Contacts of the helix formed by residues 623 - 642 (chain A) in PDB entry 4RIB
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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618A ALA* 3.2 15.2 + - + +
621A ASN* 3.0 37.2 - - - +
622A GLY* 1.3 73.2 - - - +
624A TRP* 1.3 58.1 + - - +
625A GLU* 3.2 3.4 - - - -
626A GLU* 3.1 28.1 + - + +
627A ALA* 3.0 26.3 + - - +
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Residues in contact with TRP 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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619A MET* 3.7 60.6 - - + -
622A GLY* 3.0 34.7 + - - -
623A ASN* 1.3 75.6 - - - +
625A GLU* 1.3 58.7 + - + +
627A ALA* 3.6 4.8 - - - +
628A LYS* 3.0 27.7 + - - +
675A GLU 4.6 1.8 - - - -
676A ILE* 4.1 21.0 - - + +
679A ARG* 3.6 65.7 - - + +
680A LEU* 3.9 22.1 - - + +
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Residues in contact with GLU 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 1.2 - - - -
624A TRP* 1.3 76.4 - - + +
626A GLU* 1.3 64.5 + - - +
628A LYS* 3.4 38.8 + - - +
629A GLU* 3.4 17.3 + - - +
680A LEU* 3.8 23.4 - - + +
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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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618A ALA* 4.6 7.1 - - + +
623A ASN* 3.1 29.9 + - + +
625A GLU* 1.3 77.6 - - - +
627A ALA* 1.3 64.6 + - - +
629A GLU* 3.2 12.2 + - + +
630A LEU* 3.1 39.3 + - + +
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Residues in contact with ALA 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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615A ILE* 4.5 5.6 - - + +
618A ALA* 3.9 19.0 - - + +
619A MET* 4.1 21.1 - - + +
623A ASN 3.0 12.6 + - - +
624A TRP* 3.6 13.7 - - - +
625A GLU 3.2 0.2 - - - -
626A GLU* 1.3 74.8 - - - +
628A LYS* 1.3 66.0 + - - +
629A GLU 3.3 0.2 + - - -
630A LEU* 3.3 7.0 + - - +
631A ALA* 3.0 24.9 + - - +
676A ILE* 4.2 13.4 - - + +
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Residues in contact with LYS 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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624A TRP 3.0 13.5 + - - +
625A GLU* 3.4 30.2 + - - +
626A GLU 3.3 0.2 - - - -
627A ALA* 1.3 76.1 - - - +
629A GLU* 1.3 80.8 + - - +
631A ALA* 3.4 4.4 + - - +
632A GLN* 3.0 46.2 + - - +
673A PHE* 4.3 9.8 - - + -
676A ILE* 4.3 8.7 - - + +
677A LEU* 5.0 4.7 - - + -
680A LEU* 3.6 24.7 - - + -
682A MET* 4.2 23.1 - - + -
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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 GLU* 3.6 13.7 - - - +
626A GLU* 3.2 11.8 + - + +
628A LYS* 1.3 94.0 + - - +
630A LEU* 1.3 55.0 + - + +
632A GLN* 3.0 12.4 + - - +
633A CYS* 2.6 38.3 + - - +
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Residues in contact with LEU 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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611A MET* 3.6 31.4 - - + +
614A ASP* 4.3 31.6 - - + +
615A ILE* 3.9 14.8 - - + +
618A ALA* 4.7 2.5 - - + -
626A GLU* 3.1 36.4 + - + +
627A ALA* 3.3 9.6 + - - +
629A GLU* 1.3 78.9 - - + +
631A ALA* 1.3 52.7 + - - +
633A CYS* 3.4 6.6 - - + +
634A ALA* 2.8 33.8 + - - +
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Residues in contact with ALA 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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615A ILE* 4.2 15.2 - - + +
627A ALA 3.0 18.0 + - - +
628A LYS 3.6 1.6 - - - +
630A LEU* 1.3 75.1 - - - +
632A GLN* 1.3 54.1 + - - +
634A ALA* 3.0 5.7 + - - +
635A LYS* 2.6 36.0 + - - +
669A ILE* 4.9 7.2 - - + +
670A LEU* 5.8 0.3 - - - +
673A PHE* 3.5 36.8 - - + -
676A ILE* 4.4 7.9 - - + -
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Residues in contact with GLN 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 LYS* 3.0 48.9 + - - +
629A GLU* 3.6 11.8 - - - +
631A ALA* 1.3 75.6 - - - +
633A CYS* 1.3 63.3 + - - +
635A LYS* 3.2 17.2 + - + +
636A ARG* 3.2 29.3 + - - +
673A PHE* 3.9 21.4 - - + -
677A LEU* 5.9 1.2 - - - +
682A MET* 5.9 3.0 - - - +
