Contacts of the helix formed by residues 664 - 678 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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662E LEU 4.4 0.2 - - - -
663E SER* 1.3 67.1 - - - +
665E GLN* 1.3 65.7 + - - -
666E GLU* 3.1 4.7 - - - -
667E ASP* 3.1 22.8 + - - +
668E ALA* 2.9 23.0 + - - +
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Residues in contact with GLN 665 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549E LYS* 4.0 16.6 - - - +
553E LEU* 5.1 8.0 - - + +
624E PHE* 4.3 1.8 - - + -
626E LEU* 3.5 30.5 - - + +
627E GLY 3.9 1.2 - - - +
659E GLY* 3.3 31.3 + - - -
660E ASP 3.3 14.8 + - - +
661E GLU* 3.8 17.1 - - - +
663E SER 2.5 10.8 + - - -
664E GLY* 1.3 70.7 - - - +
666E GLU* 1.3 58.4 + - + +
668E ALA* 3.4 2.7 - - - +
669E PHE* 2.9 30.4 + - - +
999E FMN 3.3 20.2 + - - -
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Residues in contact with GLU 666 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553E LEU* 3.2 30.0 - - - +
556E ASP* 5.4 4.0 - - - +
664E GLY* 3.1 1.1 - - - -
665E GLN* 1.3 77.2 - - + +
667E ASP* 1.3 68.8 + - - +
669E PHE* 3.0 9.3 + - - +
670E ARG* 2.8 63.7 + - - +
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Residues in contact with ASP 667 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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664E GLY* 3.1 21.0 + - - +
666E GLU* 1.3 77.1 - - - +
668E ALA* 1.3 63.6 + - - +
670E ARG* 3.2 17.4 + - - +
671E SER* 2.9 25.2 + - - -
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Residues in contact with ALA 668 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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624E PHE* 4.1 3.4 - - + -
658E GLU 3.7 23.3 - - - +
659E GLY* 4.4 2.0 - - - -
660E ASP 5.3 0.4 - - - +
663E SER 5.1 1.8 - - - +
664E GLY 2.9 11.9 + - - +
665E GLN* 3.4 12.6 - - - +
667E ASP* 1.3 77.2 - - - +
669E PHE* 1.3 64.1 + - - +
671E SER* 3.0 7.5 + - - -
672E TRP* 2.9 21.5 + - - +
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Residues in contact with PHE 669 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553E LEU* 3.3 59.0 - - + -
556E ASP* 4.3 4.7 - - + -
557E LEU* 4.1 13.5 - - + -
589E VAL* 4.9 4.5 - - + -
624E PHE* 3.4 38.0 - + + -
665E GLN 2.9 13.9 + - - +
666E GLU* 3.2 13.5 - - - +
668E ALA* 1.3 75.2 - - - +
670E ARG* 1.3 61.7 + - + +
672E TRP* 3.1 22.1 + + - +
673E ALA* 2.7 47.2 + - + +
698E TYR* 4.1 24.9 - + - -
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Residues in contact with ARG 670 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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666E GLU* 2.8 72.8 + - - +
667E ASP* 3.6 17.0 + - - +
669E PHE* 1.3 79.6 - - + +
671E SER* 1.3 56.8 + - - +
673E ALA* 3.7 0.5 - - - +
674E VAL* 2.8 37.6 + - - +
697E LEU* 3.1 49.1 + - - +
698E TYR* 3.9 26.7 - - + -
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Residues in contact with SER 671 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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667E ASP 2.9 13.1 + - - -
668E ALA* 3.2 12.3 - - - -
670E ARG* 1.3 78.7 - - - +
672E TRP* 1.3 62.5 + - - +
674E VAL* 3.7 5.8 + - - +
675E GLN* 3.6 21.3 + - - +
