Contacts of the helix formed by residues 611 - 630 (chain C) in PDB entry 1RR8
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 611 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609C ASP 4.1 1.2 + - - -
610C GLU* 1.3 83.7 + - - +
612C ILE* 1.3 60.1 + - - +
613C PRO* 3.3 24.6 - - + +
614C ALA* 3.1 21.7 + - - +
615C LYS* 3.0 30.9 + - - +
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Residues in contact with ILE 612 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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611C ASN* 1.3 73.5 - - - +
613C PRO* 1.4 68.8 - - + +
615C LYS* 3.4 19.6 + - + +
616C ILE* 3.5 21.9 + - + +
736C TRP 3.9 15.7 - - - +
737C GLY 3.5 25.6 - - - +
738C VAL* 4.1 21.3 - - + -
739C PRO* 4.7 10.1 - - + -
742C LYS* 4.9 12.1 - - - -
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Residues in contact with PRO 613 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611C ASN* 3.3 19.5 - - + +
612C ILE* 1.4 93.0 - - + +
614C ALA* 1.3 58.3 + - - +
616C ILE* 3.6 24.4 + - + +
617C LEU* 3.7 6.8 + - - +
742C LYS* 5.9 4.9 - - - +
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Residues in contact with ALA 614 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610C GLU* 4.2 19.4 - - + +
611C ASN* 3.1 35.0 + - - +
613C PRO* 1.3 76.7 - - - +
615C LYS* 1.3 62.5 + - - +
616C ILE 3.3 0.9 - - - -
617C LEU* 3.4 25.6 - - + +
618C SER* 3.4 15.2 + - - -
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Residues in contact with LYS 615 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606C THR* 4.1 15.5 - - + -
607C ALA 4.1 10.3 - - - -
608C PRO 4.5 5.7 + - - -
610C GLU* 3.3 28.4 + - + +
611C ASN 3.0 17.9 + - - +
612C ILE* 3.7 13.7 - - + +
613C PRO 3.3 0.2 - - - -
614C ALA* 1.3 75.1 - - - +
616C ILE* 1.3 60.6 + - - +
617C LEU 3.2 0.4 - - - -
618C SER* 3.3 7.4 + - - -
619C TYR 3.1 21.5 + - - -
732C TRP* 3.2 23.9 - - + -
736C TRP* 3.3 55.3 + - + +
738C VAL* 4.0 11.7 - - + -
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Residues in contact with ILE 616 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612C ILE* 3.5 20.1 + - + +
613C PRO* 3.7 14.4 - - + +
615C LYS* 1.3 74.6 - - - +
617C LEU* 1.3 63.2 + - - +
619C TYR* 3.3 6.7 + - - +
620C ASN* 3.0 45.1 + - - +
732C TRP* 4.8 1.1 - - - -
738C VAL* 4.6 5.8 - - + -
742C LYS* 3.9 49.8 - - + +
743C ILE* 4.4 16.6 - - + -
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Residues in contact with LEU 617 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613C PRO 3.7 6.2 + - - +
614C ALA* 3.4 23.8 - - + +
616C ILE* 1.3 78.7 - - - +
618C SER* 1.3 59.2 + - - +
620C ASN* 3.3 7.8 + - - +
621C ARG* 2.9 51.6 + - + +
710C GLU* 5.4 3.1 - - - +
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Residues in contact with SER 618 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602C LEU* 4.4 3.3 - - - +
605C LEU* 3.2 37.8 + - - +
606C THR* 4.3 11.4 - - - +
610C GLU* 5.7 4.5 + - - +
614C ALA 3.4 11.8 + - - -
615C LYS* 3.3 13.4 + - - -
617C LEU* 1.3 79.0 - - - +
619C TYR* 1.3 63.5 + - - +
621C ARG* 3.4 8.3 + - - +
622C ALA* 3.1 22.9 + - - +
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Residues in contact with TYR 619 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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598C LEU* 4.1 14.7 - - + +
602C LEU* 3.7 35.4 - - + -
615C LYS 3.1 13.0 + - - +
616C ILE 3.3 7.4 + - - +
618C SER* 1.3 74.8 - - - +
620C ASN* 1.3 71.5 + - - +
622C ALA* 3.2 4.3 + - - +
623C ASN* 3.0 44.0 + - - +
720C LYS* 4.1 11.4 + - - +
724C LEU* 5.2 2.9 - - - +
729C THR* 2.7 40.8 + - + +
732C TRP* 3.8 24.2 - + + -
743C ILE* 3.7 31.4 - - + +
744C TYR* 4.1 7.4 + - - -
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Residues in contact with ASN 620 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616C ILE* 3.0 32.4 + - - +
617C LEU* 3.6 6.5 - - - +
619C TYR* 1.3 95.2 - - - +
621C ARG* 1.3 56.5 + - - +
623C ASN* 3.6 7.9 + - - +
624C ARG* 3.0 27.4 + - - +
711C ASN* 5.4 0.2 - - - +
716C LEU* 4.2 24.2 - - + +
720C LYS* 4.8 7.9 - - - +
743C ILE* 5.6 0.8 - - - +
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Residues in contact with ARG 621 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601C GLN* 5.1 0.3 - - - +
605C LEU* 3.4 45.2 - - + +
617C LEU* 2.9 35.0 + - + +
618C SER* 3.7 8.5 - - - +
