Contacts of the helix formed by residues 607 - 627 (chain A) in PDB entry 1R1H
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 THR 607 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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461A ASP* 2.6 31.0 + - - +
463A GLU* 3.7 26.9 - - + +
464A THR* 3.2 16.1 + - - +
467A ARG* 4.9 4.3 - - - +
606A TRP* 1.3 75.1 - - - +
608A GLN* 1.3 66.0 + - - +
609A GLN* 3.7 4.1 + - - +
610A SER* 3.2 14.3 + - - -
611A ALA* 2.9 23.4 + - - +
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Residues in contact with GLN 608 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604A ASP* 5.2 7.7 + - - -
606A TRP 5.2 1.8 + - - -
607A THR* 1.3 71.6 - - - +
609A GLN* 1.3 65.8 + - - +
611A ALA* 3.4 4.6 + - - +
612A SER* 2.9 24.9 + - - -
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Residues in contact with GLN 609 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A ASP* 4.6 5.6 - - - +
607A THR* 3.2 6.4 + - - +
608A GLN* 1.3 80.4 - - - +
610A SER* 1.3 57.9 + - - +
612A SER* 3.3 10.5 + - - -
613A ASN* 2.8 63.7 + - - +
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Residues in contact with SER 610 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A TRP* 4.1 10.6 + - - -
460A MET* 3.4 6.7 - - - -
461A ASP* 2.9 40.9 + - - -
464A THR* 3.8 9.7 + - - -
606A TRP* 3.6 23.9 - - - -
607A THR* 3.2 13.5 + - - -
609A GLN* 1.3 78.9 - - - +
611A ALA* 1.3 57.9 + - - +
613A ASN* 3.3 2.3 + - - +
614A PHE* 2.9 27.7 + - - +
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Residues in contact with ALA 611 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594A ARG* 4.0 24.5 + - - +
604A ASP* 5.6 2.0 - - - +
606A TRP* 3.8 16.0 - - + -
607A THR 2.9 17.4 + - - +
608A GLN* 3.7 4.7 - - - +
610A SER* 1.3 76.0 - - - +
612A SER* 1.3 64.3 + - - +
614A PHE* 3.4 3.8 + - - +
615A LYS* 3.3 32.7 + - - +
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Residues in contact with SER 612 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608A GLN 2.9 17.1 + - - -
609A GLN* 3.6 12.9 + - - -
611A ALA* 1.3 75.5 - - - +
613A ASN* 1.3 66.6 + - - +
615A LYS* 3.4 13.9 + - - +
616A GLU* 3.1 31.0 + - - +
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Residues in contact with ASN 613 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A TRP* 3.1 44.0 + - + +
460A MET 5.8 0.2 - - - -
609A GLN* 2.8 53.1 + - - +
610A SER* 3.6 3.2 + - - +
611A ALA 3.2 0.2 - - - -
612A SER* 1.3 78.1 + - - +
614A PHE* 1.3 59.0 + - - +
616A GLU* 3.2 14.9 + - - +
617A GLN* 2.8 33.6 + - - +
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Residues in contact with PHE 614 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459A TRP* 3.8 30.2 - + + -
589A PHE 3.3 19.5 - - - -
590A ASP 3.6 23.3 - - - -
591A ASP* 3.6 19.7 - - + -
594A ARG* 3.5 31.9 - - - +
606A TRP* 4.1 8.5 - + + -
610A SER 2.9 14.3 + - - +
611A ALA* 3.5 10.5 - - - +
612A SER 3.3 0.2 - - - -
613A ASN* 1.3 76.2 - - - +
615A LYS* 1.3 70.5 + - + +
617A GLN* 3.2 4.3 + - - +
618A SER* 2.9 35.7 + - - -
648A ILE* 4.0 11.2 - - + -
748A VAL* 4.1 8.9 - - + +
749A TRP* 4.0 9.9 - + - -
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Residues in contact with LYS 615 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294A ASP* 6.1 0.9 - - - -
594A ARG* 4.0 19.5 - - - +
611A ALA* 3.3 19.1 + - - +
612A SER* 3.6 11.5 - - - +
613A ASN 3.3 0.4 - - - -
614A PHE* 1.3 83.0 - - + +
616A GLU* 1.3 56.5 + - - +
618A SER* 2.9 9.2 + - - -
619A GLN* 2.8 33.8 + - - +
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Residues in contact with GLU 616 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612A SER* 3.1 22.6 + - - +
613A ASN* 3.2 17.5 + - - +
615A LYS* 1.3 78.1 - - - +
617A GLN* 1.3 71.6 + - - +
618A SER 3.3 0.3 + - - -
619A GLN* 3.3 16.7 + - - +
620A CYS* 3.7 5.2 + - - +
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Residues in contact with GLN 617 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A TRP* 3.8 41.6 - - + +
613A ASN* 2.8 24.9 + - - +
614A PHE* 3.8 4.9 - - - +
616A GLU* 1.3 81.9 - - - +
618A SER* 1.3 62.1 + - - +
620A CYS* 3.4 19.0 + - - +
621A MET* 4.3 3.5 + - - +
747A ARG* 3.1 37.9 + - - +
748A VAL* 4.3 9.8 - - + +
