Contacts of the strand formed by residues 453 - 457 (chain A) in PDB entry 5M4G
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 GLU 453 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313A SER* 4.2 12.6 - - - +
314A ARG* 3.4 21.7 + - - -
317A MET* 4.0 19.2 - - + +
410A THR* 3.3 1.7 - - - -
411A VAL* 2.9 36.4 + - + +
451A ILE* 4.5 3.5 - - + +
452A GLU* 1.3 73.1 - - - +
454A ASP* 1.3 68.2 + - - +
455A VAL* 4.2 3.1 + - + -
464A LEU* 3.7 24.0 - - + +
466A THR* 3.2 24.4 - - - +
468A VAL* 4.7 0.5 - - - +
470A ARG* 2.9 40.9 + - - +
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Residues in contact with ASP 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A ASN* 3.1 35.9 + - - +
286A SER* 3.8 2.9 - - - -
287A ASP 2.6 45.8 + - - +
372A LEU* 4.0 11.9 - - + +
408A VAL* 5.3 4.7 - - + -
409A LEU 3.6 5.4 - - - +
410A THR* 3.5 11.0 - - - +
453A GLU* 1.3 74.9 - - - +
455A VAL* 1.3 64.6 + - - +
464A LEU* 3.7 1.2 - - - +
465A LEU* 2.8 34.0 + - + +
466A THR* 2.9 9.2 + - - -
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Residues in contact with VAL 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A MET* 4.0 17.5 - - - -
320A MET* 3.6 31.9 - - + -
408A VAL* 3.4 7.6 - - - +
409A LEU* 2.9 42.5 + - + +
411A VAL* 4.1 12.6 - - + -
453A GLU* 4.5 2.0 - - + -
454A ASP* 1.3 81.0 - - - +
456A VAL* 1.3 65.1 + - - +
457A VAL 5.1 0.2 - - - +
462A ILE* 3.8 30.5 - - + -
463A GLU 3.3 9.6 - - - +
464A LEU* 4.0 7.4 - - + -
465A LEU* 4.5 0.9 - - - +
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Residues in contact with VAL 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A LEU* 3.7 42.4 - - + -
406A GLY* 4.5 7.0 - - - -
407A MET 3.5 11.2 - - - +
408A VAL* 4.2 4.9 - - + -
455A VAL* 1.3 77.7 - - - +
457A VAL* 1.3 73.7 + - - +
458A THR* 3.8 2.6 - - + +
462A ILE* 3.1 6.5 - - - -
463A GLU* 2.8 51.0 + - + +
465A LEU* 3.7 33.2 - - + -
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Residues in contact with VAL 457 (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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320A MET* 4.5 7.9 - - + -
321A LYS* 4.3 4.3 - - - +
322A PRO* 4.0 16.8 - - + -
403A LEU* 4.2 16.8 - - + -
404A GLN 3.4 34.8 - - - +
405A PRO* 3.4 0.3 - - - +
406A GLY 2.9 24.8 + - - -
407A MET* 2.9 16.8 + - + +
409A LEU* 3.9 22.0 - - + -
456A VAL* 1.3 77.2 - - - +
458A THR* 1.3 70.9 + - - +
461A GLY 3.6 9.6 - - - +
462A ILE* 4.4 2.5 - - + -
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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