Contacts of the strand formed by residues 516 - 520 (chain B) in PDB entry 2I91
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 MET 516 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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480B ALA* 4.2 23.8 - - + +
483B LEU* 3.8 12.1 - - + -
484B LYS* 5.2 4.7 - - - -
487B ARG* 3.5 8.3 - - - +
496B LEU* 3.1 33.0 - - + +
508B ILE 4.7 0.2 - - - +
509B ALA* 4.2 8.8 - - + +
510B ASP* 3.5 39.2 - - + +
511B PRO* 6.0 0.2 - - - +
513B ASP* 3.1 50.3 + - + +
514B ARG 3.3 1.8 - - - +
515B GLY* 1.3 80.9 - - - +
517B LEU* 1.3 63.0 + - - +
518B ASP 4.4 0.2 + - - -
533B PHE* 4.1 3.5 - - - -
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Residues in contact with LEU 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B ASN* 5.6 1.1 - - - +
496B LEU 2.7 10.2 + - - +
497B ILE* 3.4 9.4 - - + -
498B VAL* 2.9 31.0 + - - +
509B ALA* 4.7 0.9 - - - -
516B MET* 1.3 76.3 - - - +
518B ASP* 1.3 72.1 + - - +
519B ILE* 3.5 25.1 + - + -
529B VAL* 4.3 13.5 - - + +
533B PHE* 3.5 55.3 - - + -
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Residues in contact with ASP 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B VAL* 2.6 38.0 - - - +
28B SER 5.2 0.6 + - - +
31B ASN* 2.6 37.0 - - + +
35B ARG* 3.4 7.5 + - - +
498B VAL* 3.2 10.7 - - - +
507B SER* 2.5 24.4 + - - -
509B ALA* 3.1 15.9 - - + +
516B MET 4.4 0.2 + - - -
517B LEU* 1.3 81.6 - - - +
519B ILE* 1.3 64.4 + - - +
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Residues in contact with ILE 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B ARG* 5.0 3.4 + - - -
399B MET* 5.8 0.2 - - + -
497B ILE* 3.8 19.1 - - + -
498B VAL 3.1 6.1 + - - +
499B CYS* 3.8 25.8 - - + -
500B ALA* 3.0 27.0 + - - +
517B LEU* 3.5 30.3 + - + -
518B ASP* 1.3 79.5 - - - +
520B CYS* 1.3 66.0 + - - +
526B ALA* 4.6 10.3 - - + +
529B VAL* 4.6 18.6 - - + -
530B ILE* 3.6 35.2 - - + -
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Residues in contact with CYS 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B ASN 5.4 0.2 - - - +
34B ARG* 4.3 11.7 - - + -
35B ARG* 3.5 34.1 - - + +
38B CYS* 3.5 30.1 - - - -
39B PHE* 3.6 8.1 - - - -
499B CYS* 4.0 5.5 - - - -
500B ALA* 4.2 4.3 - - - +
519B ILE* 1.3 78.8 - - - +
521B GLY* 1.3 77.6 + - - +
522B PHE 3.8 0.9 + - - -
523B ASP* 3.9 18.1 + - + +
526B ALA* 4.2 9.2 - - - +
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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