Contacts of the helix formed by residues 619 - 631 (chain A) in PDB entry 1WBP
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 SER 619 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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617A GLU 3.7 2.4 + - - -
618A TRP* 1.3 73.3 - - - +
620A GLN* 1.3 65.7 + - - +
621A GLU* 3.6 14.0 + - - +
622A GLU* 2.9 33.4 + - - +
623A ALA* 2.9 19.2 + - - +
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Residues in contact with GLN 620 (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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609A PHE* 3.7 30.0 - - + -
613A VAL* 4.4 18.2 - - + +
618A TRP 3.5 3.1 + - - -
619A SER* 1.3 70.9 - - - +
621A GLU* 1.3 70.7 + - - +
624A ALA* 3.1 26.3 + - - +
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Residues in contact with GLU 621 (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 SER* 3.0 12.7 + - - +
620A GLN* 1.3 88.7 + - - +
622A GLU* 1.3 64.9 + - + +
624A ALA* 3.5 4.9 - - - +
625A GLY* 3.3 17.0 + - - -
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Residues in contact with GLU 622 (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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186A LEU* 3.9 24.8 - - + +
190A LYS* 5.9 1.0 + - - -
618A TRP* 3.9 19.0 - - + -
619A SER* 2.9 29.4 + - - +
621A GLU* 1.3 80.0 - - + +
623A ALA* 1.3 65.8 + - - +
624A ALA 3.1 2.0 + - - -
625A GLY* 3.2 2.9 + - - -
626A PHE* 3.1 23.6 + - - +
652A TRP* 5.1 3.1 + - - -
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Residues in contact with ALA 623 (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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609A PHE* 3.7 9.2 - - + -
612A LEU* 3.4 26.8 - - + +
613A VAL* 3.4 33.4 - - + -
618A TRP* 3.9 9.0 - - + -
619A SER 2.9 11.0 + - - +
622A GLU* 1.3 75.7 - - - +
624A ALA* 1.3 53.0 + - - +
627A THR* 2.7 42.2 + - - -
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Residues in contact with ALA 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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609A PHE* 3.8 14.8 - - + -
620A GLN 3.1 20.3 + - - +
621A GLU* 3.5 7.2 - - - +
622A GLU 3.1 0.2 - - - -
623A ALA* 1.3 75.3 - - - +
625A GLY* 1.3 59.5 + - - +
627A THR* 4.0 2.3 - - - -
628A ASP* 2.9 30.7 + - - +
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Residues in contact with GLY 625 (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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621A GLU 3.3 7.4 + - - -
622A GLU* 3.2 6.4 + - - -
624A ALA* 1.3 79.3 - - - +
626A PHE* 1.3 62.0 + - - +
628A ASP* 3.4 7.1 + - - +
629A PHE* 3.2 21.7 + - - +
650A HIS* 4.3 2.1 - - - -
652A TRP* 3.6 18.9 - - - +
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Residues in contact with PHE 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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541A ALA* 3.8 24.2 - - + -
542A PHE* 3.8 15.3 - + - -
545A ALA* 3.8 11.4 - - + -
546A THR* 5.4 0.2 - - + -
612A LEU* 4.0 11.4 - - + -
618A TRP* 3.3 36.8 - + + -
622A GLU 3.1 16.0 + - - +
623A ALA 3.8 3.4 - - - +
625A GLY* 1.3 73.8 - - - +
627A THR* 1.3 61.2 + - - +
629A PHE* 2.8 9.8 + + - +
630A LEU* 2.8 64.5 + - + +
652A TRP* 3.5 41.4 - + - +
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Residues in contact with THR 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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608A LEU* 3.7 13.0 - - + +
609A PHE* 3.2 35.6 + - + +
612A LEU* 3.2 16.5 - - - +
623A ALA 2.7 27.4 + - - -
624A ALA* 4.0 4.7 - - - -
626A PHE* 1.3 72.8 - - - +
628A ASP* 1.3 63.3 + - - +
629A PHE 3.1 0.9 + - - -
631A LEU* 3.1 55.0 + - + +
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Residues in contact with ASP 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 ALA 2.9 20.9 + - - +
625A GLY* 3.7 7.2 - - - +
626A PHE 3.2 0.4 - - - -
627A THR* 1.3 76.6 - - - +
629A PHE* 1.3 59.0 + - - +
631A LEU* 5.4 1.8 - - - -
632A PRO* 3.6 18.1 - - - +
650A HIS* 3.1 27.3 + - + -
651A PRO* 5.5 2.1 - - - +
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Residues in contact with PHE 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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193A ILE* 4.1 16.6 - - + -
197A LEU* 4.4 4.7 - - + -
541A ALA* 5.1 2.5 - - + -
625A GLY 3.2 11.9 + - - +
626A PHE* 2.8 11.3 + + - +
628A ASP* 1.3 81.0 - - - +
630A LEU* 1.3 79.3 + - + +
632A PRO* 3.3 10.1 - - - +
633A MET* 3.7 31.4 - - + +
647A CYS* 3.8 29.5 - - + -
650A HIS* 3.4 26.4 - + + -
652A TRP* 3.3 43.3 - + + -
653A LEU* 3.8 23.1 - - + -
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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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538A ALA* 3.7 34.3 - - + +
541A ALA* 4.1 7.0 - - + -
542A PHE* 4.3 16.2 - - + -
550A LEU* 6.0 0.9 - - + -
608A LEU* 3.7 28.3 - - + -
626A PHE* 2.8 60.7 + - + +
629A PHE* 1.3 84.3 - - + +
631A LEU* 1.3 54.7 + - - +
633A MET* 2.7 38.4 + - - +
634A LEU* 3.2 12.9 + - + +
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Residues in contact with LEU 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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573A LEU* 3.8 22.4 - - + -
608A LEU* 3.3 35.0 - - + -
627A THR* 3.1 34.1 + - + +
628A ASP* 5.4 1.8 - - - -
630A LEU* 1.3 71.6 - - - +
632A PRO* 1.3 66.1 - - + +
634A LEU* 2.7 24.2 + - + +
635A GLU* 3.3 12.7 + - - +
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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