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Residues in contact with CYS 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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611A MET* 4.6 9.2 - - + -
629A GLU 2.6 21.9 + - - +
630A LEU* 3.4 10.3 - - + +
632A GLN* 1.3 72.2 - - - +
634A ALA* 1.3 61.4 + - - +
636A ARG* 3.3 33.7 + - - +
637A ASP* 3.0 33.2 + - - +
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Residues in contact with ALA 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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611A MET* 3.7 25.8 - - + +
615A ILE* 4.6 0.2 - - + -
630A LEU 2.8 20.9 + - - +
631A ALA* 3.0 7.6 + - - +
633A CYS* 1.3 73.9 - - - +
635A LYS* 1.3 62.2 + - - +
637A ASP* 3.3 13.1 + - - +
638A TRP* 3.0 19.4 + - - +
666A TYR* 3.7 13.1 - - + +
669A ILE* 4.2 20.0 - - + -
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Residues in contact with LYS 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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631A ALA 2.6 17.1 + - - +
632A GLN* 3.5 15.7 - - + +
633A CYS 3.2 0.6 - - - -
634A ALA* 1.3 71.9 - - - +
636A ARG* 1.3 64.2 + - + +
638A TRP* 3.2 9.8 + - + +
639A ASN* 3.0 38.7 + - - +
669A ILE* 5.6 0.6 - - - +
670A LEU* 4.2 29.1 - - + +
673A PHE* 4.6 7.9 - - + -
689A GLU* 2.9 37.9 + - - +
692A SER* 5.3 4.0 + - - -
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Residues in contact with ARG 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 GLN* 3.2 22.0 + - - +
633A CYS* 3.3 36.9 + - - +
635A LYS* 1.3 75.4 - - + +
637A ASP* 1.3 67.5 + - - +
639A ASN* 2.8 20.0 + - - +
640A ARG* 2.8 32.7 + - - +
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Residues in contact with ASP 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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611A MET* 4.5 6.4 - - - +
633A CYS* 3.0 31.1 + - - +
634A ALA* 3.4 12.2 - - - +
636A ARG* 1.3 78.8 - - - +
638A TRP* 1.3 60.2 + - - +
640A ARG* 3.4 25.1 + - - +
641A LEU* 3.4 25.1 + - - +
666A TYR* 3.7 18.6 - - - +
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Residues in contact with TRP 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 ALA 3.0 7.3 + - - +
635A LYS* 3.6 11.7 - - + +
636A ARG 3.1 0.4 - - - -
637A ASP* 1.3 73.6 - - - +
639A ASN* 1.3 68.1 + - - +
641A LEU* 3.3 19.1 + - + +
642A LYS* 3.6 38.0 + - + +
647A LEU* 4.1 33.2 - - + -
662A VAL* 4.5 3.1 - - + -
663A GLY* 3.5 34.3 - - - -
666A TYR* 3.2 59.7 - + + +
667A THR* 5.4 1.8 + - - +
670A LEU* 4.8 21.0 - - + +
699A TYR* 4.3 16.4 - + - -
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Residues in contact with ASN 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 LYS* 3.0 41.8 + - - +
636A ARG* 2.8 10.9 + - - +
638A TRP* 1.3 78.6 - - - +
640A ARG* 1.3 65.4 + - - +
642A LYS* 3.2 41.2 + - - +
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Residues in contact with ARG 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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636A ARG* 2.8 35.1 + - - +
637A ASP* 3.5 31.3 + - - +
639A ASN* 1.3 77.3 - - - +
641A LEU* 1.3 68.0 + - + +
642A LYS 3.4 5.5 + - - +
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Residues in contact with LEU 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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604A ARG* 3.7 34.8 - - + +
637A ASP 3.4 13.9 + - - +
638A TRP* 3.3 20.9 + - + +
639A ASN 3.2 1.2 - - - -
640A ARG* 1.3 83.6 - - + +
642A LYS* 1.3 66.5 + - - +
643A ASN 3.3 0.5 + - - -
644A HIS* 3.2 33.7 + - + +
647A LEU* 3.8 8.3 - - + +
662A VAL* 4.9 13.5 - - + -
666A TYR* 4.6 17.7 - - + +
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Residues in contact with LYS 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 TRP* 3.6 45.2 + - + +
639A ASN* 3.2 39.3 - - - +
640A ARG 3.3 6.6 - - - +
641A LEU* 1.3 78.8 - - - +
643A ASN* 1.3 79.5 + - - +
644A HIS 3.5 1.9 + - - -
647A LEU* 4.2 7.4 - - + +
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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