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Residues in contact with TRP 672 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557E LEU* 3.9 36.3 - - + -
587E LEU* 4.7 6.1 - - + -
588E VAL 4.7 3.4 - - - -
589E VAL* 5.0 0.9 - - + -
622E ALA* 3.6 13.5 - - + -
623E VAL* 3.4 36.4 + - - +
624E PHE* 3.5 40.4 - + + -
654E THR* 3.7 12.8 - - + +
655E PRO 3.3 26.3 + - - -
657E GLY* 3.7 14.6 - - - -
668E ALA 2.9 10.5 + - - +
669E PHE* 3.6 13.2 - + - +
671E SER* 1.3 74.3 - - - +
673E ALA* 1.3 80.2 + - + +
675E GLN* 3.5 13.0 - - - +
676E THR* 2.9 44.2 + - + +
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Residues in contact with ALA 673 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557E LEU* 3.7 23.8 - - + -
560E LEU* 3.8 13.7 - - + +
669E PHE* 2.7 34.5 + - + +
670E ARG* 3.7 4.0 - - - +
672E TRP* 1.3 76.6 - - + +
674E VAL* 1.3 66.8 + - - +
676E THR* 2.8 24.7 - - - +
677E PHE* 2.9 13.3 + - - +
698E TYR* 4.5 1.3 - - + -
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Residues in contact with VAL 674 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560E LEU* 4.3 7.4 - - + -
670E ARG 2.8 33.9 + - - +
671E SER* 4.0 6.5 - - - +
672E TRP 3.4 0.2 - - - -
673E ALA* 1.3 74.9 - - - +
675E GLN* 1.3 53.1 + - - +
677E PHE* 3.3 5.0 - - + +
678E LYS* 2.7 42.7 + - + +
694E ILE* 4.3 17.3 - - + -
698E TYR* 3.2 45.8 - - + +
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Residues in contact with GLN 675 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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654E THR* 3.7 17.4 + - - +
655E PRO* 5.0 4.9 - - - +
671E SER 3.6 11.5 + - - +
672E TRP* 3.5 17.3 - - - +
674E VAL* 1.3 81.4 - - - +
676E THR* 1.3 54.8 + - - +
678E LYS* 3.5 9.3 - - - -
679E ALA* 2.7 40.0 + - - +
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Residues in contact with THR 676 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557E LEU* 4.8 1.6 - - + -
561E PHE* 4.2 11.1 - - + -
587E LEU* 4.4 5.7 - - + +
622E ALA* 3.5 11.6 - - - +
653E LEU* 3.8 6.1 - - - +
654E THR* 2.9 36.4 - - - +
672E TRP* 2.9 37.9 + - + +
673E ALA* 2.8 32.1 - - - +
675E GLN* 1.3 77.5 - - - +
677E PHE* 1.3 56.9 + - - +
679E ALA* 3.5 6.0 - - - +
680E ALA* 3.2 21.7 + - - +
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Residues in contact with PHE 677 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560E LEU* 3.6 39.7 - - + -
561E PHE* 3.3 43.7 - + + -
563E CYS* 4.1 9.4 - - + -
564E ALA* 3.9 25.1 - - + -
565E PHE* 4.4 4.7 - + - -
673E ALA 2.9 17.0 + - - +
674E VAL* 3.3 5.4 - - + +
676E THR* 1.3 74.4 - - - +
678E LYS* 1.3 61.1 + - + +
679E ALA 2.7 5.7 + - - -
680E ALA* 2.6 22.5 + - - +
681E CYS* 3.1 34.6 + - - -
692E ILE* 4.3 15.0 - - + -
694E ILE* 4.0 17.7 - - + -
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Residues in contact with LYS 678 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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674E VAL* 2.7 27.7 + - + +
675E GLN* 3.5 10.1 - - - +
677E PHE* 1.3 81.4 - - + +
679E ALA* 1.3 55.5 + - - +
681E CYS* 4.3 9.5 - - + +
682E GLU* 4.2 31.6 + - - +
689E LYS 6.0 1.8 - - - +
690E GLN* 5.3 14.4 - - - +
692E ILE* 5.9 7.0 - - + -
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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