Contacts of the helix formed by residues 701 - 720 (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 ASN 701 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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699D LYS* 5.6 1.6 - - - +
700D ILE* 1.3 83.5 + - - +
702D GLU* 1.3 63.1 + - - +
703D THR* 3.5 8.1 - - - +
704D ILE* 3.2 9.1 - - + +
705D ILE* 2.8 40.6 + - - +
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Residues in contact with GLU 702 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677D GLU* 2.8 25.5 - - - +
678D GLU* 5.2 7.8 - - - +
681D ASN* 2.5 53.0 + - - +
685D GLN* 5.6 2.6 + - - -
701D ASN* 1.3 79.7 + - - +
703D THR* 1.3 59.8 + - - +
705D ILE* 5.6 0.7 - - + -
706D GLY 2.8 16.3 + - - -
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Residues in contact with THR 703 (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* 2.3 30.5 + - - -
701D ASN* 3.5 6.2 - - - +
702D GLU* 1.3 77.8 - - - +
704D ILE* 1.3 68.6 + - + +
706D GLY* 3.0 3.5 + - - -
707D ASP* 2.9 37.3 + - - +
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Residues in contact with ILE 704 (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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627D HIS* 4.2 10.8 - - + +
636D TYR* 3.8 23.2 + - + +
693D ILE* 4.1 15.7 - - + -
695D ILE* 3.5 31.6 - - + -
699D LYS 4.8 0.2 - - - +
700D ILE* 3.2 36.3 - - + +
701D ASN* 3.2 24.9 - - + +
703D THR* 1.3 79.3 - - + +
705D ILE* 1.3 59.5 + - + +
707D ASP* 3.1 4.4 + - - +
708D VAL* 2.7 36.8 + - + +
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Residues in contact with ILE 705 (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* 3.4 22.2 - - - +
684D ALA* 3.5 26.2 - - + -
685D GLN* 5.3 4.5 - - - +
689D LEU* 4.3 8.4 - - + +
690D HIS* 3.6 34.5 - - + +
693D ILE* 5.0 4.5 - - + -
700D ILE* 3.5 18.2 - - + -
701D ASN 2.8 25.8 + - - +
702D GLU* 3.7 4.0 - - + +
703D THR 3.2 0.2 - - - -
704D ILE* 1.3 80.7 - - + +
706D GLY* 1.3 57.1 + - - +
708D VAL* 3.7 7.4 - - - +
709D PHE* 2.8 26.9 + - - +
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Residues in contact with GLY 706 (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* 5.3 4.5 - - - -
680D PHE* 4.1 18.2 - - - -
681D ASN* 4.2 7.6 - - - -
702D GLU 2.8 15.4 + - - -
703D THR 3.0 3.6 + - - -
705D ILE* 1.3 75.4 - - - +
707D ASP* 1.3 59.2 + - - +
709D PHE* 3.1 11.3 + - - +
710D GLU* 2.9 30.8 + - - +
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Residues in contact with ASP 707 (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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636D TYR* 3.6 22.6 + - + -
640D GLU* 2.5 21.4 - - - +
703D THR* 2.9 29.6 + - - +
704D ILE* 3.6 6.9 - - - +
706D GLY* 1.3 71.1 - - - +
708D VAL* 1.3 54.3 + - - +
710D GLU* 2.6 10.1 + - - +
711D ALA* 2.5 34.5 + - - +
764D MG 2.0 31.2 - - - -
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Residues in contact with VAL 708 (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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624D ALA 3.3 24.5 - - - +
625D LEU* 4.2 8.5 - - + +
636D TYR* 3.6 25.3 - - + -
689D LEU* 3.3 24.2 - - + -
693D ILE* 3.3 31.0 - - + -
704D ILE* 2.7 28.4 + - + +
