Contacts of the helix formed by residues 651 - 672 (chain A) in PDB entry 3RC3
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 651 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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604A THR* 3.1 16.7 - - - +
605A PHE* 2.4 45.1 + - + +
638A TYR* 3.0 17.4 + - + +
649A PHE 3.2 0.2 - - - -
650A PRO* 1.3 92.8 - - - +
652A ALA* 1.3 64.1 + - - +
653A SER 3.4 2.5 - - - -
654A LEU* 3.2 17.2 + - + +
655A ILE* 3.0 20.3 + - - +
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Residues in contact with ALA 652 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638A TYR* 4.1 6.4 - - - -
639A LEU* 3.4 19.9 - - + +
642A SER* 3.5 28.9 - - - +
643A TYR* 5.2 2.5 - - + +
649A PHE 4.8 0.7 - - - +
650A PRO 3.5 4.9 + - - -
651A ASP* 1.3 74.9 - - - +
653A SER* 1.4 57.6 + - - +
655A ILE* 3.3 0.9 + - - -
656A ARG* 2.8 44.6 + - - +
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Residues in contact with SER 653 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651A ASP 3.4 0.8 - - - -
652A ALA* 1.4 76.7 - - - +
654A LEU* 1.3 66.3 + - - +
656A ARG* 3.4 16.2 + - - +
657A ASP* 3.1 30.4 + - - +
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Residues in contact with LEU 654 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605A PHE* 3.7 50.7 - - + -
651A ASP* 3.2 20.7 + - + +
653A SER* 1.3 80.0 - - - +
655A ILE* 1.4 66.6 + - - +
657A ASP* 3.3 15.6 + - + +
658A LEU* 3.1 21.5 + - - +
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Residues in contact with ILE 655 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605A PHE* 4.0 23.3 - - + -
608A LEU* 3.2 38.8 - - + -
635A LEU* 4.1 29.2 - - + +
638A TYR* 3.7 35.0 - - + -
639A LEU* 4.1 11.2 - - + -
651A ASP 3.0 19.9 + - - +
652A ALA 3.8 2.5 - - - +
654A LEU* 1.4 76.1 - - - +
656A ARG* 1.3 53.2 + - - +
658A LEU* 3.1 14.4 + - + +
659A GLN* 2.7 33.1 + - - +
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Residues in contact with ARG 656 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A GLU 2.9 25.9 + - - -
258A GLU* 3.7 20.4 - - + +
259A ARG 5.6 0.8 + - - -
639A LEU* 4.1 21.6 - - + +
643A TYR* 3.1 21.5 + - - -
652A ALA* 2.8 40.8 + - - +
653A SER* 3.5 14.5 + - - +
655A ILE* 1.3 74.2 - - - +
657A ASP* 1.3 59.1 + - - +
659A GLN* 3.2 12.0 + - - +
660A LYS* 2.9 29.6 + - - +
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Residues in contact with ASP 657 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653A SER* 3.1 16.8 + - - +
654A LEU* 3.5 17.8 - - + +
655A ILE 3.2 0.4 - - - -
656A ARG* 1.3 77.2 - - - +
658A LEU* 1.3 65.0 + - - +
660A LYS* 3.3 10.2 + - - +
661A GLU* 3.1 20.6 + - - +
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Residues in contact with LEU 658 (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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605A PHE* 4.2 19.1 - - + -
608A LEU* 5.4 0.2 - - + -
609A ARG* 4.4 13.7 - - + +
612A ILE* 3.8 27.1 - - + -
614A TRP* 3.7 43.3 - - + +
635A LEU* 4.2 12.6 - - + -
654A LEU 3.1 12.7 + - - +
655A ILE* 3.4 25.8 - - + +
657A ASP* 1.3 77.5 - - - +
659A GLN* 1.3 62.8 + - - +
661A GLU* 3.1 10.4 + - - +
662A LEU* 3.0 21.3 + - - +
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Residues in contact with GLN 659 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632A HIS* 3.2 49.9 + - + +
635A LEU* 3.6 21.2 - - + +
636A ASP* 2.9 34.4 + - - +
639A LEU* 3.5 18.4 - - + +
655A ILE 2.7 21.1 + - - +
656A ARG* 3.5 11.2 - - - +
658A LEU* 1.3 74.4 - - - +
660A LYS* 1.3 52.2 + - - +
662A LEU* 3.2 3.9 + - + +
663A ASP* 2.7 33.8 + - + +
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Residues in contact with LYS 660 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656A ARG 2.9 15.7 + - - +
657A ASP* 3.7 9.4 - - - +
658A LEU 3.2 0.2 - - - -
659A GLN* 1.3 78.6 - - - +
661A GLU* 1.3 61.1 + - - +
663A ASP* 3.4 9.9 + - + +
664A GLY* 3.1 18.5 + - - -
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Residues in contact with GLU 661 (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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614A TRP* 3.4 31.3 + - + -
657A ASP 3.1 10.9 + - - +
658A LEU* 3.1 12.3 + - - +
660A LYS* 1.3 76.8 - - - +
662A LEU* 1.3 60.9 + - - +
664A GLY* 3.2 4.8 + - - -
665A ILE* 3.2 27.0 + - + +
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Residues in contact with LEU 662 (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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614A TRP* 3.9 17.4 - - + -
616A LEU* 4.2 11.9 - - + -
628A LEU* 3.9 33.9 - - + +
631A VAL* 3.7 15.7 - - + -
632A HIS* 3.4 40.2 - - + +
635A LEU* 4.1 11.0 - - + -
