Contacts of the helix formed by residues 627 - 640 (chain A) in PDB entry 2WXL
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 CYS 627 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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619A LEU* 4.6 0.2 - - - -
622A GLU* 3.4 43.5 - - - +
624A TYR* 4.2 7.2 - - + +
625A LEU 3.3 7.1 + - - -
626A ASP* 1.3 80.7 + - - +
628A GLU* 1.3 66.3 + - - +
629A LEU* 4.1 1.1 - - - -
630A THR* 3.2 39.1 + - - -
631A LYS* 3.2 22.4 + - - +
663A ARG* 4.3 3.1 - - - -
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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
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590A CYS 5.8 0.2 - - - +
593A GLY 5.3 1.3 - - - +
594A SER* 4.1 31.0 + - - +
597A ILE* 4.1 18.0 - - + +
601A ARG* 3.7 22.3 + - - -
627A CYS* 1.3 70.7 - - - +
629A LEU* 1.3 61.5 + - - +
631A LYS* 3.4 15.4 + - - +
632A PHE* 2.8 30.8 + - - +
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Residues in contact with LEU 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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583A LEU* 5.4 4.9 - - + -
597A ILE* 3.6 28.1 - - + +
615A LEU* 3.3 37.0 - - + +
618A VAL* 3.8 25.6 - - + -
619A LEU* 3.8 20.0 - - + +
622A GLU* 3.7 18.1 + - - +
627A CYS* 3.3 2.1 - - - +
628A GLU* 1.3 78.8 - - - +
630A THR* 1.3 54.3 + - - +
632A PHE* 3.2 7.3 + - + +
633A LEU* 2.7 52.5 + - + +
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Residues in contact with THR 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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139A PHE* 3.8 21.8 - - + -
143A MET* 4.9 2.2 - - - -
619A LEU* 3.2 19.8 - - - +
625A LEU 4.1 5.6 + - - -
627A CYS* 3.2 26.9 + - - +
628A GLU 3.4 0.4 - - - -
629A LEU* 1.3 77.9 - - - +
631A LYS* 1.3 57.2 + - - +
633A LEU* 3.3 4.6 + - - +
634A LEU* 2.9 39.4 + - + +
663A ARG* 4.5 2.1 + - - -
667A ILE* 3.7 33.2 - - + +
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Residues in contact with LYS 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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142A LYS* 6.2 2.2 - - - +
143A MET* 4.5 21.9 - - + -
146A PHE* 3.6 41.9 - - + -
626A ASP* 5.4 1.6 - - - +
627A CYS 3.2 14.0 + - - +
628A GLU* 3.9 15.6 + - - +
630A THR* 1.3 80.1 - - - +
632A PHE* 1.3 62.4 + - - +
634A LEU* 4.5 3.8 - - - -
635A GLY* 3.0 22.3 + - - -
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Residues in contact with PHE 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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597A ILE* 3.7 27.1 - - + -
600A LEU* 3.7 21.3 - - + -
601A ARG* 4.0 40.1 - - + +
603A LEU* 4.8 6.5 - - + -
608A LEU* 4.3 18.4 - - + -
615A LEU* 4.8 7.4 - - + -
628A GLU 2.8 20.0 + - - +
629A LEU* 3.2 11.6 + - + +
631A LYS* 1.3 77.1 - - - +
633A LEU* 1.3 68.6 + - + +
635A GLY* 4.1 0.7 - - - -
636A ARG* 3.1 74.8 + - + +
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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
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608A LEU* 4.3 13.7 - - + -
612A LEU* 3.8 27.6 - - + -
615A LEU* 4.0 27.6 - - + +
616A VAL 4.5 1.3 - - - +
619A LEU* 4.0 25.4 - - + -
629A LEU* 2.7 44.5 + - + +
630A THR* 3.9 4.3 - - - +
632A PHE* 1.3 77.2 - - + +
634A LEU* 1.3 57.7 + - - +
636A ARG* 3.5 3.9 + - - +
637A ALA* 2.9 29.6 + - - +
643A ILE* 4.8 3.1 - - + +
647A LEU* 4.0 20.4 - - + +
667A ILE* 6.3 1.8 - - + -
