Contacts of the strand formed by residues 53 - 59 (chain B) in PDB entry 1JQD
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 GLU 53 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51B LYS* 3.3 15.5 - - - +
52B SER* 1.3 97.9 + - - +
54B ILE* 1.3 64.4 + - - +
55B LYS* 3.8 13.8 + - + +
81B VAL* 4.2 0.4 - - - +
82B CYS* 3.4 25.7 - - + +
84B ASN* 5.4 6.2 - - + +
112B LYS* 4.7 12.8 + - - -
137B ASP* 3.5 9.2 - - - +
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Residues in contact with ILE 54 (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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47B ILE* 4.3 15.3 - - + -
48B GLY* 3.8 21.1 - - - +
51B LYS* 5.2 0.4 - - + -
53B GLU* 1.3 74.3 - - - +
55B LYS* 1.3 58.0 + - - +
56B ILE* 4.1 14.8 - - + -
74B VAL* 4.0 25.1 - - + -
78B TYR* 3.6 40.4 - - + -
81B VAL* 3.6 20.4 - - + -
82B CYS 2.9 10.5 + - - +
83B ILE* 3.3 10.7 - - + +
84B ASN* 2.7 31.7 + - - +
137B ASP* 3.4 9.2 - - + +
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Residues in contact with LYS 55 (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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53B GLU* 4.5 13.9 - - + +
54B ILE* 1.3 73.7 - - - +
56B ILE* 1.3 62.0 + - - +
84B ASN* 3.5 29.2 - - + +
134B GLN* 3.5 30.3 + - - +
135B LYS 3.3 24.6 + - - +
136B TRP* 3.6 26.9 - - + +
137B ASP* 2.7 44.0 + - - +
138B PHE 3.2 7.1 + - - +
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Residues in contact with ILE 56 (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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54B ILE* 4.1 11.4 - - + -
55B LYS* 1.3 78.5 - - - +
57B LEU* 1.3 64.0 + - - +
58B SER 4.0 0.2 + - - -
70B ILE* 4.9 4.3 - - + -
71B LEU* 3.9 23.3 - - + -
74B VAL* 3.8 32.8 - - + -
83B ILE* 4.0 9.2 - - + -
84B ASN 2.7 12.2 + - - +
85B ASN* 3.4 20.3 - - - +
86B GLU 3.0 26.2 + - - +
136B TRP* 3.4 4.1 - - - -
138B PHE* 3.3 28.3 - - + +
140B HIS* 4.1 20.4 - - + +
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Residues in contact with LEU 57 (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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56B ILE* 1.3 73.7 - - - +
58B SER* 1.3 60.4 + - - +
59B ILE* 3.7 20.2 - - + -
86B GLU* 3.5 26.0 - - + +
88B VAL* 4.0 20.2 - - + -
123B TYR* 4.0 22.7 - - + +
136B TRP* 3.7 21.7 - - + +
138B PHE 2.8 9.5 + - - +
139B ILE* 3.3 19.4 - - + +
140B HIS* 3.1 27.5 + - - +
158B PHE* 4.0 21.5 - - + -
161B LEU* 4.2 9.9 - - + -
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Residues in contact with SER 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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56B ILE 4.0 1.0 + - - -
57B LEU* 1.3 72.7 - - - +
59B ILE* 1.3 56.4 + - - +
61B GLY* 3.4 11.8 - - - -
67B ASP* 2.6 31.5 + - - -
85B ASN* 4.5 5.6 - - - -
86B GLU 2.9 15.1 + - - +
87B VAL* 3.4 10.1 - - - +
88B VAL* 2.7 33.1 + - - +
140B HIS* 2.9 25.5 + - - -
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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
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57B LEU* 3.7 24.5 - - + -
58B SER* 1.3 71.2 + - - +
60B GLY* 1.3 68.3 + - - +
61B GLY* 3.2 1.4 - - - -
88B VAL* 3.8 20.9 - - + +
120B SER* 3.6 27.6 - - - -
139B ILE* 4.3 11.9 - - + -
140B HIS* 3.1 22.0 + - - +
141B MET* 3.7 26.8 - - + -
142B ILE 4.3 2.8 + - - -
144B MET* 3.6 27.3 - - + +
158B PHE* 3.7 21.3 - - + -
401B SAH 4.1 3.7 + - + -
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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