658A LEU 3.0 12.3 + - - +
659A GLN* 3.5 8.3 - - - +
661A GLU* 1.3 75.1 - - - +
663A ASP* 1.3 65.8 + - - +
665A ILE* 3.2 9.1 + - + +
666A ILE* 3.0 31.6 + - + +
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Residues in contact with ASP 663 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A PRO* 3.5 24.1 - - + +
401A PRO* 3.6 5.2 - - - +
402A GLY* 2.8 29.0 + - - -
403A THR* 3.0 35.5 + - - -
632A HIS* 4.5 5.4 + - + +
659A GLN* 2.7 20.6 + - + +
660A LYS* 3.4 12.3 + - + +
662A LEU* 1.3 70.8 - - - +
664A GLY* 1.3 53.1 + - - +
666A ILE* 3.3 5.9 + - - +
667A GLN* 2.8 35.3 + - - +
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Residues in contact with GLY 664 (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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660A LYS 3.1 14.2 + - - -
661A GLU* 3.2 4.9 + - - -
662A LEU 3.1 0.6 - - - -
663A ASP* 1.3 75.5 - - - +
665A ILE* 1.3 56.5 + - - +
667A GLN* 3.4 13.6 + - - +
668A ASP* 3.0 35.8 + - - +
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Residues in contact with ILE 665 (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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614A TRP* 3.8 25.8 - - + -
616A LEU 3.7 20.9 - - - +
617A LEU 4.0 13.5 - - - +
618A PRO* 4.2 15.9 - - + +
619A PRO* 4.2 3.3 - - - +
628A LEU* 3.9 26.5 - - + -
661A GLU* 3.2 18.5 + - + +
662A LEU* 3.2 11.3 + - + +
664A GLY* 1.3 71.9 - - - +
666A ILE* 1.3 62.2 + - - +
668A ASP* 3.5 7.4 + - - +
669A GLY* 3.0 23.2 + - - -
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Residues in contact with ILE 666 (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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399A LEU* 4.8 0.2 - - + -
400A PRO* 3.7 39.5 - - + -
403A THR* 3.9 3.4 - - - +
625A LEU* 3.8 20.4 - - + +
628A LEU* 3.6 50.0 - - + +
629A GLU* 4.0 6.7 - - + +
632A HIS* 4.1 7.4 - - + -
662A LEU* 3.0 30.7 + - + +
663A ASP 3.7 3.6 - - - +
665A ILE* 1.3 76.0 - - - +
667A GLN* 1.3 53.7 + - - +
669A GLY* 3.1 2.3 + - - +
670A VAL* 2.8 39.4 + - + +
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Residues in contact with GLN 667 (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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402A GLY* 4.2 11.5 + - - -
403A THR* 3.2 20.4 + - + +
406A ALA* 3.4 32.9 - - + +
407A GLN* 5.0 3.0 + - - +
663A ASP* 2.8 19.7 + - - +
664A GLY* 3.4 12.2 - - - +
666A ILE* 1.3 77.4 - - - +
668A ASP* 1.3 65.6 + - - +
670A VAL* 3.4 1.7 + - - +
671A HIS* 3.0 27.4 + - + +
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Residues in contact with ASP 668 (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 PRO* 6.4 2.5 - - + -
664A GLY 3.0 20.6 + - - +
665A ILE* 3.9 7.3 - - - +
667A GLN* 1.3 80.5 - - - +
669A GLY* 1.3 66.7 + - - +
671A HIS* 3.5 7.9 + - - +
672A ASN* 3.0 31.8 + - - +
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Residues in contact with GLY 669 (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 PRO* 3.8 29.8 - - - +
625A LEU* 5.3 0.9 - - - -
665A ILE 3.0 12.4 + - - -
666A ILE 3.1 4.2 + - - -
668A ASP* 1.3 78.4 - - - +
670A VAL* 1.3 56.0 + - - +
672A ASN* 2.9 24.0 + - - +
673A ILE* 3.0 12.8 + - - -
676A LEU* 3.5 10.6 - - - +
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Residues in contact with VAL 670 (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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394A VAL* 4.4 15.9 - - + +
396A TYR* 4.6 0.2 - - - +
399A LEU* 3.6 29.4 - - + -
403A THR* 3.7 22.9 - - + -
407A GLN* 3.9 22.7 + - + +
625A LEU* 3.9 23.6 - - + -
666A ILE* 2.8 24.4 + - + +
667A GLN 4.0 0.7 - - - +
669A GLY* 1.3 68.2 - - - +
671A HIS* 1.3 67.6 + - - +
672A ASN 3.0 1.6 - - - -
673A ILE* 2.9 29.2 + - + +
902A AZI 4.9 1.0 + - - -
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Residues in contact with HIS 671 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A GLU* 4.4 7.6 - - - -
407A GLN* 3.9 6.5 - - - +
410A LYS* 3.9 22.3 - - + +
667A GLN* 3.0 15.1 + - + +
668A ASP* 3.6 12.3 - - - +
670A VAL* 1.3 76.3 - - - +
672A ASN* 1.3 78.6 + - - +
673A ILE 3.5 1.9 + - - -
674A THR* 5.1 1.7 + - - -
901A NA 4.1 1.4 - - - -
902A AZI 3.0 60.6 + - - +
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Residues in contact with ASN 672 (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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668A ASP* 3.0 17.9 + - - +
669A GLY* 2.9 13.4 + - - +
671A HIS* 1.3 95.4 + - - +
673A ILE* 1.4 62.4 + - - +
674A THR* 3.2 4.7 - - - -
675A LYS* 2.9 50.7 + - + +
676A LEU* 3.3 13.3 + - + +
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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