Contacts of the strand formed by residues 56 - 60 (chain B) in PDB entry 1ZQ1
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 ASN 56 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B MSE 4.3 7.4 - - - +
48B VAL* 4.4 11.4 - - + +
49B LEU 3.4 1.9 + - - +
50B LYS* 2.9 47.2 - - - +
54B GLY 3.7 0.2 + - - -
55B TYR* 1.3 74.7 - - - +
57B ILE* 1.3 65.6 + - - +
120D TYR* 3.4 45.1 + - + +
122D MET* 3.5 27.7 - - - +
140D ILE* 4.8 6.9 + - - +
434D PRO* 4.0 13.7 - - - +
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Residues in contact with ILE 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B TYR* 3.6 22.2 - - + -
47B LEU 3.6 0.4 - - - +
48B VAL* 3.1 10.0 - - - +
49B LEU* 2.8 39.1 + - + +
51B LEU* 3.2 41.5 - - + -
56B ASN* 1.3 79.3 - - - +
58B GLY* 1.3 73.9 + - - +
59B ILE* 3.7 20.0 - - + -
116D VAL* 3.7 13.0 - - + -
118D GLU 4.4 1.8 - - - -
120D TYR* 3.7 6.1 - - - -
140D ILE* 3.8 28.3 - - + +
143D THR* 4.2 2.0 - - + -
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Residues in contact with GLY 58 (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 TYR* 5.3 0.2 + - - -
46B THR* 4.1 2.5 - - - -
47B LEU 3.4 4.9 - - - -
57B ILE* 1.3 77.3 - - - +
59B ILE* 1.3 66.9 + - - +
60B ALA 4.2 0.2 - - - -
116D VAL* 3.2 17.2 - - - +
117D ASP* 3.4 11.2 + - - +
118D GLU* 3.1 30.7 + - - -
120D TYR* 3.9 10.3 - - - -
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Residues in contact with ILE 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ILE* 5.6 3.1 - - + -
22B LYS* 4.3 13.5 - - + -
31B TYR* 3.2 42.6 - - + +
46B THR* 3.3 2.8 + - - -
47B LEU* 2.7 53.8 + - + +
49B LEU* 4.9 13.5 - - + -
57B ILE* 3.7 12.8 - - + -
58B GLY* 1.3 83.4 - - - +
60B ALA* 1.3 64.3 + - - +
61B LEU 3.0 6.6 + - - -
64B ILE* 3.2 39.3 - - + -
117D ASP* 3.7 2.9 - - - +
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Residues in contact with ALA 60 (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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45B ASP 3.2 13.5 - - - +
46B THR* 4.4 1.1 - - - +
59B ILE* 1.3 71.4 - - - +
61B LEU* 1.3 66.8 + - - +
62B GLU* 3.1 7.0 - - + -
63B LYS* 2.7 39.4 + - + +
64B ILE 3.5 2.8 + - - -
117D ASP* 2.8 32.1 + - + +
442D ARG* 3.8 19.3 - - - +
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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