Contacts of the strand formed by residues 524 - 529 (chain A) in PDB entry 2EIE
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 524 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A ASN* 4.2 17.7 + - - +
164A THR* 3.9 15.0 - - + +
165A ILE 3.3 15.7 - - - +
166A ASP* 4.3 4.4 - - - +
167A LEU* 4.0 9.0 - - - +
169A ILE 4.5 0.4 + - - -
171A PRO* 4.0 3.8 - - - +
491A ILE* 3.7 19.9 - - - +
493A ARG* 2.9 34.9 + - - -
511A GLY 3.1 25.3 + - - -
522A HIS* 3.0 11.0 + - - +
523A PHE* 1.3 83.2 + - - +
525A ALA* 1.3 63.4 + - - +
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Residues in contact with ALA 525 (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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164A THR* 3.4 7.6 - - - +
165A ILE* 2.7 34.9 + - + +
167A LEU* 4.5 3.8 - - + -
171A PRO* 5.3 0.2 - - + -
493A ARG* 3.4 4.0 - - - +
508A PHE* 3.5 42.0 - - + -
509A ASN 3.2 13.2 - - - +
510A GLY* 3.8 3.4 - - - -
524A ASP* 1.3 77.1 - - - +
526A GLN* 1.3 61.6 + - - +
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Residues in contact with GLN 526 (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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117A GLU* 2.8 39.2 + - - +
161A TRP* 3.8 22.4 - - + +
162A GLY* 5.1 4.2 - - - +
163A PRO 3.6 7.2 - - - +
164A THR* 3.7 22.5 + - - +
489A ASN* 3.0 30.0 + - - +
491A ILE* 3.7 24.3 - - + +
493A ARG* 4.1 4.4 + - - +
507A VAL 3.6 1.4 - - - +
508A PHE* 3.8 1.7 - - - -
509A ASN* 2.7 35.4 + - - +
525A ALA* 1.3 78.9 - - - +
527A ILE* 1.3 66.0 + - - +
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Residues in contact with ILE 527 (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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160A ARG 3.8 0.2 - - - +
161A TRP* 3.5 5.5 - - - -
162A GLY 2.8 44.0 + - - +
163A PRO* 3.2 23.5 + - + +
165A ILE* 4.4 12.6 - - + -
207A TRP* 3.8 21.5 - - + -
502A LEU* 4.0 9.4 - - + -
506A ARG* 3.7 38.4 - - + -
507A VAL 3.4 3.6 - - - +
508A PHE* 3.7 29.6 - - + -
526A GLN* 1.3 76.4 - - - +
528A PHE* 1.3 63.3 + - - +
529A THR* 4.4 1.1 - - - +
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Residues in contact with PHE 528 (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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158A LEU 3.9 10.1 - - - -
159A GLY* 3.9 17.3 - - - -
160A ARG 3.5 21.8 - - - -
161A TRP* 3.5 49.1 - + + -
453A PHE* 3.4 39.9 - + + -
473A PRO* 5.1 0.2 - - + -
475A ILE* 4.7 2.2 - - + -
486A GLN* 4.0 19.7 - - + -
487A ASN 4.4 0.9 - - - -
506A ARG* 3.5 3.3 - - - +
507A VAL* 2.9 41.8 + - + +
526A GLN 4.0 0.6 + - - -
527A ILE* 1.3 73.7 - - - +
529A THR* 1.3 59.5 - - - +
530A PRO* 3.5 34.7 - - + +
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Residues in contact with THR 529 (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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159A GLY* 3.2 2.1 - - - -
160A ARG* 2.8 38.6 + - - -
162A GLY 4.6 6.2 + - - -
506A ARG* 3.0 38.4 + - - +
527A ILE* 4.4 4.0 - - - +
528A PHE* 1.3 74.1 - - - +
530A PRO* 1.4 66.4 - - - +
533A LEU* 3.7 20.6 - - + -
534A TYR* 3.6 33.7 + - + +
540A LEU* 4.5 0.7 - - + -
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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