705D ILE* 3.7 3.8 - - - +
707D ASP* 1.3 71.4 - - - +
709D PHE* 1.3 54.1 + - - +
711D ALA* 4.0 3.6 - - - +
712D LEU* 2.7 34.2 + - + +
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Residues in contact with PHE 709 (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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647D VAL* 4.4 6.7 - - + -
680D PHE* 4.1 39.7 - + + +
683D LEU* 4.1 20.9 - - + -
684D ALA* 4.2 18.4 - - + -
687D LEU* 4.1 12.6 - - + -
689D LEU* 3.6 11.9 - - + -
705D ILE 2.8 15.4 + - - +
706D GLY* 3.1 14.1 + - - +
708D VAL* 1.3 76.8 - - - +
710D GLU* 1.3 60.6 + - - +
712D LEU* 3.8 1.8 - - + +
713D TRP* 3.0 64.5 + + - -
731D PHE* 4.0 11.4 - + - -
735D PHE* 3.5 29.2 - + - -
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Residues in contact with GLU 710 (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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640D GLU* 2.8 22.4 - - - +
643D GLY* 3.2 27.1 - - - +
644D ASP* 3.2 36.1 - - - +
647D VAL* 5.1 4.0 - - + -
680D PHE* 3.5 35.8 - - + -
706D GLY 2.9 8.2 + - - +
707D ASP* 2.6 19.2 + - - +
709D PHE* 1.3 74.0 - - + +
711D ALA* 1.3 63.9 + - - +
713D TRP* 3.7 1.9 + - - +
714D ALA 3.3 6.9 + - - -
764D MG 2.2 31.5 - - - -
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Residues in contact with ALA 711 (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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624D ALA* 3.9 9.9 - - - +
636D TYR* 3.4 33.4 - - + -
639D LEU* 3.6 16.8 - - + +
640D GLU* 3.6 16.1 - - - +
707D ASP 2.5 14.3 + - - +
708D VAL* 3.0 5.4 + - - +
710D GLU* 1.3 71.7 - - - +
712D LEU* 1.3 65.0 + - - +
714D ALA* 2.9 6.9 + - - +
715D ALA* 2.9 20.4 + - - +
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Residues in contact with LEU 712 (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* 3.7 29.6 - - + -
611D LEU* 4.1 26.7 - - + -
615D PHE* 4.6 5.6 - - + -
621D LEU* 4.5 20.2 - - + -
624D ALA* 3.8 15.9 - - + +
625D LEU* 5.0 3.6 - - + -
687D LEU* 3.8 24.0 - - + -
689D LEU* 3.9 11.4 - - + -
708D VAL* 2.7 22.6 + - + +
709D PHE 3.8 3.8 - - - +
710D GLU 3.3 0.2 - - - -
711D ALA* 1.3 71.1 - - - +
713D TRP* 1.3 61.4 + - + +
715D ALA* 2.7 25.3 + - - +
716D VAL* 3.0 12.0 + - + +
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Residues in contact with TRP 713 (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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611D LEU* 4.0 17.7 - - + -
643D GLY 5.4 0.2 - - - +
646D LEU* 3.4 15.4 - - + +
647D VAL* 3.4 27.1 - - + -
650D PHE* 5.0 0.9 - + + -
687D LEU* 4.6 2.8 - - - +
709D PHE* 3.0 62.2 + + - +
710D GLU 4.1 1.6 - - - +
711D ALA 3.4 0.6 - - - -
712D LEU* 1.3 80.4 - - + +
714D ALA* 1.3 59.8 + - - +
716D VAL* 3.8 17.1 - - + +
717D TYR 3.1 16.5 + - - -
727D THR* 3.9 36.1 - - + +
730D LEU* 3.9 13.2 - - + -
731D PHE* 3.6 23.8 - + - -
734D LEU* 3.6 20.4 - - + -
735D PHE* 3.3 24.0 - + - -
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Residues in contact with ALA 714 (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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639D LEU* 3.2 35.0 - - + +
642D LEU* 4.3 11.7 - - + -
643D GLY* 3.5 18.1 - - - +
646D LEU* 4.3 5.1 - - + +
710D GLU 3.3 2.8 + - - -
