Contacts of the helix formed by residues 623 - 642 (chain A) in PDB entry 5FG6
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 623 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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567A LEU* 3.7 15.3 - - - -
571A LEU* 4.6 0.4 - - - +
621A TYR* 3.3 8.7 - - - +
622A LYS* 1.3 106.2 - - + +
624A LEU* 1.3 64.8 + - - +
625A HIS* 3.2 15.9 + - - +
626A GLU* 2.9 44.4 + - - +
627A PHE* 3.5 8.3 + - - +
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Residues in contact with LEU 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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567A LEU* 4.0 8.4 - - + +
570A LEU* 5.0 10.3 - - + -
571A LEU* 3.7 25.8 - - + -
574A VAL* 5.1 2.5 - - + -
623A ASN* 1.3 75.5 - - - +
625A HIS* 1.3 58.0 + - - +
627A PHE* 3.1 17.1 + - + +
628A GLU* 2.8 33.0 + - - +
663A LEU* 4.4 15.9 - - + +
666A ALA* 4.2 12.8 - - + +
667A ARG* 3.7 44.2 - - + +
670A VAL* 5.1 4.7 - - + -
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Residues in contact with HIS 625 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623A ASN* 3.2 15.7 + - - +
624A LEU* 1.3 79.4 - - - +
626A GLU* 1.3 60.6 + - + +
628A GLU* 3.2 13.4 + - - +
629A GLU* 2.9 65.6 + - + +
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Residues in contact with GLU 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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615A ARG* 3.2 23.5 + - - +
620A GLY 3.9 1.4 - - - +
621A TYR* 3.6 17.5 - - + -
622A LYS* 2.9 46.6 + - - +
623A ASN* 2.9 24.5 + - - +
624A LEU 3.3 0.4 - - - -
625A HIS* 1.3 79.0 - - + +
627A PHE* 1.3 61.8 + - - +
629A GLU* 3.4 20.7 + - - +
630A ASP* 3.3 17.7 + - - +
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Residues in contact with PHE 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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571A LEU* 3.7 42.4 - - + -
574A VAL* 3.6 21.5 - - + -
575A LEU* 3.9 35.2 - - + -
578A LEU* 3.8 14.8 - - + -
612A MET* 3.5 30.2 - - + +
616A LEU* 4.3 6.5 - - + -
621A TYR* 3.5 31.7 - + + -
623A ASN 3.5 6.0 + - - +
624A LEU* 3.1 9.6 + - + +
626A GLU* 1.3 76.5 - - - +
628A GLU* 1.3 66.0 + - - +
630A ASP 3.1 3.3 + - - -
631A PHE* 3.1 18.5 + - + +
663A LEU* 4.0 12.3 - - + -
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Residues in contact with GLU 628 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624A LEU* 2.8 19.5 + - + +
625A HIS* 3.2 17.0 + - - +
627A PHE* 1.3 80.2 - - - +
629A GLU* 1.3 56.8 + - + +
631A PHE* 3.2 7.5 + - - +
632A ASP* 2.8 31.7 + - - +
663A LEU* 3.8 24.3 - - + +
667A ARG* 5.0 16.3 + - - -
703A EDO 2.8 46.6 + - - +
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Residues in contact with GLU 629 (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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625A HIS* 2.9 47.0 + - + +
626A GLU* 3.6 27.8 - - - +
627A PHE 3.2 0.2 - - - -
628A GLU* 1.3 76.9 - - + +
630A ASP* 1.3 58.8 + - - +
632A ASP* 3.3 12.2 + - - +
633A LEU* 3.0 30.7 + - - +
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Residues in contact with ASP 630 (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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607A MET* 3.4 36.4 - - + +
612A MET* 3.9 12.7 - - + -
615A ARG* 3.0 30.2 + - - -
621A TYR* 2.6 29.8 + - - +
626A GLU 3.3 3.8 + - - +
627A PHE 3.1 9.6 + - - +
629A GLU* 1.3 76.2 - - - +
631A PHE* 1.3 65.4 + - - +
633A LEU* 3.2 22.9 + - - +
634A ILE* 3.2 10.4 + - - +
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Residues in contact with PHE 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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578A LEU* 3.9 26.7 - - + -
609A PHE* 4.2 12.3 - + - -
612A MET* 3.9 13.1 - - + +
627A PHE* 3.1 10.7 + - + +
628A GLU* 3.2 7.4 + - - +
630A ASP* 1.3 74.9 - - - +
632A ASP* 1.3 73.6 + - - +
634A ILE* 3.1 17.8 + - + +
635A ILE* 3.2 32.8 + - + +
655A LEU* 3.5 47.6 - - + -
656A ARG* 4.5 5.6 - - + -
659A GLY* 4.0 11.7 - - - -
660A GLY 4.5 1.3 - - - -
663A LEU* 3.4 31.0 - - + -
703A EDO 4.0 7.6 - - - -
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Residues in contact with ASP 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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628A GLU* 2.8 24.9 + - - +
629A GLU* 3.6 10.4 - - - +
631A PHE* 1.3 81.1 - - - +
633A LEU* 1.3 57.3 + - - +
635A ILE* 3.3 5.8 + - - +
636A ASP* 2.8 48.0 + - - +
703A EDO 2.6 37.8 + - - -
