 + - - +
676A PHE* 1.3 76.7 - - - +
678A ALA* 1.3 63.0 + - - +
680A ILE* 3.2 9.7 + - + +
681A LYS* 2.8 60.6 + - + +
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Residues in contact with ALA 678 (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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564A ILE* 3.8 20.0 - - + -
566A ASN* 3.4 19.7 + - - +
567A ILE* 4.0 25.6 - - + +
674A ARG 2.9 15.0 + - - +
675A LEU 3.0 9.4 + - - +
677A THR* 1.3 76.0 - - - +
679A PHE* 1.3 63.9 + - - +
681A LYS* 5.1 0.4 - - - -
682A ALA* 3.0 25.8 + - - +
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Residues in contact with PHE 679 (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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480A LEU* 3.6 40.4 - - + -
518A ASP 5.0 0.4 - - - -
521A ALA* 4.2 12.1 - - + -
563A ARG* 3.6 32.3 - - - -
564A ILE* 3.6 29.6 - - + +
675A LEU* 3.0 48.8 + - + -
676A PHE* 3.2 7.4 + - - +
678A ALA* 1.3 78.3 - - - +
680A ILE* 1.3 56.1 + - - +
682A ALA* 3.5 1.6 + - - -
683A GLY 3.4 2.3 + - - -
684A LEU* 2.7 48.2 + - + +
685A GLY 3.7 15.0 - - - +
687A TRP* 4.3 12.8 - + - +
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Residues in contact with ILE 680 (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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494A ARG* 5.2 1.4 + - - -
676A PHE* 2.9 27.5 + - + +
677A THR* 3.7 8.3 - - + +
679A PHE* 1.3 76.3 - - - +
681A LYS* 1.3 61.4 + - + +
683A GLY* 2.7 27.5 + - - -
684A LEU 4.6 0.2 - - - +
685A GLY 3.9 18.6 - - - +
686A ALA* 3.9 22.9 - - + -
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Residues in contact with LYS 681 (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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566A ASN* 4.2 13.5 - - - +
568A GLU* 4.5 16.1 + - - +
677A THR* 2.8 43.5 + - + +
678A ALA* 5.1 0.4 - - - -
680A ILE* 1.3 74.0 - - + +
682A ALA* 1.3 56.1 + - - +
683A GLY 3.0 9.0 + - - -
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Residues in contact with ALA 682 (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 LYS* 5.3 0.3 + - - -
563A ARG 3.9 20.6 - - - +
566A ASN* 3.7 14.5 - - - +
678A ALA 3.0 19.3 + - - +
679A PHE* 3.9 3.6 - - - +
680A ILE 3.2 0.2 - - - -
681A LYS* 1.3 74.0 - - - +
683A GLY* 1.3 61.2 + - - +
684A LEU* 3.3 20.2 + - + +
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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
------------------------------------------------------------
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