Contacts of the strand formed by residues 69 - 75 (chain C) in PDB entry 3U1K
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 GLY 69 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40C GLY* 5.3 0.9 - - - -
41C SER 5.9 0.9 - - - -
67C ALA* 3.0 8.5 - - - +
68C ASP* 1.3 79.7 - - - +
70C SER* 1.3 62.9 + - - -
83C THR* 3.3 3.3 - - - -
84C ALA* 2.8 35.0 + - - +
176C ALA* 3.4 23.3 - - - -
179C LEU* 5.1 2.2 - - - -
180C SER* 3.8 4.6 - - - -
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Residues in contact with SER 70 (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 SER* 2.6 30.5 + - - -
61C GLY 5.9 1.1 - - - -
63C LEU* 3.2 19.0 + - - +
64C ALA* 3.7 23.1 + - - +
65C ARG* 5.6 0.9 - - - -
67C ALA 5.4 0.7 - - - -
69C GLY* 1.3 75.8 - - - -
71C ALA* 1.3 63.2 + - - +
72C VAL* 5.6 0.7 - - - +
81C MET* 4.1 13.9 - - - +
82C VAL 3.2 10.3 + - - -
83C THR* 4.1 4.1 - - - +
176C ALA* 3.8 6.8 + - - +
179C LEU* 4.1 7.6 - - - +
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Residues in contact with ALA 71 (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 ILE* 5.3 0.2 - - + -
59C SER 3.5 6.5 - - - +
60C SER* 4.4 1.8 - - - +
70C SER* 1.3 73.6 + - - +
72C VAL* 1.3 66.5 + - - +
73C VAL* 4.2 0.4 - - - -
80C VAL 3.8 0.2 - - - +
81C MET* 3.2 7.2 - - - +
82C VAL 2.8 32.2 + - - -
172C GLY* 3.7 22.0 - - - +
175C VAL* 3.2 39.5 - - + -
176C ALA 3.8 0.7 - - - +
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Residues in contact with VAL 72 (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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377B PHE* 5.6 2.5 - - + -
57C GLU 3.5 1.9 - - - +
58C ILE* 3.5 3.1 - - - +
59C SER* 2.9 49.7 + - - +
60C SER* 5.7 2.5 - - - -
63C LEU* 4.2 24.9 - - + -
70C SER* 5.6 0.9 - - - +
71C ALA* 1.3 78.4 - - - +
73C VAL* 1.3 70.0 + - - +
74C GLN* 5.0 5.8 - - + +
79C ALA* 4.6 8.3 - - + -
80C VAL 3.3 7.9 - - - +
81C MET* 4.1 16.6 - - + -
157C LEU* 4.0 15.3 - - + -
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Residues in contact with VAL 73 (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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56C LEU* 3.2 33.9 - - + -
57C GLU 3.4 3.8 - - - +
58C ILE* 4.3 15.7 - - + -
72C VAL* 1.3 79.3 - - - +
74C GLN* 1.3 59.5 + - - +
79C ALA* 3.4 1.3 - - - -
80C VAL* 2.8 39.3 + - - +
168C LEU* 3.7 31.5 - - + +
171C ASN* 4.2 7.0 - - + -
172C GLY* 3.6 34.5 - - - +
175C VAL* 4.4 6.1 - - + -
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Residues in contact with GLN 74 (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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377B PHE* 4.6 13.0 - - - -
55C LYS 3.8 0.9 - - - +
56C LEU* 3.7 3.8 - - - +
57C GLU* 2.8 60.6 + - + +
72C VAL* 5.1 6.2 - - + +
73C VAL* 1.3 76.8 - - - +
75C SER* 1.3 62.6 + - - +
76C GLY 3.0 24.7 + - - +
77C ASP* 4.2 12.1 + - - +
78C THR 3.2 16.6 - - - +
79C ALA* 4.0 17.8 - - + +
168C LEU* 4.5 1.3 - - - -
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Residues in contact with SER 75 (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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54C ARG* 4.5 11.4 + - - +
55C LYS 4.1 13.3 + - - -
56C LEU* 4.8 3.6 - - - -
57C GLU* 5.4 0.2 - - - -
74C GLN* 1.3 75.0 - - - +
76C GLY* 1.3 66.5 + - - +
77C ASP 3.3 0.2 + - - -
78C THR* 3.0 19.4 + - - +
163C ASN* 3.1 33.9 + - - +
168C LEU* 3.9 25.0 - - - +
203C ASN* 6.1 1.0 - - - +
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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