Contacts of the helix formed by residues 625 - 642 (chain A) in PDB entry 4NC6
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 GLY 625 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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619A TYR 5.7 2.0 - - - -
622A ASP* 3.0 29.2 + - - -
623A THR 3.4 0.6 - - - +
624A GLY* 1.3 82.0 - - - +
626A ASP* 1.3 68.0 + - - -
627A GLY 3.2 3.4 + - - -
628A GLN* 3.4 3.3 + - - +
629A ASP* 3.2 20.7 + - - +
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Residues in contact with ASP 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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619A TYR* 4.6 6.7 - - + +
624A GLY 4.8 2.4 - - - +
625A GLY* 1.3 76.7 - - - -
627A GLY* 1.3 62.9 + - - +
629A ASP* 3.7 8.5 - - - +
630A SER* 3.0 31.6 + - - +
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Residues in contact with GLY 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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619A TYR* 3.6 48.2 + - - -
620A PHE* 3.7 10.1 - - - -
625A GLY 3.2 1.0 - - - -
626A ASP* 1.3 80.7 - - - +
628A GLN* 1.3 60.9 + - - +
630A SER* 3.7 2.5 - - - -
631A LEU* 3.0 24.6 + - - +
659A LEU* 4.1 0.9 - - - +
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Residues in contact with GLN 628 (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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610A ILE* 3.3 36.0 + - - +
611A ASN* 5.4 2.1 - - - +
613A THR 4.8 3.4 + - - -
615A PRO* 5.2 4.6 - - - +
619A TYR 4.6 1.2 + - - -
620A PHE* 2.7 49.1 + - - +
622A ASP 3.5 14.1 - - - +
623A THR* 3.8 29.8 - - - +
625A GLY 3.4 5.9 + - - +
626A ASP 3.4 0.4 - - - -
627A GLY* 1.3 74.1 - - - +
629A ASP* 1.3 62.9 + - - +
631A LEU* 3.3 6.9 + - - +
632A TYR* 3.0 39.0 + - + -
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Residues in contact with ASP 629 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624A GLY 5.5 1.8 - - - +
625A GLY 3.2 14.5 + - - +
626A ASP* 3.7 11.3 - - - +
628A GLN* 1.3 80.8 - - - +
630A SER* 1.3 63.1 + - - +
632A TYR* 3.4 7.6 + - - +
633A LYS* 2.9 62.2 + - - +
664A GLU* 5.2 1.2 - - - +
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Residues in contact with SER 630 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619A TYR* 5.1 2.9 + - - -
626A ASP* 3.0 20.5 + - - +
627A GLY* 3.7 5.2 - - - -
629A ASP* 1.3 79.6 + - - +
631A LEU* 1.3 62.3 + - - +
633A LYS* 3.3 1.4 + - - +
634A ILE* 3.0 28.9 + - - +
659A LEU* 3.9 17.4 - - - +
664A GLU* 2.5 43.1 + - - +
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Residues in contact with LEU 631 (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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610A ILE* 3.9 32.5 - - + -
613A THR* 4.0 25.1 - - + +
620A PHE* 4.3 17.9 - - + -
627A GLY 3.0 17.3 + - - +
628A GLN* 3.6 7.2 - - - +
630A SER* 1.3 76.0 - - - +
632A TYR* 1.3 62.7 + - - +
634A ILE* 3.9 1.2 - - - +
635A CYS* 3.1 33.1 + - - -
652A SER 3.5 21.1 - - - +
655A ALA* 3.7 21.8 - - + -
656A ALA* 3.7 11.4 - - + +
659A LEU* 3.5 10.0 - - + +
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Residues in contact with TYR 632 (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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606A ILE* 4.3 3.4 - - + -
607A THR* 3.5 47.8 + - - +
610A ILE* 3.6 38.8 - - + +
611A ASN* 4.4 6.1 + - - -
623A THR 6.1 0.4 - - - -
628A GLN* 3.0 33.7 + - + -
629A ASP* 3.6 10.5 - - - +
631A LEU* 1.3 76.1 - - - +
633A LYS* 1.3 60.1 + - + +
635A CYS* 3.9 0.5 - - - +
636A LYS* 2.9 65.1 + - - +
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Residues in contact with LYS 633 (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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592A TYR* 3.4 14.7 + - - +
596A ILE* 4.2 30.1 - - + +
629A ASP* 2.9 49.4 + - - +
630A SER 3.3 1.8 + - - +
632A TYR* 1.3 81.7 - - + +
634A ILE* 1.3 57.9 + - - +
636A LYS* 3.9 4.8 - - - +
637A ALA* 2.8 32.6 + - - +
664A GLU* 3.6 20.4 + - - +
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Residues in contact with ILE 634 (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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592A TYR* 3.6 18.4 - - - +
630A SER 3.0 19.0 + - - +
631A LEU 3.9 3.4 - - - +
633A LYS* 1.3 74.0 - - - +
635A CYS* 1.3 59.1 + - - +
637A ALA* 3.7 1.4 - - - +
