Contacts of the helix formed by residues 665 - 682 (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 ALA 665 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531D SER* 3.2 30.7 - - - +
534D SER* 3.5 14.1 - - - +
535D ILE* 4.0 11.6 - - + +
650D SER* 4.6 3.1 - - - -
661D SER 4.0 0.6 + - - -
662D LYS 3.1 12.6 + - - +
663D LEU 3.0 4.2 - - - -
664D ALA* 1.3 74.1 - - - +
666D LYS* 1.3 63.4 + - - +
667D GLU 3.4 2.9 - - - -
668D TYR* 3.3 7.2 + - + -
669D GLN* 3.0 23.7 + - - +
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Residues in contact with LYS 666 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650D SER* 4.4 7.1 + - - +
663D LEU 4.1 8.3 - - - +
664D ALA 2.8 12.3 + - - +
665D ALA* 1.3 70.0 - - - +
667D GLU* 1.3 62.1 + - + +
669D GLN* 3.3 8.0 + - - +
670D ALA* 3.0 26.6 + - - +
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Residues in contact with GLU 667 (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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571D PRO* 3.6 21.1 - - + +
572D PRO* 3.8 33.4 - - - +
573D LEU* 5.6 0.2 - - - +
574D TYR* 4.0 14.9 - - + +
649D ARG* 3.8 20.8 + - - +
665D ALA 3.4 0.4 - - - -
666D LYS* 1.3 78.8 - - + +
668D TYR* 1.3 66.8 + - - +
670D ALA* 3.1 8.6 + - - +
671D ALA* 2.9 20.3 + - - +
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Residues in contact with TYR 668 (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* 3.8 10.4 + - - -
523D TRP* 6.1 0.3 - - - -
526D VAL* 3.3 48.2 - - + +
527D GLY 4.7 1.0 + - - -
529D GLN* 3.6 17.0 - - - -
530D GLY* 3.5 20.9 + - - -
531D SER* 3.4 29.8 - - - -
534D SER* 3.7 16.5 + - - +
574D TYR* 3.4 16.0 + - - +
665D ALA* 3.3 11.9 + - + +
667D GLU* 1.3 77.6 - - - +
669D GLN* 1.3 64.7 + - - +
671D ALA* 3.1 5.4 + - - +
672D LYS* 2.9 33.8 + - + +
801D IHP 2.6 31.3 + - - -
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Residues in contact with GLN 669 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531D SER* 4.2 12.9 - - - -
662D LYS* 3.0 33.9 + - - +
663D LEU* 4.0 25.7 - - + +
665D ALA 3.0 13.5 + - - +
666D LYS* 3.3 13.0 - - - +
668D TYR* 1.3 77.1 - - - +
670D ALA* 1.3 56.3 + - - +
672D LYS* 2.9 46.8 + - - +
673D ALA* 3.0 27.3 + - - +
801D IHP 4.3 2.3 + - - -
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Residues in contact with ALA 670 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571D PRO* 4.2 11.7 - - + -
666D LYS 3.0 13.3 + - - +
667D GLU* 3.1 11.2 + - - +
669D GLN* 1.3 72.9 - - - +
671D ALA* 1.3 65.6 + - - +
673D ALA* 3.2 1.8 + - - -
674D ARG* 3.0 53.4 + - - +
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Residues in contact with ALA 671 (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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525D VAL* 4.5 1.3 - - + +
526D VAL* 3.8 14.1 - - + +
570D LEU* 4.3 12.3 - - + +
571D PRO* 4.0 16.5 - - + +
574D TYR* 3.8 28.5 - - + -
667D GLU 2.9 12.6 + - - +
668D TYR 3.4 8.3 - - - +
670D ALA* 1.3 74.1 - - - +
672D LYS* 1.3 64.8 + - - +
674D ARG* 3.1 5.4 + - - +
675D LEU* 2.9 22.0 + - - +
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Residues in contact with LYS 672 (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* 3.6 23.1 - - - +
526D VAL* 3.8 13.9 - - + +
668D TYR* 2.9 17.5 + - + +
669D GLN* 2.9 35.9 + - - +
671D ALA* 1.3 76.0 - - - +
673D ALA* 1.3 59.4 + - - +
675D LEU* 3.1 8.3 + - + +
676D PHE* 2.9 63.3 + - + -
689D GLU* 3.7 10.0 + - - -
801D IHP 2.9 34.5 + - - +
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Residues in contact with ALA 673 (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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669D GLN 3.0 13.9 + - - +
670D ALA* 3.2 3.3 + - - +
672D LYS* 1.3 75.7 - - - +
674D ARG* 1.3 89.4 + - - +
676D PHE* 3.4 10.6 + - - +
677D THR* 3.0 27.6 + - - +
