Contacts of the strand formed by residues 978 - 983 (chain 3) in PDB entry 5Z58
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 978 (chain 3).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9703 TYR* 3.3 10.0 - - - -
9713 ASP* 3.3 30.4 + - - +
9733 GLY* 4.7 1.5 - - - +
9763 LYS* 3.7 2.0 + - - +
9773 LEU* 1.3 74.8 - - - +
9793 ARG* 1.3 63.0 + - - +
9803 LYS* 3.5 5.9 + - - +
476w GLU* 3.1 23.8 - - + +
478w GLU* 2.7 58.1 - - + +
485w ASN* 2.0 69.5 - - + +
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Residues in contact with ARG 979 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9683 ARG* 2.9 55.3 - - - +
9693 VAL 3.7 3.6 - - - +
9703 TYR* 4.0 15.2 - - + -
9783 LEU* 1.3 73.6 - - - +
9803 LYS* 1.3 60.8 + - - +
9813 CYS* 3.0 26.8 - - - +
9823 GLU* 2.7 24.7 + - - +
474w ASP* 2.6 42.0 + - - +
475w THR* 3.8 6.8 - - - -
476w GLU* 3.4 27.2 + - + +
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Residues in contact with LYS 980 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9583 ARG* 4.7 14.4 - - - +
9693 VAL* 2.6 25.2 + - + +
9713 ASP* 3.7 36.1 - - + +
9783 LEU* 3.5 6.2 + - - +
9793 ARG* 1.3 74.6 - - - +
9813 CYS* 1.3 61.6 + - - +
10143 TYR* 5.0 1.9 + - - +
10193 ASN* 4.0 23.1 + - - +
475w THR* 5.3 6.9 - - - -
476w GLU 2.5 30.1 + - - +
477w GLU* 3.2 21.2 + - - +
478w GLU* 5.3 2.4 - - - +
489w LYS* 3.9 24.4 - - + +
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Residues in contact with CYS 981 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9683 ARG* 3.1 4.0 - - - -
9693 VAL* 2.9 39.8 + - + -
9793 ARG* 3.0 18.2 - - - +
9803 LYS* 1.3 82.8 - - - +
9823 GLU* 1.3 92.4 + - - +
10143 TYR* 4.6 0.9 - - + -
10193 ASN* 2.9 27.4 - - + +
10203 GLN* 4.3 2.0 - - - -
10213 LEU* 3.5 22.2 - - - -
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Residues in contact with GLU 982 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9663 LEU* 3.1 27.2 - - + +
9673 LEU 3.1 8.5 - - - +
9683 ARG* 3.2 25.0 + - + +
9793 ARG* 2.7 37.3 + - - +
9813 CYS* 1.3 92.9 - - - +
9833 ASN* 1.3 72.4 + - - +
9843 LYS* 4.7 5.9 - - - +
10203 GLN* 6.0 0.5 - - - +
10213 LEU* 3.6 4.5 + - - +
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Residues in contact with ASN 983 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9653 LYS 4.3 1.4 - - - +
9663 LEU* 3.5 5.4 - - - -
9673 LEU* 2.8 38.3 + - + +
9823 GLU* 1.3 77.8 - - - +
9843 LYS* 1.3 63.3 + - - +
9853 HIS* 2.7 54.7 + - - -
9863 ILE* 5.0 5.0 + - + +
10213 LEU* 3.4 42.8 + - + +
10233 ILE* 4.1 20.0 - - - +
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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