Contacts of the helix formed by residues 662 - 680 (chain A) in PDB entry 3S51
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 PRO 662 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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598A ALA* 3.8 21.3 - - + +
601A ARG* 4.3 7.0 - - + -
602A LEU* 4.0 34.1 - - + +
605A TYR* 4.3 6.9 - - + -
659A LEU* 4.0 18.6 - - + -
660A GLN 3.9 0.2 - - - -
661A GLU* 1.3 83.1 - - - +
663A LEU* 1.3 66.1 + - - +
664A ASP* 3.1 13.7 - - - +
665A HIS* 2.8 24.5 + - + +
666A LEU* 3.3 7.4 + - - +
744A LEU* 4.5 0.9 - - + -
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Residues in contact with LEU 663 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630A LEU* 4.3 17.5 - - + -
633A PHE* 3.8 24.7 - - + -
644A LEU* 4.1 18.6 - - + -
645A LYS 4.4 0.2 - - - +
646A LEU* 3.8 20.4 - - + -
649A CYS* 3.6 30.1 - - - -
661A GLU* 2.6 12.8 + - - +
662A PRO* 1.3 70.5 - - - +
664A ASP* 1.3 57.5 + - - +
666A LEU* 3.0 26.0 + - + -
667A LEU* 2.9 36.1 + - + +
744A LEU* 4.1 9.5 - - + +
748A VAL* 4.7 4.3 - - + -
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Residues in contact with ASP 664 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662A PRO* 3.3 13.9 - - - +
663A LEU* 1.3 75.5 - - - +
665A HIS* 1.3 72.2 + - - -
667A LEU* 3.7 1.6 + - - +
668A SER* 3.1 9.2 + - - -
743A CYS 4.1 7.3 - - - +
744A LEU* 3.5 23.3 - - - +
747A GLY* 4.0 5.5 - - - -
748A VAL* 3.6 30.4 - - - +
751A VAL* 3.1 26.2 - - - +
803A LEU* 3.2 28.7 - - + +
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Residues in contact with HIS 665 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602A LEU* 4.3 32.9 - - + +
605A TYR* 4.2 17.9 - - + +
606A ASP* 4.8 6.3 - - - -
662A PRO* 2.8 20.0 + - + +
664A ASP* 1.3 91.7 + - - +
666A LEU* 1.3 57.5 + - - +
667A LEU 3.0 1.3 - - - -
668A SER* 3.0 8.9 + - - -
669A CYS* 2.7 36.9 + - - +
803A LEU* 3.8 29.9 - - + +
859A SER* 5.8 5.9 - - - -
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Residues in contact with LEU 666 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605A TYR* 3.2 32.5 - - + +
626A LEU* 3.8 25.1 - - + +
629A GLN* 3.6 13.7 - - + -
630A LEU* 3.9 17.7 - - + +
633A PHE* 5.3 0.2 - - + -
661A GLU* 2.9 26.0 - - - +
662A PRO 3.3 2.8 + - - -
663A LEU* 3.0 27.5 + - + +
665A HIS* 1.3 77.8 - - - +
667A LEU* 1.3 61.4 + - - +
669A CYS* 3.5 1.3 + - - +
670A ILE* 3.1 41.2 + - + +
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Residues in contact with LEU 667 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630A LEU* 4.0 25.8 - - + -
644A LEU* 4.2 11.7 - - + -
663A LEU* 2.9 23.2 + - + +
664A ASP 3.7 6.5 - - - +
666A LEU* 1.3 74.7 - - - +
668A SER* 1.3 60.1 + - - +
670A ILE* 3.3 4.4 + - + +
671A GLN* 2.8 30.1 + - - +
705A LEU* 3.5 30.0 - - + +
708A ILE* 4.4 5.8 - - + -
748A VAL* 3.7 33.7 - - + +
751A VAL* 3.6 11.3 - - + +
752A LEU* 4.4 18.8 - - + -
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Residues in contact with SER 668 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664A ASP 3.1 12.6 + - - -
665A HIS* 3.0 16.4 + - - -
667A LEU* 1.3 77.3 - - - +
669A CYS* 1.3 57.2 + - - +
671A GLN* 3.2 2.2 + - - -
672A HIS* 2.9 57.9 + - - -
751A VAL* 3.4 22.8 - - - +
803A LEU* 4.1 13.1 + - - -
861A PRO* 5.3 1.6 - - - +
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Residues in contact with CYS 669 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605A TYR* 3.4 37.9 - - + +
608A PHE* 4.3 5.6 - - - -
609A TYR* 4.7 5.2 - - - -
626A LEU* 3.5 32.3 - - + -
665A HIS 2.7 19.9 + - - +
666A LEU* 3.7 5.2 - - - +
668A SER* 1.3 73.7 - - - +
670A ILE* 1.3 57.6 + - - +
672A HIS* 3.1 6.1 + - - +
673A CYS* 2.9 42.1 + - - -
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Residues in contact with ILE 670 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623A MET* 5.0 2.2 - - - +
626A LEU* 3.7 40.8 - - + +
630A LEU* 3.4 32.1 - - + -
666A LEU* 3.1 32.7 + - + +
667A LEU* 3.8 5.4 - - + +
669A CYS* 1.3 76.0 - - - +
671A GLN* 1.3 61.7 + - - +
673A CYS* 3.9 2.1 - - - +
674A LEU* 3.0 41.2 + - + +
701A LEU* 4.1 23.3 - - + -
705A LEU* 4.7 8.3 - - + -