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Residues in contact with ARG 674 (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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567D ILE* 3.9 6.3 - - + +
568D GLU* 3.6 27.1 + - - +
569D ASP* 3.8 29.1 + - - +
570D LEU* 3.9 16.4 - - + -
571D PRO* 5.2 1.0 - - + +
670D ALA* 3.0 35.8 + - - +
671D ALA 3.3 7.2 - - - +
673D ALA* 1.3 100.6 - - - +
675D LEU* 1.3 56.6 + - - +
677D THR* 3.4 9.4 + - - -
678D ALA* 2.8 28.8 + - - +
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Residues in contact with LEU 675 (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* 3.6 41.5 - - + +
525D VAL* 4.1 18.8 - - + -
526D VAL* 4.7 8.3 - - + -
564D ILE* 3.7 22.4 - - + -
567D ILE* 3.7 11.6 - - + +
671D ALA 2.9 11.8 + - - +
672D LYS* 3.2 10.3 - - + +
674D ARG* 1.3 73.6 - - - +
676D PHE* 1.3 83.6 + - + +
678D ALA* 3.0 4.2 + - - +
679D PHE* 3.0 54.1 + - + -
687D TRP* 4.8 1.3 - - + -
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Residues in contact with PHE 676 (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* 4.0 11.2 - - - -
672D LYS* 2.9 45.9 + - + -
673D ALA* 3.4 10.5 + - - +
675D LEU* 1.3 85.4 - - + +
677D THR* 1.3 64.2 + - - +
679D PHE* 3.2 9.8 + - - +
680D ILE* 3.0 29.0 + - + +
687D TRP* 3.3 61.1 + + + +
689D GLU* 3.5 28.5 - - + -
801D IHP 5.8 0.2 - - - -
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Residues in contact with THR 677 (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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568D GLU* 5.7 3.8 - - + +
673D ALA 3.0 18.2 + - - -
674D ARG* 3.5 11.3 + - - +
676D PHE* 1.3 74.6 - - - +
678D ALA* 1.3 64.9 + - - +
680D ILE* 3.9 6.5 - - - +
681D LYS* 2.9 56.6 + - + +
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Residues in contact with ALA 678 (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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564D ILE* 3.9 17.7 - - + -
566D ASN* 3.4 17.4 + - - +
567D ILE* 3.9 30.5 - - + +
674D ARG 2.8 14.2 + - - +
675D LEU* 3.0 10.5 + - - +
677D THR* 1.3 75.4 - - - +
679D PHE* 1.3 64.3 + - - +
682D ALA* 3.1 26.2 + - - +
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Residues in contact with PHE 679 (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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480D LEU* 3.5 32.5 - - + -
518D ASP 4.8 0.9 - - - -
521D ALA* 4.4 15.0 - - + -
563D ARG* 3.8 22.0 - - - -
564D ILE* 3.7 28.5 - - + -
675D LEU* 3.0 46.1 + - + -
676D PHE* 3.2 8.9 + - - +
678D ALA* 1.3 77.6 - - - +
680D ILE* 1.3 59.7 + - - +
682D ALA* 3.4 4.5 + - - +
684D LEU* 2.9 41.4 + - + +
685D GLY 3.7 12.8 - - - +
687D TRP* 3.9 30.3 - + + +
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Residues in contact with ILE 680 (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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676D PHE* 3.0 20.2 + - + +
677D THR* 3.2 7.4 + - + +
679D PHE* 1.3 75.8 - - - +
681D LYS* 1.3 66.1 + - + +
683D GLY* 2.8 23.0 + - - -
684D LEU 4.7 0.2 - - - +
685D GLY* 3.7 18.7 + - - +
686D ALA* 4.0 22.4 - - + -
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Residues in contact with LYS 681 (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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566D ASN* 4.1 13.4 + - - +
568D GLU* 4.3 16.9 + - - +
677D THR* 2.9 38.6 + - + +
678D ALA* 5.2 0.2 - - - -
680D ILE* 1.3 80.9 - - + +
682D ALA* 1.3 57.2 + - - +
683D GLY 3.0 3.9 + - - -
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Residues in contact with ALA 682 (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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475D LYS* 4.2 15.1 - - - +
563D ARG 3.9 17.7 - - - +
566D ASN* 3.8 12.9 - - - +
678D ALA 3.1 18.9 + - - +
679D PHE 3.8 0.7 - - - +
680D ILE 3.1 0.8 - - - -
681D LYS* 1.3 75.8 - - - +
683D GLY* 1.3 60.9 - - - +
684D LEU* 3.5 27.3 + - + +
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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