Contacts of the helix formed by residues 616 - 629 (chain A) in PDB entry 1WZ2
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 616 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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503A LEU* 5.7 0.9 - - - -
529A LEU* 4.5 9.9 - - + +
612A ASP 3.9 6.2 - - - +
613A LEU* 3.1 31.9 + - - +
614A ILE 2.8 10.3 + - - -
615A PRO* 1.3 80.1 - - - +
617A HIS* 1.3 86.8 + - - +
618A LEU 3.2 0.7 - - - -
619A THR* 2.6 30.1 + - - -
620A PHE* 2.7 42.8 + - + -
987C C 4.8 8.3 + - - +
988C A 3.4 29.5 + - - +
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Residues in contact with HIS 617 (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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41A ALA* 4.6 2.0 - - + -
529A LEU* 5.1 11.2 - - + +
532A SER* 2.9 35.7 + - - -
533A THR* 4.5 7.4 - - + -
535A TYR* 5.3 0.2 - - - -
536A MET* 4.2 7.9 - - - +
607A ARG* 3.2 43.5 + - - -
609A SER* 5.5 0.9 - - - -
613A LEU* 3.3 29.2 - - + +
616A ASN* 1.3 94.7 - - - +
618A LEU* 1.3 73.7 + - + +
619A THR 2.8 0.2 + - - -
620A PHE* 3.0 12.9 + - + -
621A PHE* 2.6 33.7 + - + +
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Residues in contact with LEU 618 (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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496A PHE* 3.7 9.0 - - + -
607A ARG* 4.5 13.2 - - + +
609A SER* 3.8 18.4 - - - +
610A GLY 3.4 21.3 - - - +
613A LEU* 2.6 43.1 + - + +
614A ILE* 3.4 21.5 - - + +
617A HIS* 1.3 78.9 - - + +
619A THR* 1.3 55.5 + - - +
621A PHE* 3.0 28.5 - - + +
622A ILE* 3.5 8.5 - - - +
638A ILE* 3.5 38.7 - - + +
640A VAL* 4.1 7.6 - - + -
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Residues in contact with THR 619 (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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496A PHE* 4.6 8.3 - - + -
499A ILE* 3.1 30.4 - - + +
500A ILE* 4.8 9.6 - - + -
503A LEU* 4.6 5.6 - - + -
614A ILE* 2.5 23.8 + - - +
616A ASN* 2.6 16.7 + - - -
618A LEU* 1.3 69.7 - - - +
620A PHE* 1.3 56.6 + - - +
621A PHE 2.8 4.0 - - - -
622A ILE* 2.7 34.6 + - + +
623A PHE* 3.1 33.2 + - + -
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Residues in contact with PHE 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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469A TYR* 3.1 48.7 - + - +
503A LEU* 4.2 24.5 - - + -
506A LYS* 3.8 33.2 - - + -
529A LEU* 4.0 20.2 - - + -
533A THR* 4.1 11.0 - - + -
615A PRO 5.1 0.2 - - - -
616A ASN* 2.7 54.1 + - + -
617A HIS* 3.2 9.6 - - - +
619A THR* 1.3 71.3 - - - +
621A PHE* 1.3 56.8 + - - +
623A PHE* 3.2 5.8 + - - -
624A ASN* 2.8 41.8 + - - +
985C A 5.8 1.1 - - - -
987C C 5.8 0.2 - - - -
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Residues in contact with PHE 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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533A THR* 3.5 20.2 - - - +
536A MET* 3.9 21.1 - - + -
604A LEU* 4.2 8.5 - - + -
607A ARG* 3.8 32.8 - - + -
617A HIS* 2.6 20.6 + - - +
618A LEU* 3.0 24.9 - - - +
619A THR 2.8 0.4 - - - -
620A PHE* 1.3 79.3 - - - +
622A ILE* 1.3 60.2 + - + -
625A HIS* 2.9 60.4 + + - +
635A PRO* 3.6 26.5 - - + -
638A ILE* 3.7 27.1 - - + -
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Residues in contact with ILE 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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478A ALA* 4.4 14.4 - - + +
481A ALA* 4.1 25.4 - - + -
482A LEU* 4.4 17.7 - - + +
485A MET* 4.3 24.7 - - + -
496A PHE* 3.8 31.9 - - + -
500A ILE* 5.2 3.6 - - + -
618A LEU 3.5 10.1 - - - +
619A THR* 2.7 23.0 + - + +
621A PHE* 1.3 75.5 - - + +
623A PHE* 1.3 68.8 + - + +
625A HIS* 3.2 6.8 - - - +
626A VAL* 3.0 20.7 + - + +
635A PRO* 4.9 6.3 - - + -
638A ILE* 4.6 0.4 - - + -
