Contacts of the helix formed by residues 617 - 626 (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 ASP 617 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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615D PHE* 4.0 4.1 - - - -
616D LYS* 1.3 77.3 - - + +
618D LYS* 1.3 53.4 + - - +
619D SER* 2.8 30.3 + - - -
620D LEU* 2.8 45.0 + - + +
621D LEU 4.0 0.5 + - - -
719D ASP* 3.1 14.3 + - - +
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Residues in contact with LYS 618 (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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605D GLU* 5.0 13.7 - - + +
608D GLU* 3.2 35.6 + - - +
614D THR* 3.7 10.5 - - - +
615D PHE* 2.7 38.0 + - - -
616D LYS 3.7 10.0 + - - -
617D ASP* 1.3 72.9 + - - +
619D SER* 1.3 56.1 + - - +
620D LEU 2.9 6.1 + - - -
621D LEU* 2.9 19.9 + - + +
622D GLU* 3.1 18.8 + - - +
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Residues in contact with SER 619 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617D ASP* 2.8 24.8 + - - -
618D LYS* 1.3 76.1 - - - +
620D LEU* 1.3 60.5 + - - +
622D GLU* 3.7 21.3 + - - +
623D LYS* 3.2 21.5 + - - +
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Residues in contact with LEU 620 (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* 4.2 8.5 - - + -
617D ASP* 2.8 26.0 + - + +
619D SER* 1.3 77.3 + - - +
621D LEU* 1.3 66.2 + - - +
623D LYS* 3.1 20.4 + - + +
624D ALA* 3.2 13.3 + - - +
639D LEU* 3.8 16.8 - - + +
715D ALA* 3.9 7.6 - - + +
718D ILE* 4.3 28.3 - - + -
719D ASP* 3.5 43.7 - - + +
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Residues in contact with LEU 621 (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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605D GLU* 3.5 20.4 - - + +
607D LEU* 5.0 8.5 - - + -
608D GLU* 3.6 30.1 - - + +
611D LEU* 5.7 1.3 - - + -
615D PHE* 3.3 48.2 - - + -
618D LYS* 2.9 13.1 + - + +
620D LEU* 1.3 78.0 - - - +
622D GLU* 1.3 62.7 + - - +
624D ALA* 3.3 8.3 + - - +
625D LEU* 3.1 46.4 + - + +
712D LEU* 4.5 10.3 - - + -
715D ALA* 4.6 0.2 - - - -
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Residues in contact with GLU 622 (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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65A GLY* 5.3 8.6 - - - +
605D GLU* 4.4 24.7 - - - +
618D LYS* 3.1 14.3 + - - +
619D SER* 3.7 26.3 + - - +
620D LEU 3.1 0.4 - - - -
621D LEU* 1.3 76.0 - - - +
623D LYS* 1.3 56.5 + - - +
625D LEU* 3.0 7.4 + - + +
626D THR* 2.4 37.3 + - - -
694D ARG* 3.6 33.3 + - - +
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Residues in contact with LYS 623 (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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619D SER 3.2 11.3 + - - +
620D LEU* 3.1 14.7 + - + +
622D GLU* 1.3 78.5 - - - +
624D ALA* 1.3 59.6 + - - +
626D THR 3.5 4.7 - - - +
633D LYS 4.9 1.1 - - - -
634D GLU* 3.1 52.2 + - + +
635D HIS* 2.8 53.4 - - - +
636D TYR* 3.0 2.3 + - - -
638D THR* 5.7 10.5 - - - -
639D LEU* 4.0 18.8 - - + +
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Residues in contact with ALA 624 (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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620D LEU 3.2 7.4 + - - +
621D LEU* 3.5 10.8 - - - +
622D GLU 3.1 0.4 - - - -
623D LYS* 1.3 77.6 - - - +
625D LEU* 1.3 57.3 + - - +
626D THR 3.3 0.2 - - - -
636D TYR* 3.4 7.6 - - - +
639D LEU* 3.6 20.8 - - + +
708D VAL* 3.3 27.9 - - - +
711D ALA* 3.9 6.4 - - - +
712D LEU* 3.8 34.1 - - + +
715D ALA* 4.0 4.9 - - + -
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Residues in contact with LEU 625 (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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604D LEU 6.0 0.2 - - - +
605D GLU* 4.4 14.6 - - - +
607D LEU* 4.6 3.8 - - + -
621D LEU* 3.1 42.2 + - + +
622D GLU* 3.0 7.2 + - - +
624D ALA* 1.3 75.7 - - - +
626D THR* 1.3 57.0 + - - +
689D LEU* 3.8 29.6 - - + -
692D PHE* 3.2 36.6 - - + +
693D ILE* 3.4 24.2 - - + +
694D ARG* 2.5 37.1 + - - +
708D VAL* 4.2 6.7 - - + +
712D LEU* 5.0 4.9 - - + -
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Residues in contact with THR 626 (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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622D GLU 2.4 23.4 + - - -
623D LYS 3.7 2.2 - - - -
624D ALA 3.3 0.6 - - - -
625D LEU* 1.3 78.3 - - - +
627D HIS* 1.3 65.3 + - - +
630D TYR* 4.1 7.6 - - + -
631D SER* 3.3 26.0 - - - -
634D GLU 2.9 27.3 + - - +
635D HIS* 3.2 1.1 - - - -
636D TYR* 2.8 34.7 + - - -
694D ARG* 2.5 34.4 + - - +
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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