Contacts of the helix formed by residues 664 - 684 (chain A) in PDB entry 3HR4
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 GLY 664 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660A ASP 3.8 0.2 + - - -
661A GLU 5.1 1.0 + - - -
662A LEU 3.8 4.2 + - - -
663A SER* 1.3 76.9 - - - +
665A GLN* 1.3 67.6 + - - +
666A GLU 3.5 1.8 - - - -
667A ASP* 3.6 21.4 + - - +
668A ALA* 3.2 18.5 + - - +
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Residues in contact with GLN 665 (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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549A LYS* 3.3 17.9 - - - +
553A LEU* 4.7 6.5 - - + +
624A PHE* 5.4 0.4 - - + -
626A LEU* 3.3 31.7 - - + +
627A GLY 3.6 4.6 + - - -
659A GLY* 3.0 42.6 + - - +
660A ASP 3.8 5.5 + - - +
661A GLU* 3.4 23.3 + - - +
663A SER 3.7 1.0 + - - -
664A GLY* 1.3 69.6 - - - +
666A GLU* 1.3 67.5 + - + +
668A ALA* 2.8 7.3 + - - +
669A PHE* 2.7 23.0 + - - +
999A FMN 3.4 20.6 + - - -
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Residues in contact with GLU 666 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553A LEU* 4.0 20.8 - - + +
556A ASP* 4.3 9.2 - - - +
664A GLY 3.5 0.2 - - - -
665A GLN* 1.3 77.3 - - + +
667A ASP* 1.3 67.3 + - - +
669A PHE* 2.7 20.2 + - - -
670A ARG* 2.7 69.6 + - - +
697A LEU* 5.6 0.5 - - - +
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Residues in contact with ASP 667 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664A GLY* 3.6 21.7 + - - +
665A GLN 3.2 0.4 + - - -
666A GLU* 1.3 77.4 - - - +
668A ALA* 1.3 63.2 + - - +
670A ARG* 3.7 14.8 + - - +
671A SER* 3.0 24.4 + - - -
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Residues in contact with ALA 668 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624A PHE* 4.0 4.7 - - + -
658A GLU 3.6 25.8 - - - +
659A GLY* 3.9 5.8 - - - -
660A ASP 5.2 0.4 - - - +
663A SER 5.4 1.1 - - - +
664A GLY 3.2 9.0 + - - +
665A GLN 2.8 9.6 + - - +
667A ASP* 1.3 76.0 - - - +
669A PHE* 1.3 70.1 + - - +
671A SER* 3.0 9.4 + - - -
672A TRP* 2.9 18.7 + - - +
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Residues in contact with PHE 669 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553A LEU* 3.0 66.6 - - + -
556A ASP* 3.8 14.4 - - + -
557A LEU* 4.0 16.6 - - + -
589A VAL* 4.5 11.7 - - + -
624A PHE* 3.3 42.0 - + + -
665A GLN 2.7 10.6 + - - +
666A GLU* 2.7 13.2 + - - +
668A ALA* 1.3 75.1 - - - +
670A ARG* 1.3 68.8 + - + +
672A TRP* 2.7 12.0 + + - +
673A ALA* 2.6 45.5 + - + +
698A TYR* 3.9 11.0 - + - -
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Residues in contact with ARG 670 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
666A GLU* 2.7 78.5 + - - +
667A ASP* 4.0 13.8 + - - +
669A PHE* 1.3 77.8 - - + +
671A SER* 1.3 62.5 + - - +
673A ALA* 3.9 8.7 - - - -
674A VAL* 2.9 31.5 + - + +
697A LEU* 3.7 50.1 + - - +
698A TYR* 4.1 18.8 - - + -
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Residues in contact with SER 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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667A ASP 3.0 16.2 + - - -
668A ALA* 3.1 13.2 - - - -
670A ARG* 1.3 75.3 - - - +
672A TRP* 1.3 57.9 + - - +
674A VAL* 4.0 3.6 - - - +
675A GLN* 2.9 35.2 + - - +
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Residues in contact with TRP 672 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A LEU* 3.8 32.5 - - + -
587A LEU* 4.8 4.5 - - + -
588A VAL 4.6 3.4 - - - -
589A VAL* 4.8 0.4 - - + -
622A ALA* 3.6 18.4 - - + -
623A VAL 3.2 37.1 + - - -
624A PHE* 3.6 35.9 - + + -
654A THR* 3.2 16.2 - - + +
655A PRO 3.0 28.2 + - - -
657A GLY* 3.6 14.4 - - - -
668A ALA 2.9 9.4 + - - +
669A PHE* 2.7 18.7 + + - +
671A SER* 1.3 70.0 - - - +
673A ALA* 1.3 70.5 + - - +
675A GLN* 3.3 20.8 - - - +
676A THR* 2.8 39.2 + - + +
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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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557A LEU* 3.9 14.1 - - + -
560A LEU* 3.5 10.9 - - + +
669A PHE* 2.6 25.0 + - + +
670A ARG* 3.5 9.2 - - - +
672A TRP* 1.3 76.2 - - - +
674A VAL* 1.3 62.5 + - - +
676A THR* 2.8 28.5 - - - +
677A PHE* 3.0 9.4 + - - +
698A TYR* 3.7 23.6 - - + -
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Residues in contact with VAL 674 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560A LEU* 4.1 6.7 - - + -
670A ARG 2.9 19.5 + - - +
671A SER* 4.0 4.0 - - - +
673A ALA* 1.3 76.0 - - - +
675A GLN* 1.3 62.9 + - - +
677A PHE* 3.1 6.8 + - + +
678A LYS* 3.0 25.5 + - + +
694A ILE* 4.2 18.4 - - + -
698A TYR* 3.5 40.8 - - + +
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Residues in contact with GLN 675 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654A THR* 3.5 21.3 + - - +