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Residues in contact with GLN 671 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667A LEU 2.8 14.4 + - - +
668A SER* 3.2 12.1 - - - +
670A ILE* 1.3 78.9 - - - +
672A HIS* 1.3 82.2 + - + +
674A LEU* 3.3 2.2 + - - +
675A ALA* 2.8 34.4 + - - +
705A LEU* 4.6 10.9 - - + +
751A VAL* 4.4 7.6 - - + +
754A GLU* 3.6 12.6 + - + +
755A TYR* 3.1 47.0 - - + +
758A SER* 2.8 28.9 + - - -
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Residues in contact with HIS 672 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609A TYR* 3.0 39.9 + - + +
668A SER* 2.9 43.1 + - - +
669A CYS* 3.1 3.8 + - - +
671A GLN* 1.3 104.2 + - + +
673A CYS* 1.3 59.5 + - - +
675A ALA* 3.9 5.6 - - - +
676A TRP* 3.1 18.5 + - - +
751A VAL* 6.1 0.2 - - - +
754A GLU* 3.7 19.4 + - - +
803A LEU 5.1 0.8 + - - -
805A SER* 3.4 19.9 + - - -
860A GLY* 5.4 0.2 - - - -
861A PRO* 2.9 45.0 - - + +
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Residues in contact with CYS 673 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609A TYR* 4.2 17.5 - - - -
612A LEU* 3.5 23.9 - - + +
622A ILE* 4.9 2.7 - - - -
623A MET* 3.3 24.7 - - + -
626A LEU* 3.9 20.6 - - - -
669A CYS* 2.9 31.4 + - - +
670A ILE* 3.9 3.8 - - - +
672A HIS* 1.3 74.3 - - - +
674A LEU* 1.3 55.8 + - - +
676A TRP* 2.9 6.9 + - - +
677A TYR* 2.7 36.5 + - - +
698A TYR* 4.5 0.2 - - - -
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Residues in contact with LEU 674 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623A MET* 4.8 1.1 - - - +
670A ILE* 3.0 21.0 + - + +
671A GLN* 3.6 3.4 - - - +
673A CYS* 1.3 75.1 - - - +
675A ALA* 1.3 64.3 + - - +
676A TRP 3.1 0.3 + - - -
677A TYR* 3.1 1.6 + - - +
678A LYS* 2.9 43.1 + - + +
698A TYR* 3.3 54.9 - - + +
701A LEU* 3.6 27.1 - - + -
702A ASP* 3.8 20.0 - - - +
705A LEU* 3.7 27.4 - - + -
755A TYR* 5.2 1.8 - - + -
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Residues in contact with ALA 675 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671A GLN* 2.8 37.8 + - - +
672A HIS* 3.9 6.7 - - - +
674A LEU* 1.3 71.5 - - - +
676A TRP* 1.3 56.5 + - - +
678A LYS* 4.0 12.3 - - - +
679A SER* 2.9 31.2 + - - -
755A TYR* 6.2 0.6 - - + -
758A SER* 4.8 9.6 - - - +
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Residues in contact with TRP 676 (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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609A TYR* 4.3 11.2 - + + +
612A LEU* 3.8 33.5 + - + +
613A ARG* 3.4 55.0 - - + -
616A SER* 6.1 1.9 - - - +
672A HIS 3.1 15.8 + - - +
673A CYS* 2.9 11.3 + - - +
675A ALA* 1.3 75.6 - - - +
677A TYR* 1.3 66.2 + - + +
679A SER* 4.0 5.2 - - - -
680A ARG* 2.5 89.1 + - + +
681A VAL* 4.1 13.7 - - + +
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Residues in contact with TYR 677 (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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612A LEU* 6.0 1.1 - - + -
619A ALA* 4.8 4.9 - - + -
673A CYS 2.7 12.3 + - - +
674A LEU 3.7 0.9 - - - +
676A TRP* 1.3 81.2 - + + +
678A LYS* 1.3 70.4 + - + +
681A VAL* 3.3 54.5 + - + +
694A GLU* 3.3 29.6 + - - +
695A GLU* 3.2 32.2 + - + +
698A TYR* 3.3 68.0 - + + +
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Residues in contact with LYS 678 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674A LEU* 2.9 36.5 + - + +
675A ALA* 4.0 7.8 - - - +
677A TYR* 1.3 86.5 - - + +
679A SER* 1.3 67.8 + - - +
682A VAL* 3.7 14.4 - - - +
698A TYR* 5.9 0.7 - - + -
702A ASP* 3.6 33.7 + - - +
755A TYR* 4.1 16.0 - - - -
758A SER 5.6 1.4 + - - -
759A ILE* 4.5 14.3 + - - +
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Residues in contact with SER 679 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675A ALA 2.9 23.3 + - - -
676A TRP* 3.5 7.4 + - - -
678A LYS* 1.3 81.0 - - - +
680A ARG* 1.3 85.2 + - - +
682A VAL* 4.3 3.6 - - - +
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Residues in contact with ARG 680 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676A TRP* 2.5 69.8 + - + +
679A SER* 1.3 89.2 + - - +
681A VAL* 1.3 64.5 + - + +
682A VAL* 2.8 14.2 + - - +
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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