Contacts of the strand formed by residues 471 - 475 (chain A) in PDB entry 4N7E
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 ASP 471 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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458A HIS* 3.6 4.5 - - - -
459A GLY 3.4 24.6 + - - -
469A VAL 4.4 4.7 - - - +
470A PRO* 1.3 78.4 - - - +
472A VAL* 1.3 64.6 + - - +
473A TYR* 3.3 16.2 + - + -
484A LYS* 3.1 44.7 + - + -
486A LEU 3.5 9.2 - - - +
487A GLU* 3.8 5.6 - - - +
488A GLY* 3.4 18.9 + - - +
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Residues in contact with VAL 472 (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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456A ILE* 3.8 19.3 - - + -
457A ALA 3.7 6.1 - - - +
458A HIS* 3.5 30.1 - - + +
471A ASP* 1.3 73.4 - - - +
473A TYR* 1.3 57.9 + - - +
484A LYS* 3.5 4.3 - - - +
485A MET* 2.6 56.8 + - + -
486A LEU* 2.8 23.6 + - + +
488A GLY 3.4 17.7 - - - +
490A HIS* 3.9 15.7 - - + +
492A TYR* 4.1 5.6 - - + -
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Residues in contact with TYR 473 (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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410A PRO* 3.8 25.6 - - + -
413A SER* 3.9 6.4 + - - -
427A LEU* 3.9 16.8 - - + -
429A ILE* 5.9 0.9 - - + -
456A ILE* 3.6 3.3 - - - +
457A ALA 2.8 35.3 + - - +
459A GLY* 3.5 39.2 + - - -
460A SER* 4.6 0.7 - - - -
461A VAL* 3.4 25.3 + - + +
471A ASP* 3.3 32.4 + - + -
472A VAL* 1.3 75.9 - - - +
474A ILE* 1.3 60.0 + - - +
482A TRP* 4.0 18.1 - - + -
483A THR 3.3 5.6 - - - +
484A LYS* 3.6 31.0 + - + -
485A MET* 4.4 1.1 - - - -
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Residues in contact with ILE 474 (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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454A ILE* 4.7 6.5 - - + -
455A VAL 3.3 11.4 - - - +
456A ILE* 3.9 10.3 - - + -
473A TYR* 1.3 74.1 - - - +
475A SER* 1.3 71.2 + - - +
476A ASP* 5.6 1.8 - - + +
482A TRP* 3.4 6.2 - - - -
483A THR* 2.8 53.3 + - - +
485A MET* 3.9 38.5 - - + +
501A ILE* 4.0 16.2 - - + -
520A GLU* 3.3 27.6 - - + +
521A GLY 4.8 5.6 - - - +
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Residues in contact with SER 475 (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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453A GLY 3.2 1.3 - - - +
454A ILE* 3.3 3.3 - - - +
455A VAL* 2.9 35.0 + - - +
474A ILE* 1.3 80.8 - - - +
476A ASP* 1.3 58.4 + - - +
477A ASP* 3.0 7.4 + - - -
478A GLY 3.6 0.2 + - - -
479A GLY* 2.8 29.1 + - - -
481A SER 2.8 24.9 + - - -
482A TRP* 3.6 21.5 - - - -
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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