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Residues in contact with SER 618 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614A PHE* 2.9 23.8 + - - -
615A LYS* 2.9 22.9 + - - -
617A GLN* 1.3 74.9 - - - +
619A GLN* 1.3 60.3 + - - +
620A CYS 3.1 2.2 - - - -
621A MET* 2.8 27.6 + - - +
622A VAL* 3.2 13.4 + - - +
644A LEU* 3.8 14.3 - - - +
648A ILE* 4.0 26.5 - - - -
748A VAL* 5.0 7.0 - - - -
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Residues in contact with GLN 619 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615A LYS 2.8 18.0 + - - +
616A GLU* 3.5 10.5 - - - +
617A GLN 3.3 0.2 - - - -
618A SER* 1.3 78.3 + - - +
620A CYS* 1.3 61.0 + - - +
622A VAL* 3.2 23.1 + - - +
623A TYR* 3.1 67.2 + - + +
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Residues in contact with CYS 620 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616A GLU 3.7 3.8 + - - +
617A GLN* 3.4 15.1 + - - +
618A SER 3.1 0.8 - - - -
619A GLN* 1.3 78.9 - - - +
621A MET* 1.3 57.1 + - - +
623A TYR* 3.5 8.4 + - - +
624A GLN* 3.0 22.3 + - - +
744A LYS* 3.4 33.2 - - - +
745A LYS 4.3 1.8 - - - -
746A CYS* 2.0 60.9 - - + -
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Residues in contact with MET 621 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617A GLN 4.8 2.9 - - - +
618A SER* 2.8 12.0 + - - +
620A CYS* 1.3 74.8 - - - +
622A VAL* 1.3 66.9 + - - +
624A GLN* 4.3 9.4 - - - +
625A TYR* 3.1 36.1 + - + +
640A GLY 4.7 1.0 - - - +
644A LEU* 4.1 10.1 - - + -
647A ASN* 4.1 4.0 + - + +
648A ILE* 4.0 21.5 - - - -
651A ASN* 3.7 37.9 - - + +
746A CYS* 3.7 20.9 - - + -
747A ARG* 4.1 10.8 - - - -
748A VAL* 3.2 45.8 - - + +
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Residues in contact with VAL 622 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618A SER* 3.2 12.2 + - - +
619A GLN* 3.5 34.3 - - - +
621A MET* 1.3 76.3 - - - +
623A TYR* 1.3 61.3 + - + +
626A GLY* 3.0 27.7 + - - -
640A GLY* 3.5 26.0 - - - +
641A ILE* 3.9 27.6 - - + -
644A LEU* 3.9 22.6 - - + +
754A NAG 4.0 1.7 - - - +
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Residues in contact with TYR 623 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619A GLN* 3.1 45.7 + - + +
620A CYS* 3.8 8.7 - - - +
622A VAL* 1.3 80.3 - - + +
624A GLN* 1.3 65.0 + - - +
627A ASN* 2.8 30.0 + - - +
754A NAG 3.4 63.9 - - - +
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Residues in contact with GLN 624 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620A CYS 3.0 17.5 + - - +
621A MET* 3.4 3.2 + - - +
623A TYR* 1.3 77.8 - - - +
625A TYR* 1.3 80.5 + - + +
627A ASN* 3.4 13.8 + - - +
628A PHE* 3.6 15.5 + - + -
720A GLY* 3.0 25.7 + - - -
723A GLN* 3.0 29.3 + - - +
724A ASN* 2.9 30.7 + - - +
746A CYS* 3.6 13.7 - - - +
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Residues in contact with TYR 625 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621A MET* 3.1 25.4 + - + +
624A GLN* 1.3 99.2 - - - +
626A GLY* 1.3 62.1 + - - +
627A ASN 3.0 1.6 - - - -
628A PHE* 2.9 39.9 + + - +
638A LEU* 3.4 17.8 - - + +
640A GLY* 4.6 2.0 - - - -
643A THR* 4.4 5.8 - - - +
647A ASN* 3.1 49.8 + - + +
650A ASP* 5.2 0.2 - - - +
651A ASN* 3.1 24.4 + - - -
712A SER* 3.3 15.3 - - - -
716A PHE 3.7 18.7 + - - -
717A ARG* 4.3 1.9 + - - -
720A GLY* 3.3 22.0 - - - -
721A THR* 3.5 8.8 + - - +
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Residues in contact with GLY 626 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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622A VAL 3.0 20.4 + - - -
625A TYR* 1.3 76.9 - - - +
627A ASN* 1.3 48.4 + - - +
628A PHE 3.3 0.2 - - - -
637A HIS* 2.7 38.8 - - - +
638A LEU 3.5 15.3 - - - -
640A GLY* 3.9 7.7 - - - -
754A NAG 3.4 20.7 - - - +
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Residues in contact with ASN 627 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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623A TYR 2.8 18.5 + - - +
624A GLN* 3.5 7.6 - - - +
625A TYR 3.0 1.0 - - - -
626A GLY* 1.3 75.5 - - - +
628A PHE* 1.3 64.6 + - + +
629A SER* 3.5 4.0 + - - -
637A HIS* 3.5 16.7 + - - -
754A NAG 1.4 64.9 + - - +
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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
------------------------------------------------------------
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