711D ALA 2.9 8.3 + - - +
713D TRP* 1.3 79.5 - - - +
715D ALA* 1.3 58.0 + - - +
717D TYR* 3.4 7.2 + - - +
718D ILE* 3.0 33.6 + - - +
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Residues in contact with ALA 715 (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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615D PHE* 3.1 16.6 - - + -
620D LEU* 3.8 30.7 - - + +
621D LEU* 4.6 0.2 - - - -
624D ALA* 4.0 7.0 - - + -
639D LEU* 3.9 15.9 - - + +
711D ALA 2.9 9.8 + - - +
712D LEU* 2.7 17.6 + - - +
714D ALA* 1.3 70.3 - - - +
716D VAL* 1.3 57.9 + - - +
718D ILE* 3.9 2.4 - - - -
719D ASP* 2.9 30.1 + - - +
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Residues in contact with VAL 716 (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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611D LEU* 3.9 18.8 - - + -
613D TYR* 4.2 11.9 - - + -
615D PHE* 3.3 30.1 - - + -
712D LEU* 3.0 11.3 + - + +
713D TRP* 3.8 19.3 - - + +
714D ALA 3.3 0.2 - - - -
715D ALA* 1.3 76.0 - - - +
717D TYR* 1.3 60.0 + - - +
719D ASP* 3.1 2.4 + - - +
720D SER* 2.8 30.6 + - - -
727D THR* 3.4 25.1 - - + +
730D LEU* 4.0 21.1 - - + -
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Residues in contact with TYR 717 (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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449C PHE* 3.3 30.6 - + - -
453C ASP* 2.4 36.6 + - - -
528C ARG* 2.5 23.1 + - - -
642D LEU* 4.1 16.8 - - + -
646D LEU* 3.8 19.1 - - + -
713D TRP 3.1 13.0 + - - +
714D ALA* 3.5 7.4 - - - +
716D VAL* 1.3 78.5 - - - +
718D ILE* 1.3 64.2 + - + +
720D SER* 2.9 19.2 + - - -
722D ARG* 2.9 53.6 + - + +
723D ASP 3.9 3.1 - - - -
724D ALA* 3.8 16.4 - - - -
727D THR* 3.4 12.8 - - - +
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Residues in contact with ILE 718 (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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456C VAL* 6.2 0.9 - - + -
620D LEU* 4.3 21.5 - - + +
639D LEU* 3.7 30.1 - - + -
642D LEU* 4.3 12.3 - - + -
714D ALA 3.0 11.2 + - - +
715D ALA 4.2 2.5 - - - +
717D TYR* 1.3 76.2 - - + +
719D ASP* 1.3 64.4 + - - +
721D GLY* 3.1 12.3 + - - -
722D ARG* 3.6 47.5 + - - +
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Residues in contact with ASP 719 (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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613D TYR* 2.9 22.8 + - + +
615D PHE* 3.0 24.9 - - + -
616D LYS* 2.7 39.6 + - - +
617D ASP* 3.1 23.6 + - - +
620D LEU* 3.5 17.1 - - + +
715D ALA 2.9 21.6 + - - +
716D VAL 3.1 3.5 + - - +
718D ILE* 1.3 76.9 - - - +
720D SER* 1.3 57.3 + - - +
721D GLY 3.0 5.4 + - - -
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Residues in contact with SER 720 (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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613D TYR* 3.6 11.4 - - - -
616D LYS* 5.0 2.7 - - - +
716D VAL 2.8 12.4 + - - -
717D TYR 2.9 7.8 + - - -
718D ILE 3.1 0.2 - - - -
719D ASP* 1.3 76.0 - - - +
721D GLY* 1.3 58.9 + - - +
723D ASP* 2.8 46.5 + - - +
726D PHE* 3.9 22.4 - - - -
727D THR* 3.5 3.8 + - - -
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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