Contacts of the helix formed by residues 676 - 688 (chain D) in PDB entry 1RC5
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 676 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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672D ALA 3.8 11.0 - - - -
673D TYR* 2.6 28.5 + - - -
674D LEU 3.5 1.4 - - - -
675D ILE* 1.3 79.1 - - - +
677D GLU* 1.3 60.0 + - - +
678D GLU* 3.7 9.7 + - - +
679D PHE* 3.4 13.5 + - - +
680D PHE* 2.7 39.9 + - - +
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Residues in contact with GLU 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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676D SER* 1.3 73.8 - - - +
678D GLU* 1.3 57.2 + - - +
680D PHE* 4.3 6.3 - - - -
681D ASN* 2.8 38.7 + - - +
702D GLU* 2.8 45.3 - - + +
703D THR* 2.3 42.4 + - - -
706D GLY* 5.3 3.6 - - - -
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Residues in contact with GLU 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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673D TYR* 3.8 25.7 + - + +
676D SER* 3.0 9.3 + - - +
677D GLU* 1.3 81.7 - - - +
679D PHE* 1.3 59.6 + - - +
681D ASN* 3.2 5.0 + - - +
682D LEU* 2.9 27.6 + - + +
702D GLU* 5.2 8.1 - - - +
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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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673D TYR* 3.3 51.6 - + + +
674D LEU* 3.3 29.4 - - + +
676D SER* 3.4 4.3 + - - +
678D GLU* 1.3 77.2 - - - +
680D PHE* 1.3 63.0 + - - +
682D LEU* 2.8 40.4 + - + +
683D LEU* 3.0 38.8 + - + +
738D ASP* 4.6 4.0 - - + -
739D ILE* 4.1 28.5 - - + -
742D ALA* 3.7 31.0 - - + -
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Residues in contact with PHE 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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644D ASP 5.9 0.4 - - - -
647D VAL* 3.7 30.3 - - + -
648D ASN* 5.5 0.9 - - - -
651D ILE* 4.4 2.7 - - + -
674D LEU 3.5 12.1 - - - -
675D ILE* 3.3 37.7 - - + -
676D SER 2.7 26.6 + - - +
677D GLU* 3.9 6.1 - - - +
679D PHE* 1.3 75.8 - + - +
681D ASN* 1.3 62.2 + - - +
683D LEU* 2.9 17.6 + - + +
684D ALA* 2.9 13.5 + - - +
706D GLY* 4.1 19.7 - - - -
709D PHE* 4.1 22.7 - + + -
710D GLU* 3.5 42.0 - - + -
731D PHE* 6.0 0.2 - + - -
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Residues in contact with ASN 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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677D GLU* 2.8 26.9 + - - +
678D GLU 3.5 5.2 - - - +
680D PHE* 1.3 76.9 - - - +
682D LEU* 1.3 53.4 + - - +
683D LEU 3.0 1.1 + - - -
684D ALA* 3.2 10.0 + - - +
685D GLN* 2.7 47.3 + - - +
702D GLU* 2.5 65.9 + - + +
705D ILE* 3.4 23.9 - - - +
706D GLY* 3.8 6.1 - - - +
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Residues in contact with LEU 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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673D TYR* 4.8 6.3 - - - +
678D GLU* 2.9 16.4 + - + +
679D PHE* 2.8 35.3 + - + +
681D ASN* 1.3 76.7 - - - +
683D LEU* 1.3 62.1 + - + +
685D GLN* 4.3 19.3 - - + +
686D LYS* 3.8 16.1 + - - +
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Residues in contact with LEU 683 (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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651D ILE* 6.3 0.4 - - + -
674D LEU 5.3 0.4 - - - +
679D PHE* 3.3 42.2 - - + +
680D PHE* 2.9 10.4 + - + +
682D LEU* 1.3 82.6 - - + +
684D ALA* 1.3 62.7 + - - +
685D GLN 3.4 0.4 - - - -
686D LYS* 2.8 43.7 - - - +
687D LEU* 3.4 9.9 + - - +
709D PHE* 4.1 19.7 - - + -
731D PHE* 5.1 2.7 - - + -
735D PHE* 3.5 50.6 - - + -
738D ASP* 4.3 12.8 - - + -
739D ILE* 4.9 3.6 - - + -
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Residues in contact with ALA 684 (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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680D PHE 2.9 12.4 + - - +
681D ASN* 3.2 9.4 + - - +
683D LEU* 1.3 77.6 - - - +
685D GLN* 1.3 51.8 + - + +
687D LEU* 2.5 30.1 + - - +
688D GLU 2.6 13.3 + - - -
689D LEU* 3.3 15.3 + - + +
690D HIS 5.7 0.4 - - - +
705D ILE* 3.5 32.5 - - + +
709D PHE* 4.2 14.5 - - + -
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Residues in contact with GLN 685 (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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681D ASN* 2.7 36.0 + - - +
682D LEU* 4.2 20.9 - - + +
684D ALA* 1.3 74.8 - - - +
686D LYS* 1.3 60.5 + - - +
688D GLU* 3.1 25.8 + - - +
690D HIS* 4.3 20.4 + - + +
702D GLU* 5.6 3.2 + - - +
705D ILE* 5.3 4.5 - - - +
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Residues in contact with LYS 686 (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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610D LYS* 3.6 27.4 + - - +
682D LEU* 3.8 15.7 + - - +
683D LEU* 2.8 35.6 + - + +
685D GLN* 1.3 76.7 - - - +
687D LEU* 1.3 57.5 + - + +
688D GLU* 5.0 2.0 - - - +
734D LEU* 4.2 10.5 - - + +
735D PHE* 4.0 16.2 - - + -
738D ASP* 2.6 38.5 + - - -
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Residues in contact with LEU 687 (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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607D LEU* 3.5 24.3 - - + +
610D LYS* 4.5 17.9 - - + +
611D LEU* 3.9 19.5 - - + +
683D LEU 3.9 6.7 - - - +
684D ALA* 2.5 15.2 + - - +
686D LYS* 1.3 77.7 - - - +
688D GLU* 1.3 64.9 + - - +
689D LEU* 4.1 8.1 - - + +
692D PHE* 3.0 21.0 - - - -
709D PHE* 4.1 24.5 - - + -
712D LEU* 3.8 28.5 - - + -
713D TRP* 4.6 0.9 - - - +
734D LEU* 4.2 19.5 - - + -
735D PHE* 4.2 7.9 - - + -
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Residues in contact with GLU 688 (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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610D LYS* 5.6 6.2 - - - +
684D ALA 2.6 12.0 + - - -
685D GLN* 3.1 20.7 + - - +
686D LYS 5.0 1.5 - - - +
687D LEU* 1.3 77.2 - - - +
689D LEU* 1.3 63.6 + - - +
690D HIS* 3.0 11.7 - - + -
691D LYS* 2.5 62.6 + - + +
692D PHE* 3.1 16.5 - - + -
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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