619C TYR 3.2 0.2 - - - -
620C ASN* 1.3 75.5 - - - +
622C ALA* 1.3 62.2 + - - +
624C ARG* 3.5 25.1 + - - +
625C ALA* 3.6 8.5 + - - +
710C GLU* 3.9 30.7 + - - +
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Residues in contact with ALA 622 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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598C LEU* 4.0 9.1 - - + +
601C GLN* 3.8 35.3 - - + +
602C LEU* 3.9 20.0 - - + +
605C LEU* 3.9 2.2 - - + +
618C SER 3.1 12.5 + - - +
619C TYR 3.5 8.3 - - - +
621C ARG* 1.3 77.6 - - - +
623C ASN* 1.3 62.8 + - - +
624C ARG 3.2 0.2 - - - -
625C ALA* 3.4 12.7 + - - +
626C VAL* 3.4 16.3 + - - +
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Residues in contact with ASN 623 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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598C LEU* 4.1 7.4 - - + +
619C TYR* 3.0 35.4 + - + +
620C ASN* 3.7 10.6 + - - +
622C ALA* 1.3 73.8 - - - +
624C ARG* 1.3 64.7 - - - +
626C VAL* 3.3 3.6 + - - +
627C ALA* 3.1 18.7 + - - +
716C LEU* 3.7 27.1 + - + +
719C SER* 3.1 24.2 + - - -
720C LYS* 4.0 21.2 + - - +
724C LEU* 3.6 16.7 - - - +
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Residues in contact with ARG 624 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620C ASN 3.0 17.8 + - - +
621C ARG* 3.5 19.0 + - - +
623C ASN* 1.3 76.7 - - - +
625C ALA* 1.3 56.0 + - - +
627C ALA* 3.1 5.2 + - - +
628C ILE* 3.0 53.9 + - - +
710C GLU* 3.0 62.9 + - - +
711C ASN* 3.7 23.6 - - - +
714C ILE* 3.8 18.9 - - + +
716C LEU* 3.7 6.9 - - - +
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Residues in contact with ALA 625 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597C THR* 4.5 10.0 - - + +
601C GLN* 3.3 31.4 - - + +
621C ARG 3.6 6.5 + - - +
622C ALA 3.4 10.7 + - - +
623C ASN 3.3 0.2 - - - -
624C ARG* 1.3 78.1 - - - +
626C VAL* 1.3 61.2 + - - +
628C ILE* 3.5 12.1 + - - +
629C LEU* 3.2 23.0 + - - +
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Residues in contact with VAL 626 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594C ALA* 3.6 35.2 - - + +
597C THR* 4.3 6.3 - - + -
598C LEU* 3.8 22.9 - - + +
622C ALA 3.4 15.3 - - - +
623C ASN* 3.3 11.6 + - - +
624C ARG 3.2 0.2 - - - -
625C ALA* 1.3 76.0 - - - +
627C ALA* 1.3 57.8 + - - +
629C LEU* 3.5 7.4 + - - +
630C CYS* 3.1 30.3 + - - +
719C SER* 3.8 16.6 - - - +
724C LEU* 3.7 24.0 - - + -
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Residues in contact with ALA 627 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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623C ASN 3.1 11.8 + - - +
624C ARG* 3.1 11.1 + - - +
626C VAL* 1.3 75.8 - - - +
628C ILE* 1.3 57.9 + - - +
631C ASN* 3.1 7.1 + - - -
632C HIS* 2.9 39.9 + - + +
714C ILE* 3.5 17.3 - - + +
715C ALA 3.4 26.9 - - - +
716C LEU* 4.5 2.5 - - + -
719C SER* 4.6 5.8 + - - +
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Residues in contact with ILE 628 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537C TYR* 5.8 1.4 - - - -
624C ARG* 3.0 56.9 + - - +
625C ALA* 3.9 9.9 - - - +
626C VAL 3.3 0.2 - - - -
627C ALA* 1.3 73.2 - - - +
629C LEU* 1.3 65.3 + - - +
631C ASN* 3.4 14.9 + - - +
714C ILE* 4.1 21.3 - - + -
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Residues in contact with LEU 629 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484C LYS 4.9 10.1 - - - +
485C LEU 3.9 17.3 - - - +
486C ALA* 4.2 13.7 - - + +
537C TYR* 4.9 5.9 + - - -
590C ARG* 5.0 0.9 + - - -
593C ASN* 4.2 19.1 - - + +
594C ALA* 4.0 24.7 - - - +
597C THR* 4.3 16.6 - - + +
625C ALA 3.2 13.6 + - - +
626C VAL* 3.8 17.0 - - - +
627C ALA 3.4 0.2 - - - -
628C ILE* 1.3 80.0 - - - +
630C CYS* 1.3 71.3 + - - +
631C ASN* 3.4 2.4 + - - +
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Residues in contact with CYS 630 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486C ALA* 5.2 1.6 - - - -
488C ARG* 4.3 2.3 + - - -
590C ARG* 2.8 51.0 + - - +
594C ALA* 4.0 19.7 - - - -
626C VAL* 3.1 22.3 + - - +
627C ALA 4.3 0.2 - - - +
628C ILE 3.4 0.2 - - - -
629C LEU* 1.3 89.5 - - - +
631C ASN* 1.3 65.4 + - - +
632C HIS* 3.4 33.9 - - + +
723C PTR 4.6 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
------------------------------------------------------------
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