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Residues in contact with LEU 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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139A PHE* 4.9 0.2 - - + -
143A MET* 3.9 24.9 - - + -
146A PHE* 4.3 7.9 - - + -
147A CYS* 3.8 15.0 - - - -
630A THR* 2.9 29.0 + - + +
631A LYS 3.9 2.2 - - - +
633A LEU* 1.3 74.0 - - - +
635A GLY* 1.3 59.6 + - - +
637A ALA* 3.2 4.1 + - - +
638A LEU* 2.9 34.7 + - - +
647A LEU* 4.3 7.4 - - + -
667A ILE* 3.6 36.1 - - + +
670A ALA* 3.9 20.0 - - + -
671A TYR* 3.9 21.8 - - + +
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Residues in contact with GLY 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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146A PHE* 3.6 24.0 - - - -
150A ALA* 5.8 2.1 - - - +
631A LYS 3.0 13.8 + - - -
632A PHE 4.1 0.4 - - - -
634A LEU* 1.3 75.8 - - - +
636A ARG* 1.3 63.6 + - - +
638A LEU* 3.3 6.2 + - - +
639A ALA* 3.0 24.4 + - - +
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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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600A LEU 4.3 0.2 + - - -
601A ARG* 3.2 26.4 + - - +
603A LEU* 2.8 23.4 + - - +
604A THR 3.5 12.7 + - - -
605A ASP* 3.1 28.7 + - - +
608A LEU* 3.5 27.7 - - + +
632A PHE* 3.1 57.2 + - + +
633A LEU* 3.9 4.0 - - - +
635A GLY* 1.3 75.7 - - - +
637A ALA* 1.3 56.6 + - - +
639A ALA* 3.2 8.2 + - - +
640A ASN* 3.1 30.1 + - - +
643A ILE* 4.0 4.5 - - + +
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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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165A TYR* 4.8 1.0 - - - -
633A LEU 2.9 19.3 + - - +
634A LEU 3.2 4.9 + - - +
636A ARG* 1.3 73.2 - - - +
638A LEU* 1.3 63.2 + - - +
640A ASN 2.8 20.1 + - - +
641A ARG* 4.4 0.5 - - - -
643A ILE* 3.8 13.1 - - + +
644A GLY* 3.7 23.7 - - - +
647A LEU* 3.6 23.6 - - + -
671A TYR* 3.9 15.7 + - + -
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Residues in contact with LEU 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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146A PHE* 5.0 2.9 - - + -
147A CYS* 3.5 45.8 - - + +
150A ALA* 3.7 26.6 - - + +
154A ARG* 3.8 13.5 + - - +
165A TYR* 3.3 19.8 - - - -
634A LEU* 2.9 21.7 + - + +
635A GLY* 3.9 4.7 - - - +
637A ALA* 1.3 77.9 - - - +
639A ALA* 1.3 57.7 + - - +
640A ASN 3.4 0.2 - - - -
671A TYR* 3.8 26.9 - - + +
674A GLY* 3.5 33.7 - - - +
675A SER* 4.3 3.6 - - - +
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Residues in contact with ALA 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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164A GLN 5.0 0.3 - - - +
165A TYR* 3.5 23.4 - - - +
605A ASP* 5.2 1.4 - - - +
635A GLY 3.0 16.0 + - - +
636A ARG* 3.2 7.3 + - - +
638A LEU* 1.3 79.8 - - - +
640A ASN* 1.3 59.6 + - - +
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Residues in contact with ASN 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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164A GLN 4.7 2.7 + - - +
165A TYR* 3.7 4.5 - - - -
168A PRO* 3.4 27.7 - - - +
605A ASP* 3.0 38.4 + - - +
636A ARG 3.1 5.5 + - - +
637A ALA 2.8 15.8 - - - +
638A LEU 3.4 0.8 - - - -
639A ALA* 1.3 82.1 - - - +
641A ARG* 1.3 58.8 + - - +
642A LYS* 2.9 23.5 + - - +
643A ILE* 3.1 28.7 + - + +
644A GLY 2.9 15.6 + - - -
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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