Contacts of the strand formed by residues 478 - 483 (chain A) in PDB entry 4FLH
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 478 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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477A ARG* 1.3 75.0 - - - +
479A GLU* 1.3 60.9 + - - -
480A TYR* 3.4 15.0 - - - -
519A LEU* 3.4 13.2 - - - -
520A LEU* 2.7 36.8 + - - +
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Residues in contact with GLU 479 (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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366A ARG* 2.7 44.9 + - - -
478A GLY* 1.3 72.1 - - - -
480A TYR* 1.3 71.7 + - - +
481A VAL* 6.3 0.9 - - + -
517A SER* 5.9 0.2 - - - -
518A ILE 2.9 21.4 + - - +
519A LEU* 4.1 12.9 - - + +
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Residues in contact with TYR 480 (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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169A HIS* 3.8 50.7 + + + -
170A ASP* 6.0 0.5 - - - +
466A LEU* 4.4 13.2 - - + -
476A ARG* 3.2 40.4 + - + +
477A ARG 3.4 20.9 + - - -
478A GLY 3.4 17.9 - - - -
479A GLU* 1.3 79.0 - - - +
481A VAL* 1.3 65.0 + - - +
482A LEU* 3.9 13.0 - - + -
516A ILE 3.8 0.7 - - - +
517A SER* 3.4 4.3 - - - -
518A ILE* 3.0 49.1 + - + +
520A LEU* 4.5 4.0 - - + -
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Residues in contact with VAL 481 (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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169A HIS* 6.2 1.1 - - - +
479A GLU* 6.0 1.1 - - + -
480A TYR* 1.3 75.0 - - - +
482A LEU* 1.3 61.0 + - - +
483A HIS* 3.8 17.0 + - - +
510A LYS* 5.4 2.6 + - - -
515A SER* 4.3 17.5 - - - +
516A ILE 3.4 5.2 - - - +
517A SER* 3.5 24.0 - - - +
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Residues in contact with LEU 482 (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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169A HIS* 3.6 36.1 - - + +
431A LEU* 4.1 26.2 - - + -
464A VAL* 4.0 20.9 - - + -
465A ASN 4.5 1.1 - - - +
466A LEU* 4.3 24.2 - - + -
480A TYR* 4.3 13.0 - - + -
481A VAL* 1.3 74.1 - - - +
483A HIS* 1.3 61.9 + - - +
484A MET* 3.6 4.3 + - - +
506A THR* 3.8 11.9 - - + -
515A SER* 3.2 5.2 - - - -
516A ILE* 3.0 38.2 + - + +
518A ILE* 4.4 10.1 - - + -
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Residues in contact with HIS 483 (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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464A VAL* 4.1 3.2 - - - +
481A VAL* 3.8 19.7 + - + +
482A LEU* 1.3 70.9 - - - +
484A MET* 1.3 60.5 + - - +
485A TRP* 5.2 0.2 + - - -
506A THR* 3.4 14.0 + - - +
507A ASN* 2.9 43.9 + - - +
510A LYS* 3.3 57.7 + - + +
513A SER* 3.2 29.0 + - - +
514A MET 3.4 2.0 - - - -
515A SER* 3.8 19.2 - - - -
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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