Contacts of the helix formed by residues 628 - 639 (chain A) in PDB entry 3AR2
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 628 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518A PRO* 6.0 0.9 - - + -
519A GLU* 3.6 24.0 + - - +
549A ILE* 5.4 10.1 - - - +
561A CYS* 6.3 3.4 - - + +
627A ASP* 1.3 86.6 + - - +
629A LYS* 1.3 66.5 + - - +
630A GLY* 2.5 35.0 + - - -
631A THR* 3.1 18.6 + - + +
632A ALA* 3.0 18.9 + - - +
678A ARG* 3.3 27.0 - - - +
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Residues in contact with LYS 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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627A ASP 3.3 2.6 + - - -
628A ASN* 1.3 73.1 + - - +
630A GLY* 1.3 56.5 + - - +
632A ALA* 3.2 3.5 - - + +
633A ILE* 2.8 42.2 + - + +
652A ALA* 3.5 33.1 + - + -
653A TYR 3.9 4.9 - - - +
654A THR* 3.4 22.0 - - + -
657A GLU* 2.9 36.3 + - - -
675A CYS* 5.5 1.1 - - - -
677A ALA* 3.1 24.9 - - + +
678A ARG* 4.0 4.8 - - + +
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Residues in contact with GLY 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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554A THR* 4.0 25.7 - - - +
628A ASN* 2.5 17.3 + - - +
629A LYS* 1.3 70.9 - - - +
631A THR* 1.4 53.7 + - - -
632A ALA 3.1 0.2 + - - -
633A ILE* 3.1 7.7 + - - +
634A ALA* 2.8 35.9 + - - +
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Residues in contact with THR 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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352A LYS* 4.9 2.4 + - - -
553A GLY* 3.2 30.7 - - - +
558A THR 4.5 6.5 - - - -
559A LEU 2.9 29.2 - - - +
560A ARG* 4.8 2.5 - - - -
561A CYS* 5.1 4.5 - - + +
627A ASP* 3.4 26.4 + - - +
628A ASN* 3.1 24.1 + - + +
630A GLY* 1.4 74.9 - - - +
632A ALA* 1.3 54.1 + - - +
634A ALA* 3.5 0.9 + - - +
635A ILE* 2.7 40.9 + - - +
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Residues in contact with ALA 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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352A LYS* 5.7 2.5 - - - -
623A MET* 4.1 8.5 - - - -
625A THR* 4.1 23.6 - - + -
627A ASP* 5.6 0.2 - - + -
628A ASN 3.0 13.1 + - - +
629A LYS 3.2 10.3 - - - +
630A GLY 3.0 1.0 - - - -
631A THR* 1.3 75.1 + - - +
633A ILE* 1.3 67.7 + - - +
634A ALA 3.0 1.2 + - - -
635A ILE* 3.0 7.6 + - - +
636A CYS* 2.8 23.8 + - - +
675A CYS* 3.7 22.2 - - - -
677A ALA* 4.1 4.0 - - + -
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Residues in contact with ILE 633 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629A LYS* 2.8 32.8 + - + +
630A GLY* 3.8 5.2 - - - +
632A ALA* 1.3 72.3 - - - +
634A ALA* 1.3 67.5 + - - +
636A CYS* 3.1 8.9 + - - +
637A ARG* 3.0 52.5 + - + +
642A PHE* 4.3 8.1 - - + -
648A VAL* 3.7 19.3 - - + +
652A ALA* 3.6 32.8 - - + -
675A CYS* 4.1 7.4 - - - -
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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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553A GLY 3.9 10.5 - - - +
554A THR* 4.0 15.7 - - - +
558A THR* 3.4 27.1 - - + -
630A GLY 2.8 16.8 + - - +
631A THR 3.6 4.7 - - - +
633A ILE* 1.3 82.2 - - - +
635A ILE* 1.3 63.9 + - - +
637A ARG* 3.0 19.4 + - - +
638A ARG* 3.1 12.5 + - - +
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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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352A LYS* 5.4 8.7 - - + -
356A LEU* 5.7 1.8 - - + -
357A THR* 4.8 17.9 - - + -
558A THR* 3.2 37.2 - - - +
601A ASP 4.9 10.5 - - - +
603A PRO* 4.8 5.6 - - + -
623A MET* 3.7 21.1 - - + -
631A THR* 2.7 24.9 - - - +
632A ALA* 3.4 6.3 - - - +
634A ALA* 1.3 74.3 - - - +
636A CYS* 1.3 58.4 + - - +
638A ARG* 2.8 31.3 + - - +
639A ILE* 2.8 34.3 + - + +
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Residues in contact with CYS 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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623A MET* 3.5 45.8 - - - -
632A ALA 2.8 15.0 + - - +
633A ILE 3.1 9.4 + - - +
635A ILE* 1.3 72.4 - - - +
637A ARG* 1.3 59.9 + - - +
639A ILE* 3.7 7.7 + - - +
640A GLY 3.1 2.8 + - - -
641A ILE* 2.7 48.1 + - + -
642A PHE* 3.1 20.9 + - + -
675A CYS* 3.9 17.9 - - - -
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Residues in contact with ARG 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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608A MET* 4.7 2.4 - - - +
633A ILE* 3.0 34.9 + - - +
634A ALA* 3.0 12.4 + - - +
636A CYS* 1.3 75.7 - - - +
638A ARG* 1.3 65.6 + - + +
640A GLY* 3.0 13.9 + - - -
642A PHE* 3.4 26.1 - - + +
643A GLY 2.9 27.4 + - - +
644A GLU* 4.2 25.0 + - + +
645A ASN* 5.3 1.1 - - - -
646A GLU* 3.2 30.7 + - - +
648A VAL* 3.7 11.7 - - - +
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Residues in contact with ARG 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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556A ARG 4.1 13.6 + - - -
557A ASP* 4.1 6.0 + - - -
558A THR* 2.9 42.4 + - + +
601A ASP 4.9 2.8 + - - -
602A PRO* 5.0 4.4 - - - +
603A PRO* 3.5 40.4 - - + +
608A MET* 3.6 16.8 - - - +
634A ALA 3.1 12.0 + - - +
635A ILE* 2.8 19.7 + - - +
637A ARG* 1.3 73.5 - - + +
639A ILE* 1.3 62.4 + - + +
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Residues in contact with ILE 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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356A LEU* 4.2 17.3 - - + +
603A PRO* 3.6 34.5 - - + -
604A ARG 5.4 0.9 - - - +
607A VAL* 4.1 23.6 - - + -
608A MET* 3.3 34.4 - - + +
611A ILE* 3.8 16.9 - - + +
623A MET* 4.9 1.3 - - + -
635A ILE* 2.8 29.9 + - + +
636A CYS* 3.7 9.9 - - - +
638A ARG* 1.3 78.2 - - - +
640A GLY* 1.3 60.6 + - - +
641A ILE* 3.8 26.2 - - + -
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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
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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