Contacts of the strand formed by residues 57 - 63 (chain B) in PDB entry 3RCZ
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 57 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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378A GLU* 6.4 2.2 - - + -
381A GLY* 5.9 2.0 - - - +
23B GLY 3.5 24.5 - - - +
25B TYR* 4.0 26.2 - - + -
44B GLY* 3.8 12.8 - - - -
45B ILE 3.7 18.6 - - - -
46B PRO* 3.8 4.0 - - + -
55B GLY 3.9 0.2 + - - -
56B GLY* 1.3 72.7 - - - -
58B TYR* 1.3 61.2 + - - +
59B LYS* 3.7 15.8 + - + +
155B ASN* 2.8 29.2 + - - +
157B PRO* 3.8 33.0 - - + -
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Residues in contact with TYR 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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44B GLY* 3.4 2.2 - - - -
45B ILE* 2.7 48.0 + - + +
47B GLY* 3.7 10.3 - - - -
53B TRP* 2.7 53.8 + + + -
56B GLY* 3.6 16.8 - - - -
57B LEU* 1.3 71.7 - - - +
59B LYS* 1.3 62.6 + - - +
60B LEU* 3.5 6.9 - - - +
77B PHE* 3.9 22.9 - + + -
81B LEU* 3.9 21.8 - - + -
120B LEU* 4.0 14.1 - - + -
151B GLN* 4.3 4.0 - - + -
152B ALA* 3.3 23.4 + - - +
155B ASN* 3.9 31.2 - - + -
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Residues in contact with LYS 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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381A GLY 5.1 5.3 + - - -
25B TYR* 2.5 43.4 + - + +
43B VAL 3.4 6.1 - - - +
44B GLY* 5.2 1.1 - - - -
57B LEU* 3.7 16.7 + - + +
58B TYR* 1.3 73.8 - - - +
60B LEU* 1.3 60.9 + - - +
77B PHE* 3.4 9.9 - - - -
78B THR* 2.9 45.9 + - - +
79B PRO 4.9 0.2 - - - +
155B ASN* 5.0 5.3 + - - +
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Residues in contact with LEU 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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42B LYS* 3.7 3.8 - - - +
43B VAL* 2.9 45.1 + - + +
45B ILE* 3.3 28.0 - - + -
58B TYR 3.5 10.3 - - - +
59B LYS* 1.3 72.1 - - - +
61B THR* 1.3 68.1 + - - +
62B MET* 5.5 1.1 - - + -
75B CYS* 4.2 9.0 - - + -
76B ARG 3.2 5.8 - - - +
77B PHE* 3.3 43.5 - - + +
78B THR* 4.3 2.5 - - - -
92B VAL* 3.8 30.3 - - + -
113B LEU* 5.7 0.4 - - + -
116B ILE* 3.9 14.1 - - + -
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Residues in contact with THR 61 (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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41B TRP 3.4 10.5 - - - +
42B LYS* 4.9 11.4 - - + -
60B LEU* 1.3 78.1 - - - +
62B MET* 1.3 64.8 + - - +
63B ALA* 4.1 2.2 + - - +
74B LYS 3.5 1.4 + - - +
75B CYS* 3.4 4.5 - - - +
76B ARG* 2.9 48.8 + - - +
78B THR* 3.9 20.6 - - + +
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Residues in contact with MET 62 (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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39B MET 3.6 1.2 - - - +
40B ASN* 3.4 5.0 - - - -
41B TRP* 3.0 33.8 + - + -
43B VAL* 3.9 31.6 - - + -
60B LEU* 5.5 0.9 - - + -
61B THR* 1.3 77.9 - - - +
63B ALA* 1.3 61.1 + - - +
64B PHE* 3.7 27.6 - - + -
73B PRO* 3.6 28.9 - - + -
74B LYS 3.4 5.6 - - - +
75B CYS* 3.8 15.3 - - + -
109B ILE* 4.4 15.9 - - + -
112B ILE* 3.8 21.3 - - + -
113B LEU* 4.3 13.5 - - + -
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Residues in contact with ALA 63 (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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39B MET 3.5 4.5 - - - -
40B ASN* 3.7 15.0 - - - +
61B THR* 4.1 3.0 - - - +
62B MET* 1.3 71.8 - - - +
64B PHE* 1.3 62.9 + - - +
65B PRO* 3.7 1.9 - - - +
73B PRO* 3.2 2.8 - - - +
74B LYS* 2.8 51.7 + - + +
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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