Contacts of the helix formed by residues 557 - 568 (chain A) in PDB entry 3HZJ
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 557 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555A HIS 3.0 9.5 + - - +
556A ASP* 1.3 75.8 - - - +
558A GLN* 1.3 62.9 + - - +
559A ALA* 3.2 15.8 + - - +
560A MSE 2.9 34.2 + - + +
561A LEU* 3.3 20.3 + - - +
637A GLU* 4.7 2.9 - - - +
641A CYS* 5.7 1.9 - - - -
907A UNX 3.9 21.1 - - - -
542C ALA 5.8 0.2 - - - -
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Residues in contact with GLN 558 (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 ASP 3.5 3.9 + - - +
557A ASN* 1.3 73.1 - - - +
559A ALA* 1.3 67.4 + - - +
560A MSE 3.2 0.2 - - - -
561A LEU* 3.2 10.0 + - - +
562A ASP* 2.8 61.2 + - - +
541C GLU* 4.6 23.3 + - + +
542C ALA* 4.3 25.0 + - + +
545C ALA* 4.8 3.6 + - - +
632C LEU 3.3 17.1 + - - -
633C HIS* 3.2 34.7 - - - +
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Residues in contact with ALA 559 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A ASN* 3.2 11.4 + - - +
558A GLN* 1.3 79.0 - - - +
560A MSE 1.3 59.4 + - + +
562A ASP* 3.9 6.1 - - - +
563A ARG* 3.0 28.6 + - - +
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Residues in contact with MSE 560 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A ASN* 2.9 21.2 + - + +
558A GLN 3.2 0.2 - - - -
559A ALA* 1.3 75.1 - - + +
561A LEU* 1.3 58.1 + - - +
563A ARG* 3.6 12.8 - - + +
564A TYR* 2.9 29.6 + - - +
613A TYR* 4.5 23.8 - - + +
637A GLU* 3.6 1.3 - - - +
640A PHE* 4.3 20.6 - - + -
641A CYS* 3.3 30.7 - - + -
644A VAL* 5.4 7.4 - - + -
907A UNX 3.9 11.9 - - - -
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Residues in contact with LEU 561 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A ASN 3.3 14.1 + - - +
558A GLN* 3.2 21.5 + - - +
560A MSE 1.3 76.2 - - - +
562A ASP* 1.3 62.4 + - - +
564A TYR* 3.3 3.3 + - - +
565A ARG* 3.1 63.9 + - - +
637A GLU* 3.4 39.6 + - + +
632C LEU 4.1 0.2 - - - +
633C HIS 3.5 9.9 - - - +
634C MSE 3.3 30.5 - - - +
635C PRO* 4.1 13.2 - - + -
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Residues in contact with ASP 562 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558A GLN* 2.8 50.1 + - - +
559A ALA* 3.9 6.1 - - - +
561A LEU* 1.3 77.9 - - - +
563A ARG* 1.3 62.0 + - - +
565A ARG* 3.5 13.4 + - - +
566A ILE* 3.3 30.6 + - + +
632C LEU 4.2 5.0 - - - +
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Residues in contact with ARG 563 (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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559A ALA 3.0 18.3 + - - +
560A MSE 3.6 19.5 - - + +
562A ASP* 1.3 77.7 - - - +
564A TYR* 1.3 62.0 + - - +
566A ILE* 3.1 14.4 + - - +
567A LEU* 2.9 53.1 + - + +
612A VAL* 5.2 1.4 + - - +
613A TYR* 3.5 35.9 + - + +
615A GLU* 5.5 5.1 + - - -
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Residues in contact with TYR 564 (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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560A MSE 2.9 18.4 + - - +
561A LEU 3.6 3.8 - - - +
563A ARG* 1.3 77.0 - - - +
565A ARG* 1.3 69.7 + - + +
567A LEU* 3.1 8.7 + - - -
568A ILE* 3.1 42.8 + - + +
605A LYS* 3.3 18.0 - - - +
606A ILE* 3.7 2.7 + - - -
609A ALA* 3.5 26.9 - - + -
636A GLU* 2.6 38.2 + - + +
637A GLU* 3.6 32.8 - - + -
640A PHE* 3.4 40.8 - + + -
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Residues in contact with ARG 565 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561A LEU* 3.1 36.5 + - + +
562A ASP* 3.9 11.2 + - - +
563A ARG 3.3 0.4 - - - -
564A TYR* 1.3 84.2 - - + +
566A ILE* 1.3 59.7 + - + +
568A ILE* 3.5 18.3 - - + +
569A THR* 3.2 22.3 - - - +
906A UNX 3.3 21.6 - - - -
591C TYR* 3.3 47.1 + - + +
598C ASP* 5.0 0.7 - - + +
631C LEU* 2.7 39.0 + - - +
632C LEU* 3.7 17.8 + - - +
634C MSE 3.0 18.6 + - - -
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Residues in contact with ILE 566 (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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562A ASP* 3.3 16.3 + - + +
563A ARG* 3.1 16.6 + - - +
565A ARG* 1.3 78.9 - - + +
567A LEU* 1.3 67.3 + - + +
568A ILE 3.2 0.4 - - - -
569A THR* 2.8 29.4 + - - +
570A LYS* 3.6 6.0 + - + +
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Residues in contact with LEU 567 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563A ARG* 2.9 58.4 + - + +
564A TYR* 3.1 7.1 + - - +
566A ILE* 1.3 78.2 - - + +
568A ILE* 1.3 60.7 + - - +
569A THR 3.1 1.3 + - - -
570A LYS* 3.3 22.5 + - + +
608A LYS* 4.9 2.3 - - - +
609A ALA* 3.8 25.8 - - + +
612A VAL* 3.7 33.0 - - + +
613A TYR* 3.9 11.7 - - + +
640A PHE* 3.8 31.6 - - + -
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Residues in contact with ILE 568 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564A TYR* 3.1 56.8 + - + +
565A ARG* 3.5 26.2 - - + +
567A LEU* 1.3 74.6 - - - +
569A THR* 1.3 57.8 + - - +
570A LYS 3.5 3.2 - - - +
605A LYS* 3.8 33.9 - - + +
608A LYS* 6.0 3.4 - - - -
609A ALA* 4.0 3.8 - - + +
636A GLU* 4.8 0.7 - - - +
598C ASP* 3.7 38.8 - - + +
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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