Contacts of the strand formed by residues 101 - 106 (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 LEU 101 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95C TRP* 3.4 9.4 - - - -
96C SER* 2.9 41.5 + - - +
98C ASP* 4.9 1.6 - - - +
100C ASN* 1.3 89.1 - - + +
102C LEU* 1.3 64.5 + - - +
113C ILE* 4.1 11.7 - - + -
114C TRP 3.2 9.0 - - - +
115C ASP* 4.3 5.8 - - - +
116C VAL* 3.9 1.1 - - - -
122C LEU* 3.6 31.2 - - + -
137C PHE* 3.9 13.2 - - + -
141C SER* 5.4 1.6 - - - +
158C VAL* 4.0 26.7 - - + -
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Residues in contact with LEU 102 (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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61C ALA* 3.8 4.9 - - + -
69C ILE* 4.1 14.6 - - + -
71C ILE* 3.6 30.1 - - + -
83C ILE* 4.2 8.5 - - + -
93C VAL* 3.8 17.9 - - + -
94C ALA 3.2 18.6 - - - +
95C TRP* 3.5 33.4 - - + +
101C LEU* 1.3 71.2 - - - +
103C VAL* 1.3 58.6 + - - +
113C ILE* 3.3 6.6 - - - +
114C TRP* 2.7 46.7 + - + -
116C VAL* 3.7 22.0 - - + +
137C PHE* 4.0 2.9 - - - -
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Residues in contact with VAL 103 (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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93C VAL* 3.2 7.4 - - - +
94C ALA* 2.9 40.1 + - + +
102C LEU* 1.3 74.7 - - - +
104C SER* 1.3 64.5 + - - +
111C LEU* 4.0 28.9 - - + -
112C LYS 3.2 12.3 - - - +
113C ILE* 4.4 2.2 - - + -
114C TRP* 4.7 0.4 - - - -
125C LEU* 4.6 0.2 - - + -
135C CYS* 3.7 17.8 - - + -
136C ASN 4.5 2.0 - - - +
137C PHE* 3.5 26.4 - - + -
144C ILE* 3.7 30.7 - - + -
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Residues in contact with SER 104 (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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69C ILE* 3.6 22.7 - - - -
86C HIS* 2.6 29.7 + - - -
90C ILE* 3.8 8.1 - - - -
92C ASP 3.3 10.1 - - - -
93C VAL* 4.4 1.6 - - - -
103C VAL* 1.3 75.5 - - - +
105C ALA* 1.4 59.5 + - - +
111C LEU* 3.0 28.5 - - - +
112C LYS 3.0 8.3 + - - -
114C TRP* 2.8 20.3 + - - -
135C CYS* 4.0 3.8 - - - -
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Residues in contact with ALA 105 (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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90C ILE* 3.3 4.5 - - - +
91C SER 2.9 26.5 + - - -
92C ASP* 2.9 12.5 + - + +
104C SER* 1.4 72.1 - - - +
106C SER* 1.4 59.3 + - - +
110C THR 4.1 2.7 - - - -
111C LEU* 4.2 1.8 - - - -
132C VAL* 3.5 34.8 - - + +
133C PHE 4.0 2.7 - - - -
134C CYS 3.9 12.6 - - - +
135C CYS* 3.8 17.9 - - + -
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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
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86C HIS* 3.3 32.0 + - - -
88C LEU 3.0 14.8 + - - -
89C GLY 2.9 14.6 + - - -
90C ILE* 4.3 1.6 - - - -
91C SER 4.7 0.2 - - - +
105C ALA* 1.4 73.8 - - - +
107C ASP* 1.3 69.3 + - - +
108C ASP* 3.0 23.1 + - - -
109C LYS* 3.2 8.0 + - - -
110C THR 3.1 8.6 + - - +
132C VAL* 3.0 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