655A PRO* 4.8 6.6 - - - +
671A SER* 2.9 25.1 + - - +
672A TRP* 3.3 31.7 + - - +
674A VAL* 1.3 74.7 - - - +
676A THR* 1.3 62.2 + - - +
678A LYS* 3.5 6.2 + - - +
679A ALA* 3.2 22.7 + - - +
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Residues in contact with THR 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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557A LEU* 4.5 0.2 - - + -
561A PHE* 4.0 15.9 - - + -
587A LEU* 4.3 4.0 - - + +
622A ALA* 3.5 15.2 - - - +
653A LEU* 3.4 16.1 - - - +
654A THR* 3.4 32.2 - - - +
672A TRP* 2.8 37.2 + - + +
673A ALA* 2.8 30.7 - - - +
675A GLN* 1.3 74.4 - - - +
677A PHE* 1.3 57.1 + - - +
679A ALA* 3.6 1.5 + - - +
680A ALA* 3.1 21.5 + - - +
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Residues in contact with PHE 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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560A LEU* 3.5 41.1 - - + -
561A PHE* 3.5 21.8 - + + -
563A CYS* 4.3 9.2 - - + -
564A ALA* 4.3 7.2 - - + -
565A PHE* 3.5 31.9 - + - -
673A ALA 3.0 17.1 + - - +
674A VAL* 3.1 7.6 + - + +
676A THR* 1.3 75.1 - - - +
678A LYS* 1.3 71.2 + - + +
679A ALA 3.1 1.6 - - - -
680A ALA* 3.1 2.4 + - - +
681A CYS* 2.9 44.1 + - - -
689A LYS 5.9 0.7 - - - -
692A ILE* 4.4 9.2 - - + -
694A ILE* 3.7 28.5 - - + -
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Residues in contact with LYS 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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674A VAL* 3.0 18.6 + - + +
675A GLN* 4.1 6.5 - - - +
677A PHE* 1.3 84.0 - - + +
679A ALA* 1.3 61.2 + - - +
681A CYS* 3.7 6.4 + - + +
682A GLU* 3.4 18.4 + - - +
689A LYS* 4.2 32.8 - - + +
690A GLN* 4.3 22.9 - - - +
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Residues in contact with ALA 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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653A LEU* 3.1 30.1 - - + +
654A THR* 5.2 2.7 - - - +
675A GLN 3.2 16.8 + - - +
676A THR* 3.7 3.1 - - - +
677A PHE 3.1 0.2 - - - -
678A LYS* 1.3 77.1 - - - +
680A ALA* 1.3 63.4 + - - +
682A GLU* 3.0 15.6 + - - +
683A THR* 3.0 22.3 + - + +
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Residues in contact with ALA 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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561A PHE* 3.8 15.7 - - + -
565A PHE* 3.6 20.0 - - + -
585A LEU* 4.1 8.7 - - + -
653A LEU* 3.9 15.9 - - + +
676A THR 3.1 17.8 + - - +
677A PHE 3.1 4.2 + - - +
679A ALA* 1.3 70.5 - - - +
681A CYS* 1.3 62.5 + - - +
682A GLU 2.9 5.9 + - - -
683A THR* 4.7 1.3 - - - +
684A PHE* 3.2 35.4 + - + +
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Residues in contact with CYS 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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564A ALA* 4.2 2.2 - - - -
565A PHE* 3.9 8.7 - - - -
677A PHE* 2.9 54.6 + - - +
678A LYS* 3.9 7.0 - - + +
679A ALA 3.3 0.2 - - - -
680A ALA* 1.3 75.4 - - - +
682A GLU* 1.3 56.7 + - - +
685A ASP 4.3 0.2 - - - -
686A VAL* 2.8 57.9 + - + +
689A LYS* 3.7 26.5 - - + -
692A ILE* 5.0 5.2 - - - -
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Residues in contact with GLU 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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678A LYS 3.4 11.6 + - - +
679A ALA* 3.0 12.5 + - - +
680A ALA 2.9 2.4 - - - -
681A CYS* 1.3 78.3 - - - +
683A THR* 1.3 67.8 + - + +
684A PHE 3.0 2.0 + - - -
685A ASP* 3.1 18.0 + - - +
689A LYS* 3.0 33.5 + - + +
690E GLN* 5.8 0.2 - - - +
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Residues in contact with THR 683 (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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620A ARG* 3.1 41.4 + - - +
653A LEU* 4.2 14.8 - - + +
679A ALA* 3.0 19.4 + - + +
680A ALA* 4.8 0.4 - - - -
682A GLU* 1.3 78.4 - - + +
684A PHE* 1.3 70.8 + - - +
685A ASP* 3.8 2.4 + - - +
685E ASP* 4.7 4.2 - - - +
689E LYS* 3.4 30.7 + - - +
690E GLN* 5.8 2.5 - - - -
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Residues in contact with PHE 684 (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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537A VAL* 3.9 24.6 - - + +
565A PHE* 4.3 17.0 - + + -
584A ARG* 3.3 41.1 - - + -
585A LEU* 4.0 23.8 - - + -
620A ARG* 4.4 12.3 - - - -
653A LEU* 5.9 0.7 - - + -
680A ALA* 3.2 28.0 + - - +
681A CYS 4.3 0.2 - - - -
682A GLU 3.0 0.8 - - - -
683A THR* 1.3 89.2 - - - +
685A ASP* 1.3 75.5 + - - +
686A VAL* 3.6 4.5 - - + +
682E GLU 5.4 1.4 - - - +
685E ASP* 3.3 41.9 - - + +
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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
------------------------------------------------------------
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