Contacts of the strand formed by residues 630 - 636 (chain A) in PDB entry 2PTM
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 630 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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564A GLU 4.0 0.3 - - - +
565A VAL* 3.3 6.8 - - - +
566A PHE* 2.9 34.6 + - + +
585A ILE* 5.7 0.4 - - - -
587A GLN 3.3 4.9 - - - +
588A GLY* 3.8 2.9 - - - -
589A ILE 3.7 32.1 - - - -
590A VAL* 3.8 9.9 - - - -
626A CYS* 3.7 25.1 - - - -
628A THR 3.5 14.1 + - - -
629A TYR* 1.3 76.6 - - - +
631A THR* 1.3 63.4 + - - +
632A LEU* 4.0 19.3 + - + +
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Residues in contact with THR 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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507A TYR* 4.2 22.0 - - + +
563A PHE* 3.8 14.8 - - + -
564A GLU 3.6 3.6 - - - -
565A VAL* 4.0 18.2 - - + -
586A GLN* 2.9 42.9 + - - +
587A GLN* 2.9 33.8 + - + +
629A TYR 4.4 0.2 + - - -
630A CYS* 1.3 75.5 - - - +
632A LEU* 1.3 62.7 + - - +
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Residues in contact with LEU 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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563A PHE* 3.6 6.9 - - - -
564A GLU* 2.8 36.7 + - + +
566A PHE* 3.6 28.5 - - + -
572A VAL* 4.2 7.0 - - + -
583A PHE* 3.8 29.4 - - + -
584A PHE 3.2 7.0 - - - +
585A ILE* 3.9 30.7 - - + -
586A GLN 4.4 0.2 - - - +
590A VAL* 5.4 0.9 - - + -
609A PHE* 4.0 18.6 - - + -
630A CYS* 4.1 21.8 - - + -
631A THR* 1.3 81.5 - - - +
633A PHE* 1.3 65.0 + - - +
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Residues in contact with PHE 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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535A ASN* 5.2 4.3 - - + -
536A CYS* 4.2 18.2 - - - -
539A LEU* 3.9 20.4 - - + -
561A LEU* 3.8 38.6 - - + -
562A GLU 3.2 4.0 - - - -
563A PHE* 3.6 45.5 - + + -
583A PHE* 3.6 1.1 - - - -
584A PHE* 2.8 42.5 + - + +
586A GLN* 3.5 42.8 - - + -
632A LEU* 1.3 76.5 - - - +
634A SER* 1.3 62.6 + - - +
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Residues in contact with SER 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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560A LEU 4.0 1.2 - - - +
561A LEU* 3.3 9.6 - - - -
562A GLU* 2.8 46.6 + - - +
564A GLU* 2.6 29.2 + - - +
581A ARG* 3.9 17.0 - - - -
582A MET 3.1 13.2 - - - -
583A PHE* 3.9 9.2 - - - +
632A LEU 4.2 0.6 - - - -
633A PHE* 1.3 74.7 - - - +
635A LEU* 1.3 59.1 + - - +
636A SER 4.2 0.6 + - - -
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Residues in contact with LEU 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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557A VAL* 4.4 13.7 - - + +
560A LEU* 3.8 27.1 - - + +
561A LEU* 4.2 15.9 - - + -
581A ARG* 3.3 3.1 - - - -
582A MET* 2.9 41.9 + - + +
584A PHE* 4.6 13.7 - - + -
614A LEU* 4.2 1.4 - - - +
633A PHE 4.2 0.2 + - - -
634A SER* 1.3 72.8 - - - +
636A SER* 1.3 64.6 + - - +
639A HIS* 3.8 18.8 - - + -
640A PHE* 3.7 38.6 - - + +
643A VAL* 4.3 14.6 - - + -
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Residues in contact with SER 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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560A LEU 5.5 0.2 + - - -
580A ASP 3.5 9.0 - - - -
581A ARG* 3.7 5.8 - - - +
634A SER* 4.2 0.6 + - - -
635A LEU* 1.3 76.8 - - - +
637A VAL* 1.3 60.1 + - - +
638A GLN* 3.2 21.2 - - - +
639A HIS* 3.0 38.1 + - - +
640A PHE* 2.8 27.7 + - - +
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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