Contacts of the strand formed by residues 56 - 61 (chain C) in PDB entry 4UC5
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 56 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C LEU* 4.3 0.9 - - - -
54C LYS 4.6 0.2 - - - -
55C ARG* 1.3 72.9 - - - +
57C LEU* 1.3 68.9 + - - +
58C VAL* 3.4 6.7 + - + +
88C GLU 3.1 7.7 + - - -
89C LEU* 3.4 26.1 - - + -
90C LEU 2.9 23.5 + - - -
291C LEU* 4.1 23.1 - - + -
298C ILE* 3.7 24.5 - - + +
299C MET 3.8 2.7 - - - -
300C GLY* 3.6 26.2 - - - +
301C VAL* 4.2 17.0 - - + -
339C LEU* 4.3 18.2 - - + -
343C ASN* 3.6 10.9 - - + +
346C ARG* 4.5 5.6 - - - +
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Residues in contact with LEU 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C ILE* 4.0 26.7 - - + -
48C LEU* 3.7 15.1 - - + +
56C LEU* 1.3 70.7 - - - +
58C VAL* 1.3 62.2 + - - +
59C ILE* 3.9 19.1 - - + -
90C LEU* 3.4 21.8 - - + +
92C VAL* 3.9 22.0 - - + -
161C TRP* 4.0 17.9 - - + +
265C MET* 3.4 24.9 - - + -
299C MET* 3.0 24.6 + - + +
300C GLY* 2.9 4.4 - - - -
301C VAL 2.8 27.7 + - - +
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Residues in contact with VAL 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C LEU* 3.7 15.5 - - + +
57C LEU* 1.3 77.8 - - - +
59C ILE* 1.3 63.9 + - - +
60C ILE* 3.6 20.3 + - + +
89C LEU* 4.2 26.7 - - + -
90C LEU 2.8 12.5 + - - +
91C ILE* 3.6 8.4 - - + -
92C VAL 3.0 27.6 + - - +
301C VAL* 3.5 22.9 - - + -
303C VAL* 4.6 4.0 - - + -
336C LEU* 3.8 22.2 - - + -
339C LEU* 4.6 3.8 - - + -
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Residues in contact with ILE 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C LEU* 3.9 15.3 - - + -
58C VAL* 1.3 71.7 - - - +
60C ILE* 1.3 61.4 + - - +
92C VAL* 3.5 27.6 - - + -
94C ARG* 3.7 15.3 - - + -
96C TYR* 5.0 2.0 - - - +
143C SER* 3.3 21.3 - - - +
161C TRP* 3.9 36.6 - - + -
265C MET* 3.7 26.2 - - + -
301C VAL 2.9 9.7 + - - +
302C MET* 3.2 13.4 - - + +
303C VAL* 2.9 25.0 + - - +
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Residues in contact with ILE 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C VAL* 3.9 21.8 - - + +
59C ILE* 1.3 78.1 - - - +
61C GLY* 1.3 58.6 + - - +
74C TYR* 3.7 9.9 - - - +
78C LEU* 4.0 22.7 - - + +
91C ILE* 4.0 8.1 - - + -
92C VAL 3.1 8.0 + - - +
93C MET* 3.2 9.2 - - - +
94C ARG* 2.8 24.9 + - - +
303C VAL* 3.3 33.0 - - + +
305C SER* 3.8 4.5 - - - -
332C THR* 4.0 26.7 - - + +
335C LEU* 5.0 2.5 - - + -
336C LEU* 4.1 20.4 - - + -
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Residues in contact with GLY 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C ILE* 1.3 78.5 - - - +
62C PRO* 1.3 79.2 - - - +
74C TYR* 3.6 11.0 - - - -
93C MET* 4.8 0.2 - - - -
94C ARG* 3.5 10.1 - - - +
303C VAL 3.1 6.0 + - - +
304C GLU* 3.2 7.1 - - - -
305C SER 2.8 26.4 + - - -
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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