Contacts of the strand formed by residues 629 - 633 (chain A) in PDB entry 1YC0
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 GLY 629 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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583A CYS* 3.3 5.9 - - - +
584A ALA 2.9 39.0 + - - -
585A GLY* 4.8 0.2 - - - -
592A ASP* 3.6 20.9 + - - -
618A TRP 4.1 0.7 - - - -
628A PRO* 1.3 72.9 - - - +
630A VAL* 1.3 61.4 + - - -
631A TYR* 3.4 9.8 - - - -
260I ARG* 3.7 11.4 - - - -
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Residues in contact with VAL 630 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573A TYR* 3.4 38.8 - - + -
577A ILE* 3.8 7.9 - - + -
581A MET* 3.8 22.9 - - + -
582A LEU 3.5 6.7 - - - +
583A CYS* 4.5 1.8 - - - -
617A SER* 3.3 7.3 + - - -
618A TRP* 2.9 82.7 + - + +
629A GLY* 1.3 71.5 - - - +
631A TYR* 1.3 68.9 + - - +
260I ARG* 5.3 0.9 + - - -
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Residues in contact with TYR 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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537A ILE* 3.2 38.4 - - + +
559A VAL* 4.3 5.5 - - - +
581A MET* 3.2 7.2 - - - -
582A LEU* 2.8 48.6 + - + +
584A ALA* 3.6 24.4 + - + -
592A ASP* 4.4 5.4 + - - -
593A ALA* 4.3 8.2 - - + +
602A LEU* 3.6 24.7 - - + -
614A GLY* 4.3 1.8 - - - -
615A ILE 3.3 12.3 - - - +
616A ILE* 3.6 41.3 - - + -
617A SER* 4.1 2.9 - - - -
629A GLY* 3.4 26.7 - - - -
630A VAL* 1.3 78.6 - - - +
632A THR* 1.3 62.6 + - - +
260I ARG* 5.3 1.1 - - - -
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Residues in contact with THR 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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497A ASP* 2.7 50.5 + - - +
498A LEU* 4.3 2.9 - - + -
580A ASN 3.6 8.1 - - - +
581A MET* 4.7 1.1 - - - +
582A LEU* 4.3 0.9 - - - +
613A TYR 3.8 0.2 - - - +
614A GLY* 3.1 21.0 - - - -
615A ILE* 3.1 32.1 + - + +
617A SER* 4.0 3.5 - - - -
631A TYR* 1.3 72.5 - - - +
633A ARG* 1.3 63.1 + - - +
634A VAL 3.0 9.4 + - - +
637A TYR* 3.8 25.6 - - + -
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Residues in contact with ARG 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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528A THR* 4.8 12.1 - - - +
564A ASP* 2.7 39.2 + - - -
577A ILE* 6.2 0.2 - - - +
578A SER 5.5 0.2 + - - -
579A PRO* 3.3 10.6 + - - +
580A ASN 2.8 23.1 + - - +
581A MET 2.8 29.8 + - - +
582A LEU* 3.5 26.2 - - + +
613A TYR* 4.2 14.9 + - + +
631A TYR 3.5 1.0 + - - -
632A THR* 1.3 68.6 - - - +
634A VAL* 1.3 63.6 + - - +
635A ALA* 3.1 11.3 + - + +
636A ASN* 3.1 48.0 + - - +
637A TYR* 3.5 7.5 - - - -
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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