638A TYR* 2.9 29.1 + - - +
655A ALA* 4.0 14.4 - - + +
659A LEU* 3.5 39.7 - - + -
664A GLU* 3.8 19.5 - - + +
667A ALA* 3.9 8.7 - - + -
668A PHE* 4.0 18.0 - - + +
671A LEU* 3.7 26.7 - - + -
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Residues in contact with CYS 635 (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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606A ILE* 3.7 24.2 - - + +
610A ILE* 4.2 5.2 - - - -
631A LEU* 3.1 29.2 + - - +
632A TYR 3.9 0.2 - - - +
634A ILE* 1.3 78.5 - - - +
636A LYS* 1.3 62.0 + - - +
638A TYR* 3.3 6.9 + - - +
639A SER* 3.1 22.0 + - - -
647A TYR* 3.8 29.7 - - + -
651A GLN* 4.9 0.4 - - - -
652A SER* 3.8 28.3 - - - -
655A ALA* 4.3 7.2 - - - -
671A LEU* 5.6 1.6 - - - -
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Residues in contact with LYS 636 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595A LEU 5.7 0.4 - - - -
596A ILE* 6.5 1.1 - - - -
598A LYS 5.3 8.5 - - - +
599A GLU* 5.9 3.4 + - - +
600A SER* 3.9 22.2 - - - +
603A ASP* 3.4 26.6 + - - +
606A ILE* 3.9 12.8 - - + -
632A TYR* 2.9 49.5 + - - +
633A LYS* 3.9 5.2 - - - +
635A CYS* 1.3 77.6 - - - +
637A ALA* 1.3 62.1 + - - +
639A SER* 2.7 24.8 + - - -
640A VAL* 3.3 11.4 + - + +
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Residues in contact with ALA 637 (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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592A TYR* 3.6 28.9 - - + -
595A LEU* 4.0 25.7 + - + +
596A ILE* 4.4 5.3 - - + +
633A LYS 2.8 23.2 + - - +
634A ILE 3.7 2.2 - - - +
636A LYS* 1.3 74.6 - - - +
638A TYR* 1.3 56.4 + - - +
640A VAL* 3.2 5.7 + - - +
641A TYR* 2.9 28.8 + - - +
668A PHE* 3.8 7.0 - - + -
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Residues in contact with TYR 638 (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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634A ILE 2.9 18.6 + - - +
635A CYS* 3.7 6.1 - - - +
636A LYS 3.3 0.2 - - - -
637A ALA* 1.3 73.1 - - - +
639A SER* 1.3 65.9 + - - +
641A TYR* 4.2 4.3 - + - -
642A ASP* 2.7 55.4 + - + +
646A GLY 3.4 23.3 - - - -
647A TYR* 4.3 1.1 - - + -
648A CYS* 5.2 0.4 - - - -
651A GLN* 3.4 28.7 - - - +
668A PHE* 3.8 6.9 - + + -
671A LEU* 4.2 17.7 - - + -
672A VAL* 4.2 22.4 - - + -
675A MET* 3.3 43.5 - - + +
676A PHE* 3.4 16.0 - + - -
681A ARG* 4.2 1.6 + - - -
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Residues in contact with SER 639 (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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600A SER* 2.8 27.0 + - - -
601A PRO* 3.9 8.8 - - - +
602A GLN* 3.4 21.0 - - - +
606A ILE* 4.3 1.1 - - - -
635A CYS 3.1 12.6 + - - -
636A LYS 2.7 18.4 + - - -
638A TYR* 1.3 77.3 - - - +
640A VAL* 1.3 61.3 + - - +
642A ASP 3.7 12.8 - - - +
643A GLU* 4.9 1.7 - - - -
646A GLY* 3.9 4.9 - - - -
647A TYR* 3.7 21.3 - - - +
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Residues in contact with VAL 640 (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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595A LEU* 3.7 22.3 - - + +
598A LYS* 4.3 23.8 - - + +
599A GLU 3.4 27.4 - - - +
600A SER* 4.4 1.6 - - - -
601A PRO* 4.6 4.5 - - + -
636A LYS 3.3 11.6 + - - +
637A ALA* 3.2 9.7 + - - +
638A TYR 3.1 0.4 - - - -
639A SER* 1.3 83.6 + - - +
641A TYR* 1.3 61.9 + - - +
642A ASP 3.5 0.2 - - - -
643A GLU* 3.6 21.8 - - - +
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Residues in contact with TYR 641 (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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588A LEU* 3.9 21.2 - - + +
591A LYS* 4.3 20.7 + - + -
595A LEU* 3.8 27.5 - - + +
637A ALA 2.9 16.7 + - - +
638A TYR* 3.8 7.9 - + - +
640A VAL* 1.3 77.3 - - - +
642A ASP* 1.3 58.9 + - - +
643A GLU* 3.3 9.9 + - - +
668A PHE* 4.2 10.5 - + + -
672A VAL* 3.7 30.6 - - + +
676A PHE* 3.7 34.1 - + - -
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Residues in contact with ASP 642 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638A TYR* 2.7 49.7 + - + +
639A SER 3.7 4.3 - - - +
641A TYR* 1.3 74.6 - - - +
643A GLU* 1.3 57.6 - - - +
644A GLU* 3.4 2.8 + - - +
645A ILE* 3.1 25.3 + - - +
646A GLY* 2.8 27.6 + - - +
676A PHE* 3.7 10.2 - - + -
681A ARG* 2.8 40.7 + - - +
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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