Contacts of the strand formed by residues 59 - 64 (chain C) in PDB entry 3UVN
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 TRP 59 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C PHE* 3.3 8.7 - - - -
54C SER* 2.7 42.7 + - - +
56C ASN* 4.2 12.5 + - - +
57C GLY 4.7 0.2 - - - -
58C GLU* 1.3 113.4 - - + +
60C LEU* 1.3 56.5 - - - +
71C ILE* 3.9 17.3 - - + -
72C TRP 3.4 15.5 - - - +
73C GLY* 4.5 5.2 - - - -
74C ALA* 4.2 4.7 - - - -
80C GLU* 3.7 35.7 - - + -
95C TRP* 3.6 33.4 - + + -
99C SER 5.0 4.1 + - - -
116C VAL* 5.1 8.0 - - + +
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Residues in contact with LEU 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C LEU* 4.1 13.9 - - + -
51C VAL* 4.1 7.0 - - + -
52C LYS* 3.5 28.9 - - - +
53C PHE* 3.8 19.7 - - + +
59C TRP* 1.3 73.6 - - - +
61C ALA* 1.3 64.3 + - - +
71C ILE* 3.4 4.2 - - - +
72C TRP* 2.9 47.2 + - + +
73C GLY 5.5 0.2 - - - -
74C ALA* 4.5 5.3 - - - +
95C TRP* 4.3 2.0 - - - -
308C ALA* 4.8 0.2 - - + -
317C ALA* 3.5 28.7 - - + -
327C ILE* 3.6 31.0 - - + -
329C LEU* 4.2 6.3 - - + -
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Residues in contact with ALA 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C SER 3.9 0.5 - - - +
51C VAL* 3.3 5.0 - - - +
52C LYS 2.8 32.0 + - - +
60C LEU* 1.3 74.2 - - - +
62C SER* 1.3 60.4 + - - +
69C ILE* 4.6 1.3 - - + -
70C LYS 3.3 4.9 - - - -
71C ILE* 3.7 13.7 - - + -
93C VAL* 4.1 13.4 - - + +
95C TRP* 3.5 30.9 - - + +
102C LEU* 3.8 13.7 - - + -
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Residues in contact with SER 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C HIS* 2.7 28.7 + - - -
48C VAL* 4.3 2.2 - - - -
50C SER 3.3 4.3 - - - -
51C VAL* 3.8 9.9 - - - -
60C LEU 4.2 0.2 + - - -
61C ALA* 1.3 76.7 - - - +
63C SER* 1.3 60.7 + - - +
68C LEU 3.8 0.7 - - - +
69C ILE* 3.1 8.0 - - - +
70C LYS* 2.8 36.3 + - - +
72C TRP* 2.9 19.3 + - - -
93C VAL* 4.3 2.9 - - - -
327C ILE* 3.5 20.6 - - - -
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Residues in contact with SER 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C HIS* 4.4 0.2 - - - -
48C VAL* 3.3 9.2 - - - +
49C SER* 2.8 40.4 + - - -
50C SER* 2.9 25.2 + - - -
62C SER* 1.3 74.7 - - - +
64C SER* 1.3 62.9 + - - +
68C LEU 3.7 4.9 - - - -
69C ILE* 4.6 3.1 - - - +
90C ILE* 3.6 24.9 - - - -
92C ASP 3.8 6.1 + - - -
93C VAL* 3.9 16.6 - - - +
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Residues in contact with SER 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C HIS* 3.2 18.7 + - - -
46C LYS 3.3 8.3 + - - -
47C ALA 2.7 22.2 + - - -
48C VAL* 4.3 0.2 - - - -
49C SER* 3.6 3.3 + - - -
63C SER* 1.3 78.7 - - - +
65C ALA* 1.4 57.5 + - - +
66C ASP* 3.0 34.7 + - - -
67C LYS* 3.1 15.6 + - - -
68C LEU 3.2 5.5 + - - -
90C ILE* 3.1 25.6 + - - +
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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