Contacts of the strand formed by residues 480 - 485 (chain A) in PDB entry 4XE4
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 LEU 480 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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478A THR 3.3 17.7 - - - +
479A THR* 1.3 74.7 - - - +
481A CYS* 1.3 59.0 + - - +
504A GLN* 3.9 24.2 - - - +
505A VAL 5.0 0.4 - - - -
506A PRO* 6.0 0.4 - - - -
550A CYS* 3.4 5.9 - - - +
551A GLU* 3.1 58.0 + - + +
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Residues in contact with CYS 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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475A PRO* 6.0 0.2 - - - -
479A THR* 4.4 9.0 - - - -
480A LEU* 1.3 77.8 - - - +
482A GLN* 1.3 61.8 + - - +
504A GLN* 3.4 13.6 + - - +
505A VAL* 2.9 42.3 + - + +
506A PRO 5.2 0.2 - - - -
507A PHE* 4.4 21.3 - - - +
530A ALA* 5.4 0.4 - - + -
548A LEU* 4.1 15.5 - - + -
549A VAL 3.4 4.9 - - - -
550A CYS* 2.1 45.8 - - - +
562A GLN* 5.6 0.2 - - - -
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Residues in contact with GLN 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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365A HIS* 4.0 17.9 - - + -
481A CYS* 1.3 77.1 - - - +
483A VAL* 1.3 61.3 + - - +
502A GLU* 3.3 30.3 + - - +
503A ALA 3.2 25.1 - - - +
504A GLN* 4.2 18.7 + - - +
547A PRO 4.0 0.5 - - - +
548A LEU* 3.4 6.5 - - - -
549A VAL* 2.7 52.3 + - + +
559A LEU* 5.2 9.3 - - - +
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Residues in contact with VAL 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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365A HIS* 5.4 0.4 - - - -
482A GLN* 1.3 74.8 - - - +
484A ALA* 1.3 60.9 + - - +
502A GLU* 3.3 3.2 - - - +
503A ALA* 2.7 51.0 + - + +
505A VAL* 4.7 10.3 - - + +
541A GLN* 4.6 13.4 - - + +
542A GLY* 5.0 3.4 - - - -
547A PRO 3.4 17.5 - - - +
548A LEU* 4.0 9.0 - - + -
565A ILE* 3.6 26.9 - - + -
580A TYR* 3.9 21.8 - - + +
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Residues in contact with ALA 484 (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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365A HIS* 3.7 36.8 - - + +
368A ILE* 3.5 23.9 - - + +
483A VAL* 1.3 77.6 - - - +
485A GLY* 1.3 58.0 + - - +
500A LEU* 4.3 3.4 - - + -
501A GLN 3.3 12.6 - - - +
502A GLU* 4.2 0.2 - - - +
541A GLN* 5.6 0.2 - - - -
542A GLY* 4.3 10.7 - - - -
543A ASP* 4.4 1.2 - - - +
546A GLY* 4.8 0.7 - - - -
547A PRO* 3.7 19.7 + - + +
565A ILE* 4.7 2.6 - - - +
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Residues in contact with GLY 485 (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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368A ILE* 4.3 3.8 - - - -
484A ALA* 1.3 73.0 - - - +
486A TRP* 1.3 62.2 + - - -
487A GLY 3.8 0.2 - - - -
500A LEU* 3.3 16.2 - - - -
501A GLN* 2.8 33.8 + - - +
541A GLN* 4.1 2.2 - - - +
542A GLY 3.9 13.1 - - - +
543A ASP* 3.0 14.1 - - - -
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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