Contacts of the strand formed by residues 104 - 109 (chain C) in PDB entry 2UYK
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 THR 104 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A VAL* 3.7 7.8 - - - +
20A GLY* 3.5 15.7 - - - -
21A VAL* 3.5 38.1 - - + +
28A PHE* 3.6 13.0 - - + +
29A THR 4.0 1.3 - - - -
30A SER* 3.3 18.6 - - - +
72C ILE 2.9 17.3 + - - -
73C LYS* 3.0 20.4 - - - +
74C MET 2.9 22.9 + - - -
103C PRO* 1.3 78.4 - - - +
105C ARG* 1.3 60.8 + - - +
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Residues in contact with ARG 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A GLY* 4.8 0.4 - - - -
16A PRO* 3.8 7.6 - - - +
17A TYR* 3.9 27.8 - - + -
30A SER* 2.9 8.7 + - - -
31A GLY 2.9 13.0 + - - -
73C LYS* 4.2 2.4 - - - +
74C MET 3.2 11.4 - - - +
76C VAL* 3.9 12.9 - - + +
84C PHE* 3.5 13.3 - - - -
87C ILE* 5.7 1.8 - - - +
88C ASN* 2.8 32.3 + - - +
91C TYR* 3.3 56.6 - - - +
104C THR* 1.3 77.7 - - - +
106C SER* 1.3 71.3 + - - +
107C CYS* 4.6 2.7 - - - +
1129C SER* 2.8 55.2 + - - +
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Residues in contact with SER 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A GLY* 3.3 19.9 + - - -
77A PHE* 4.4 10.5 - - - -
120A GLU* 3.4 13.7 - - - -
122A GLU* 2.7 30.2 + - - +
73C LYS* 3.7 5.0 + - - +
74C MET 3.2 5.9 + - - -
75C THR* 3.4 12.3 - - - -
76C VAL 2.9 24.8 + - - -
105C ARG* 1.3 73.9 - - - +
107C CYS* 1.3 61.8 + - - +
108C VAL* 5.4 0.2 - - - -
1129C SER 3.5 2.7 - - - -
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Residues in contact with CYS 107 (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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114A PRO* 3.2 11.5 - - + +
120A GLU* 2.7 28.1 + - - +
76C VAL* 3.2 18.8 - - + +
78C ILE* 4.3 19.5 - - - -
81C LEU* 5.3 1.1 - - - -
84C PHE* 3.2 35.9 - - + -
105C ARG* 4.6 3.4 - - - +
106C SER* 1.3 74.8 - - - +
108C VAL* 1.3 63.3 + - - +
1129C SER* 2.8 32.6 + - - +
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Residues in contact with VAL 108 (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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77A PHE* 3.6 32.5 - - + -
110A VAL* 4.2 13.7 - - + -
112A ARG 4.2 0.4 - - - -
113A LEU* 3.5 26.5 - - + -
114A PRO* 4.7 2.0 - - - -
120A GLU* 3.7 6.3 - - - +
75C THR* 5.5 1.6 - - + -
76C VAL 3.2 3.2 + - - +
77C PHE* 3.6 32.6 - - + -
78C ILE* 3.0 29.5 + - - +
81C LEU* 5.9 0.4 - - - -
106C SER* 5.2 0.7 - - - -
107C CYS* 1.3 82.9 - - - +
109C GLN* 1.3 59.3 + - - +
110C VAL* 3.9 11.4 - - + -
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Residues in contact with GLN 109 (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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110A VAL* 3.4 3.9 - - - +
111A ALA* 2.8 42.1 + - - +
112A ARG* 2.9 42.9 + - + +
113A LEU* 4.9 0.4 - - - +
78C ILE* 3.1 6.0 - - + +
79C THR 3.4 35.5 + - - +
80C ASP* 3.8 3.2 - - - +
81C LEU* 3.0 42.1 + - + +
108C VAL* 1.3 70.6 - - - +
110C VAL* 1.3 62.2 + - - +
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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