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Residues in contact with PHE 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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469A TYR* 3.6 32.8 - + + -
474A TRP* 3.5 31.3 + + + -
475A LYS* 3.5 29.8 - - + -
478A ALA* 3.4 27.8 - - + -
500A ILE* 3.8 22.2 - - + -
503A LEU* 3.8 24.2 - - + -
619A THR* 3.1 32.5 + - + -
620A PHE* 3.2 6.5 + - - +
622A ILE* 1.3 75.0 - - + +
624A ASN* 1.3 68.0 + - - +
625A HIS 2.6 5.6 + - - -
626A VAL* 2.7 25.9 + - - +
627A ALA 3.0 3.6 + - - -
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Residues in contact with ASN 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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166A GLN* 3.2 13.2 + - - +
170A LEU* 4.6 14.9 - - + +
467A ILE* 5.0 2.0 - - - +
469A TYR* 2.7 38.6 + - - -
474A TRP* 3.8 4.7 - - - -
530A SER 4.1 5.0 - - - +
533A THR* 2.8 31.3 + - - +
534A ILE* 3.7 13.3 - - + +
620A PHE* 2.8 17.7 + - - +
621A PHE 4.7 0.4 - - - +
623A PHE* 1.3 69.5 - - - +
625A HIS* 1.3 61.8 + - - +
627A ALA* 3.3 10.0 + - - +
628A ILE* 3.2 27.1 + - + +
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Residues in contact with HIS 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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533A THR 3.7 8.5 + - - -
534A ILE* 4.0 7.2 - - + +
536A MET* 3.8 8.3 - - + -
602A TYR* 3.1 30.9 + - - -
604A LEU* 5.7 2.4 - - - +
621A PHE* 2.9 48.0 + + - +
622A ILE 3.2 11.0 + - - +
623A PHE 2.6 4.6 + - - -
624A ASN* 1.3 75.5 - - - +
626A VAL* 1.3 57.5 + - + +
627A ALA 3.0 0.2 - - - -
628A ILE 2.9 4.0 + - - -
629A PHE* 2.8 54.5 + + + +
633A HIS 4.0 10.1 + - - -
634A TRP* 4.4 2.9 - - - -
635A PRO* 3.5 31.3 - - + +
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Residues in contact with VAL 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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474A TRP* 3.6 17.5 - - + +
477A LYS* 3.6 31.2 - - + +
478A ALA* 4.0 14.1 - - - +
481A ALA* 3.5 22.4 - - + -
622A ILE* 3.0 15.4 + - + +
623A PHE* 2.7 33.5 + - - +
625A HIS* 1.3 73.1 - - + +
627A ALA* 1.3 59.1 + - - +
628A ILE 3.4 0.4 + - - -
629A PHE 4.6 2.3 + - - +
634A TRP* 3.3 48.2 + - + +
635A PRO* 5.8 0.2 - - + -
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Residues in contact with ALA 627 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169A LYS 5.5 1.0 - - - +
170A LEU* 4.7 4.7 - - + -
173A LYS* 3.8 20.8 - - - +
175A TYR* 3.9 15.0 - - + -
474A TRP* 3.2 36.1 - - + +
477A LYS* 5.3 1.6 - - - +
623A PHE 3.0 4.5 + - - +
624A ASN* 3.3 12.1 - - - +
625A HIS 3.0 0.4 - - - -
626A VAL* 1.3 81.2 - - - +
628A ILE* 1.3 63.1 + - + +
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Residues in contact with ILE 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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165A TRP* 3.5 31.0 - - + -
166A GLN* 3.8 43.3 - - + +
169A LYS* 4.4 19.3 - - + +
170A LEU* 4.7 9.2 - - + -
534A ILE* 4.0 12.3 - - + -
569A LEU* 4.1 19.2 - - + +
624A ASN 3.2 13.6 + - - +
625A HIS 2.9 4.6 + - - -
626A VAL 5.0 0.2 - - - -
627A ALA* 1.3 87.6 - - + +
629A PHE* 1.3 72.5 + - + +
630A ARG* 3.9 1.6 + - - +
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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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162A PHE* 5.1 0.7 - + - -
165A TRP* 4.1 12.6 - + - -
534A ILE* 3.9 47.3 - - + -
537A ALA* 4.7 10.1 - - + -
568A PHE* 4.4 16.6 - + + -
569A LEU* 5.7 0.2 - - + -
598A PHE* 4.1 25.1 - + - -
602A TYR* 4.5 5.8 - + - -
625A HIS* 2.8 46.3 + + - +
626A VAL 4.6 2.3 - - - +
628A ILE* 1.3 93.5 - - + +
630A ARG* 1.3 52.3 - - - +
631A GLU 2.2 22.7 + - - -
633A HIS* 3.6 23.1 - - + +
634A TRP* 2.8 17.5 + - + -
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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