Contacts of the strand formed by residues 644 - 648 (chain A) in PDB entry 1ZM9
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 644 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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593A ILE* 5.2 1.1 - - - -
601A ILE* 4.6 0.8 - - - +
636A PHE* 3.1 26.0 - - - -
637A GLY 2.8 24.5 + - - +
638A PRO* 4.1 1.4 - - - +
642A GLY 2.8 5.1 + - - +
643A PRO* 1.3 79.2 + - - +
645A LEU* 1.3 67.6 + - - +
667A PHE* 3.8 16.8 - - + -
671A THR* 4.0 8.2 - - + +
681A MET* 3.2 21.7 - - - +
682A ARG* 3.5 9.1 - - - +
683A SER 3.4 5.3 - - - +
684A VAL* 2.9 48.1 - - - +
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Residues in contact with LEU 645 (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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593A ILE* 4.0 19.0 - - + +
597A VAL* 5.6 1.8 - - + -
601A ILE* 4.4 13.2 - - + -
606A ILE* 6.0 0.4 - - + -
619A MET* 5.1 5.4 - - - -
625A TRP* 3.8 27.8 - - + -
633A ILE* 4.3 15.7 - - + -
635A CYS 3.6 8.5 - - - +
636A PHE* 3.1 50.7 - - + -
644A ASN* 1.3 79.3 - - - +
646A VAL* 1.3 64.9 + - - +
647A ILE* 4.1 12.1 - - + -
667A PHE* 3.5 10.8 - - - -
684A VAL 3.1 7.6 + - - +
685A ARG* 4.9 1.1 - - - -
686A VAL* 3.0 24.2 + - - +
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Residues in contact with VAL 646 (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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633A ILE* 3.7 0.9 - - - +
634A TRP* 2.9 40.4 + - + -
635A CYS* 3.4 16.0 + - - -
645A LEU* 1.3 72.2 - - - +
647A ILE* 1.3 68.7 + - - +
663A VAL* 4.7 6.7 - - + -
667A PHE* 3.3 51.8 - - + -
686A VAL* 3.2 12.8 - - + +
688A ILE* 3.6 32.1 - - + -
709A MET* 4.4 5.4 - - + -
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Residues in contact with ILE 647 (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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625A TRP* 3.8 16.4 - - + -
629A ASP* 3.7 27.1 - - + +
632A LYS* 3.8 4.9 - - + -
633A ILE* 3.5 35.0 - - + -
645A LEU* 4.5 4.7 - - + -
646A VAL* 1.3 82.7 - - - +
648A ASP* 1.3 59.5 + - - +
649A GLN* 3.2 15.0 + - + -
685A ARG* 3.0 32.1 - - - +
686A VAL 2.7 8.9 + - - -
687A ASN* 3.1 21.7 - - - +
688A ILE* 2.9 26.5 + - - +
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Residues in contact with ASP 648 (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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632A LYS* 3.1 48.1 + - + +
634A TRP* 3.4 39.8 + - + +
646A VAL* 4.1 1.2 + - - +
647A ILE* 1.3 68.6 - - - +
649A GLN* 1.3 59.9 + - - +
650A THR* 2.7 39.6 + - - +
656A LEU* 3.5 13.7 - - - +
688A ILE* 4.6 7.8 - - + +
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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