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Residues in contact with LEU 633 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605A HIS* 3.7 43.5 - - + +
607A MET* 3.8 16.8 - - + -
629A GLU 3.0 15.7 + - - +
630A ASP* 3.2 27.8 + - - +
632A ASP* 1.3 74.3 - - - +
634A ILE* 1.3 66.0 + - - +
636A ASP* 4.5 4.3 - - + +
637A ASN* 2.8 42.1 + - - +
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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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587A PHE* 3.4 37.3 - - + +
607A MET* 3.7 28.0 - - + +
608A ASP* 3.7 25.8 - - - -
609A PHE* 3.7 18.8 - - + +
612A MET* 3.7 21.3 - - - -
630A ASP 3.2 9.4 + - - +
631A PHE* 3.1 10.4 + - + +
633A LEU* 1.3 80.1 - - - +
635A ILE* 1.3 70.0 + - + +
637A ASN* 4.0 2.7 - - - +
638A CYS* 3.3 20.8 + - - +
655A LEU* 4.6 3.4 - - + -
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Residues in contact with ILE 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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587A PHE* 5.4 0.7 - - + -
631A PHE* 3.2 31.1 + - + +
632A ASP* 3.7 7.0 - - - +
633A LEU 3.2 0.6 - - - -
634A ILE* 1.3 77.3 - - + +
636A ASP* 1.3 67.6 + - - +
638A CYS* 3.2 3.1 + - - +
639A MET* 3.0 51.1 + - + +
652A ALA* 3.6 25.7 - - - +
655A LEU* 3.8 26.7 - - + -
656A ARG* 3.7 35.7 - - + +
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Residues in contact with ASP 636 (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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632A ASP* 2.8 36.2 + - - +
633A LEU* 4.3 5.3 - - + +
635A ILE* 1.3 79.8 - - - +
637A ASN* 1.3 66.7 + - - +
639A MET* 3.4 7.7 + - - +
640A LYS* 2.9 26.7 + - - +
656A ARG* 6.0 0.2 - - - -
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Residues in contact with ASN 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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599A TYR* 3.5 17.6 + - - +
603A ILE* 3.6 28.3 - - + +
605A HIS 2.8 28.2 + - - +
606A PRO* 3.6 14.1 - - - +
607A MET 3.7 7.9 + - - +
633A LEU* 2.8 35.8 + - - +
634A ILE* 4.0 3.7 - - - +
636A ASP* 1.3 77.4 - - - +
638A CYS* 1.3 58.9 + - - +
640A LYS* 3.3 1.0 + - - +
641A TYR* 2.9 33.1 + - - +
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Residues in contact with CYS 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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587A PHE* 3.9 16.8 - - + -
599A TYR* 4.8 1.3 + - - -
634A ILE 3.3 16.2 + - - +
635A ILE 3.2 5.4 + - - +
637A ASN* 1.3 78.6 - - - +
639A MET* 1.3 58.0 + - - +
641A TYR* 4.9 0.4 - - - -
642A ASN* 2.9 53.7 + - - +
648A PHE* 3.3 30.5 - - - -
649A TYR* 4.6 1.0 - - - -
652A ALA* 3.6 13.2 - - + -
705A 5XE 3.7 14.8 - - - +
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Residues in contact with MET 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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635A ILE* 3.0 38.1 + - - +
636A ASP* 4.1 7.9 - - - +
638A CYS* 1.3 76.3 - - - +
640A LYS* 1.3 60.4 + - - +
642A ASN 3.4 6.2 - - - +
649A TYR* 3.3 55.3 - - + +
652A ALA* 3.9 15.5 - - + -
653A VAL* 3.8 16.2 - - + -
656A ARG* 3.8 26.5 - - - +
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Residues in contact with LYS 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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602A HIS* 3.0 35.0 + - + +
603A ILE* 4.0 10.9 - - + +
604A LYS 5.7 0.8 - - - +
636A ASP 2.9 18.8 + - - +
637A ASN* 3.7 4.0 - - - +
639A MET* 1.3 79.6 - - - +
641A TYR* 1.3 64.0 + - - +
642A ASN 3.6 1.9 + - - +
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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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596A VAL* 3.1 17.3 - - + +
598A ASP* 2.6 38.9 + - - -
599A TYR* 3.7 28.9 - + + -
602A HIS* 4.0 27.6 - + + -
603A ILE* 4.3 5.2 - - + -
637A ASN 2.9 17.7 + - - +
640A LYS* 1.3 79.9 - - - +
642A ASN* 1.3 81.5 + - - +
643A ALA 4.1 0.5 + - - -
705A 5XE 3.9 22.4 - - - -
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Residues in contact with ASN 642 (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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638A CYS* 2.9 31.8 + - - +
639A MET 3.4 16.6 - - - +
640A LYS 4.3 1.5 - - - +
641A TYR* 1.3 96.1 - - - +
643A ALA* 1.3 65.6 + - - +
644A ARG 3.7 0.2 + - - -
646A THR* 3.6 18.3 + - + +
648A PHE* 3.5 28.3 - - + +
649A TYR* 3.5 8.6 - - + +
705A 5XE 2.9 29.2 + - - -
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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