Contacts of the strand formed by residues 518 - 523 (chain A) in PDB entry 1IEQ
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 CYS 518 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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403A LEU* 3.1 16.6 - - - +
480A ALA 3.3 8.7 - - - +
482A VAL* 4.6 5.6 - - + -
512A VAL* 4.4 9.4 - - + -
513A CYS* 2.0 54.3 - - - +
516A VAL 3.9 5.2 - - - +
517A ARG* 1.3 74.3 - - - +
519A ALA* 1.3 59.5 + - - +
520A THR* 4.3 1.6 - - - -
536A ALA 3.9 0.4 - - - -
537A SER* 3.6 17.9 - - - -
538A ASP* 2.8 13.4 + - - -
539A ALA 3.3 13.3 + - - +
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Residues in contact with ALA 519 (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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403A LEU* 3.7 15.3 - - + -
404A LEU* 3.9 21.5 - - + -
406A LEU* 4.4 11.2 - - + -
480A ALA 2.8 13.5 + - - +
481A ILE* 3.4 9.9 - - + +
482A VAL 3.1 21.3 + - - +
518A CYS* 1.3 73.3 - - - +
520A THR* 1.3 62.6 + - - +
521A VAL* 3.7 1.3 + - - +
539A ALA* 3.4 8.1 - - + -
541A VAL* 6.2 0.9 - - + -
557A LEU* 4.4 9.9 - - + -
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Residues in contact with THR 520 (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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482A VAL* 3.4 11.9 + - - +
484A VAL* 4.5 5.2 - - + -
509A VAL* 3.6 29.6 - - + +
513A CYS* 4.2 4.7 - - - -
518A CYS* 3.9 0.6 - - - -
519A ALA* 1.3 72.7 - - - +
521A VAL* 1.3 67.1 + - - +
522A LEU* 4.4 2.9 - - + +
533A LEU* 4.5 8.1 - - + -
537A SER* 2.8 27.2 + - - +
539A ALA 2.8 11.8 + - - -
540A LEU* 3.3 19.1 - - + -
541A VAL* 2.7 34.5 + - - +
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Residues in contact with VAL 521 (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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447A ILE* 4.0 22.4 - - + -
481A ILE* 4.1 25.1 - - + -
482A VAL 2.8 11.2 + - - +
483A ALA* 3.3 7.8 - - + +
484A VAL 3.2 26.3 + - - +
519A ALA 4.4 1.3 - - - +
520A THR* 1.3 77.7 - - - +
522A LEU* 1.3 59.8 + - - +
523A ILE* 3.7 4.3 + - + -
541A VAL* 3.7 10.1 - - + +
543A ALA* 3.8 24.9 - - + -
553A VAL* 4.3 11.2 - - + -
557A LEU* 4.1 21.5 - - + -
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Residues in contact with LEU 522 (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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484A VAL* 3.5 14.8 - - + +
485A GLY* 4.2 10.3 - - - -
501A ILE* 4.4 13.0 - - + -
520A THR* 3.9 3.5 - - + -
521A VAL* 1.3 71.1 - - - +
523A ILE* 1.3 64.4 + - - +
524A SER* 3.7 9.8 + - - +
528A VAL* 3.9 20.2 - - + -
530A VAL* 4.4 15.0 - - + -
533A LEU* 4.0 20.4 - - + -
540A LEU* 4.7 11.4 - - + -
541A VAL 2.7 18.3 + - - +
542A ALA* 3.8 3.6 - - + -
543A ALA* 2.9 27.6 + - - -
544A TRP 3.6 2.8 + - - -
571A TRP* 3.9 25.4 - - + -
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Residues in contact with ILE 523 (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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419A HIS* 3.5 36.1 - - + +
425A TYR 3.5 26.9 - - - +
426A GLN* 4.4 9.4 - - + -
447A ILE* 4.5 11.9 - - + -
484A VAL 2.9 10.0 + - - +
485A GLY* 3.0 4.3 - - - -
486A GLU* 2.9 25.7 + - - +
521A VAL* 4.1 13.7 - - + +
522A LEU* 1.3 69.9 - - - +
524A SER* 1.3 63.1 + - - +
543A ALA* 3.6 26.2 - - + -
544A TRP 3.3 9.6 - - - +
545A LEU* 4.0 7.4 - - + -
546A PRO* 3.8 16.6 - - + -
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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