Contacts of the helix formed by residues 634 - 643 (chain A) in PDB entry 1AUQ
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 PHE 634 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594A THR* 3.9 8.5 - - - -
595A SER* 3.3 28.6 + - - +
598A LEU* 3.4 22.2 - - + -
631A SER* 3.2 17.1 + - - +
632A ARG 3.4 0.4 + - - -
633A ASN* 1.3 76.8 - - - +
635A VAL* 1.3 70.3 + - + +
637A TYR* 3.1 14.6 + - - +
638A VAL* 3.1 27.1 + - + +
661A GLN* 3.5 58.8 - - + +
664A LEU* 4.2 21.1 - - + -
665A ILE* 3.6 27.8 - - + -
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Residues in contact with VAL 635 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632A ARG 5.3 0.6 + - - -
633A ASN 3.4 0.8 - - - -
634A PHE* 1.3 79.5 - - + +
636A ARG* 1.3 53.7 + - + +
638A VAL* 3.2 5.7 + - - +
639A GLN* 2.7 61.0 + - + +
664A LEU* 3.8 37.9 - - + -
668A GLN* 4.0 15.0 - - - +
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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
----------------------------------------------------------
602A LEU* 4.7 1.2 - - - +
632A ARG* 3.4 20.7 + - - +
633A ASN* 2.9 39.3 + - + +
635A VAL* 1.3 79.8 - - + +
637A TYR* 1.3 58.4 + - + +
639A GLN* 3.3 14.8 + - - +
640A GLY* 2.8 26.7 + - - -
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Residues in contact with TYR 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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595A SER* 3.3 35.0 - - - -
596A GLU* 4.3 9.0 + - - -
598A LEU* 4.1 20.2 - - + +
599A LYS* 3.3 38.0 + - + +
602A LEU* 3.7 19.5 - - + +
603A PHE* 4.0 11.9 - + - -
633A ASN* 3.0 58.2 + - + -
634A PHE* 3.6 4.7 - - - +
636A ARG* 1.3 78.4 - - + +
638A VAL* 1.3 58.5 + - - +
640A GLY* 3.2 1.6 + - - -
641A LEU* 3.0 33.7 + - - +
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Residues in contact with VAL 638 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598A LEU* 3.5 29.8 - - + -
634A PHE* 3.1 30.0 + - + +
635A VAL* 3.6 9.6 - - - +
637A TYR* 1.3 75.2 - - - +
639A GLN* 1.3 59.6 + - - +
641A LEU* 3.6 8.5 + - - +
642A LYS* 3.1 25.3 + - - +
648A VAL* 5.1 7.6 - - + +
664A LEU 5.4 0.2 - - - -
665A ILE* 4.0 24.7 - - + -
668A GLN* 3.6 28.7 - - + +
672A ASN* 4.6 4.2 + - - +
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Residues in contact with GLN 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 VAL* 2.7 40.7 + - - +
636A ARG* 3.7 18.3 - - - +
638A VAL* 1.3 71.2 - - - +
640A GLY* 1.3 63.2 + - - +
642A LYS* 3.2 13.2 + - + +
643A LYS* 3.1 41.9 + - - +
668A GLN* 3.6 25.5 + - + +
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Residues in contact with GLY 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 LEU* 3.7 22.4 - - - +
636A ARG 2.8 15.6 + - - -
637A TYR 3.6 4.0 - - - -
638A VAL 3.2 0.2 - - - -
639A GLN* 1.3 77.6 - - - +
641A LEU* 1.3 60.3 + - - +
643A LYS* 3.2 23.3 + - - +
644A LYS* 3.3 11.4 + - - +
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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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598A LEU* 3.8 38.6 - - + +
601A THR* 3.9 14.8 - - + +
602A LEU* 3.6 36.8 - - + +
606A PHE* 4.5 0.9 - - + -
618A ALA* 5.4 0.4 - - + -
637A TYR 3.0 20.7 + - - +
638A VAL* 4.0 5.2 - - - +
640A GLY* 1.3 75.4 - - - +
642A LYS* 1.3 57.4 + - - +
644A LYS* 3.4 1.5 + - - +
645A LYS 3.2 3.5 + - - -
646A VAL* 2.7 69.7 + - + +
648A VAL* 3.9 15.0 - - + -
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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 VAL 3.1 16.2 + - - +
639A GLN* 3.3 17.7 - - + +
640A GLY 3.1 0.2 - - - -
641A LEU* 1.3 79.5 - - - +
643A LYS* 1.3 66.2 + - + +
645A LYS* 3.1 22.0 + - - +
646A VAL 4.2 6.5 + - - +
647A ILE* 6.5 0.4 - - - -
668A GLN* 3.7 24.2 - - + +
669A ALA* 4.0 24.7 - - + +
672A ASN* 5.6 1.8 - - - +
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Residues in contact with LYS 643 (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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639A GLN* 3.1 27.5 + - - +
640A GLY* 3.2 11.5 + - - +
642A LYS* 1.3 81.0 - - + +
644A LYS* 1.3 59.4 + - + +
645A LYS* 3.0 10.2 + - - +
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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