Contacts of the strand formed by residues 524 - 528 (chain L) in PDB entry 4E2I
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 524 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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408L PHE* 4.2 3.7 - - - -
412L MET* 4.0 4.7 - - - -
420L ARG 3.9 2.6 - - - +
421L TYR* 3.1 33.8 - - - -
422L TRP 3.2 4.0 + - - -
469L LEU* 3.9 9.0 - - - -
470L VAL 3.1 14.1 - - - -
523L PRO* 1.3 81.6 - - - +
525L ILE* 1.3 67.3 + - - +
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Residues in contact with ILE 525 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408L PHE* 3.5 28.9 - - + -
421L TYR* 4.1 0.8 - - - -
422L TRP* 3.6 11.4 - - + +
424L PHE* 3.4 41.1 - - + -
436L ALA* 4.6 7.9 - - + +
439L LEU* 3.5 36.3 - - + -
469L LEU* 6.5 1.1 - - + -
470L VAL 2.8 10.7 + - - +
471L VAL* 3.4 13.5 - - + +
472L PHE* 2.9 25.6 + - - +
524L GLY* 1.3 79.9 - - - +
526L VAL* 1.3 72.0 + - - +
527L THR* 4.2 6.7 - - + -
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Residues in contact with VAL 526 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421L TYR* 3.6 18.6 - - + -
422L TRP 3.0 6.3 + - - -
423L LEU* 3.2 9.9 - - - +
424L PHE 3.0 21.2 + - - -
472L PHE* 3.5 36.6 - - + -
475L VAL* 4.1 9.6 - - + -
494L LEU* 3.8 31.4 - - + -
501L LEU* 5.1 2.9 - - + -
525L ILE* 1.3 74.3 - - - +
527L THR* 1.3 65.1 + - - +
528L MET* 4.8 2.9 - - + -
541L PHE* 3.7 26.9 - - + -
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Residues in contact with THR 527 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424L PHE* 3.5 30.1 - - + -
432L LYS* 4.9 10.8 - - + -
433L THR* 6.1 0.4 - - - -
436L ALA* 3.7 26.0 - - + -
471L VAL* 5.0 1.3 - - + -
472L PHE 2.8 25.5 + - - +
473L GLU* 3.2 14.2 + - - +
474L ASP* 2.8 23.2 + - - -
475L VAL* 3.2 24.9 + - - +
525L ILE* 4.2 3.6 - - + -
526L VAL* 1.3 76.3 - - - +
528L MET* 1.3 62.4 + - - +
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Residues in contact with MET 528 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423L LEU* 3.5 22.2 - - + -
424L PHE 3.3 5.0 + - - +
425L LYS* 3.5 32.2 - - + -
426L GLY 3.0 21.5 + - - -
432L LYS* 3.9 0.7 - - - +
474L ASP* 4.3 3.1 - - - +
475L VAL* 3.5 26.9 - - + +
491L ILE* 3.6 25.8 - - + -
494L LEU* 4.9 3.4 - - + -
526L VAL* 4.8 4.9 - - + -
527L THR* 1.3 78.2 - - - +
529L ASN* 1.3 74.6 + - - +
531L TYR* 4.1 12.1 - - + +
533L VAL* 3.5 33.4 - - + -
537L LEU* 5.3 0.2 - - + -
541L PHE* 5.0 2.9 - - + -
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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
------------------------------------------------------------
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