Contacts of the strand formed by residues 135 - 140 (chain C) in PDB entry 1VBF
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 TYR 135 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C LYS* 3.6 16.6 - - + +
74C VAL 3.9 0.4 - - - -
75C LEU* 3.7 37.7 - - + -
96C VAL* 3.7 24.8 - - + +
129C TYR* 2.6 42.2 + - - +
132C GLU* 3.5 22.6 - - - +
133C LYS 3.0 23.9 + - - -
134C PRO* 1.3 77.0 - - - +
136C ASP* 1.3 62.1 + - - +
137C ARG 3.8 14.1 - - - +
138C VAL* 4.4 6.7 - - + -
154C GLN* 3.1 31.1 + - + +
155C LEU* 3.6 2.2 - - - -
156C LYS* 2.7 29.9 + - - +
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Residues in contact with ASP 136 (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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71C GLY 4.5 1.2 - - - +
72C GLN* 3.4 28.6 - - + +
73C LYS* 2.9 36.3 + - - +
134C PRO 5.9 0.2 - - - -
135C TYR* 1.3 75.0 - - - +
137C ARG* 1.3 79.0 + - - +
155C LEU* 4.1 2.9 - - - -
156C LYS* 3.1 37.1 + - + +
159C GLY* 3.4 4.5 - - - -
160C ILE 3.2 13.2 + - - -
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Residues in contact with ARG 137 (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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66C LEU* 2.7 43.3 + - + +
67C ASP* 2.4 47.7 + - - +
68C LEU* 4.4 2.0 - - + -
69C HIS* 5.4 1.8 - - - -
72C GLN* 3.2 36.4 + - - +
73C LYS 3.6 2.2 + - - -
74C VAL* 3.6 16.2 - - + -
75C LEU 3.1 20.5 + - - -
135C TYR* 3.5 3.3 - - - +
136C ASP* 1.3 94.0 + - + +
138C VAL* 1.3 73.5 + - - +
156C LYS* 4.2 18.0 - - - +
158C GLY 5.4 1.6 + - - -
160C ILE* 3.2 33.6 - - - +
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Residues in contact with VAL 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C LEU* 3.7 6.6 - - - +
75C LEU* 3.2 32.3 - - + +
77C ILE* 4.4 5.8 - - + -
135C TYR* 4.4 6.7 - - + -
137C ARG* 1.3 82.5 - - - +
139C VAL* 1.3 67.0 + - - +
151C PRO* 4.3 13.5 - - + +
155C LEU* 4.0 23.6 - - + -
160C ILE 2.9 5.9 + - - -
161C MSE 3.3 41.4 - - + -
162C ILE 2.9 23.3 + - - -
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Residues in contact with VAL 139 (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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62C MSE 5.0 6.5 - - + -
63C LEU* 4.7 4.9 - - + -
66C LEU* 3.2 34.1 - - + -
74C VAL* 4.5 1.6 - - + -
75C LEU 3.2 8.8 + - - +
76C GLU* 3.7 4.8 - - - +
77C ILE* 2.9 27.0 + - - +
88C ILE* 4.4 18.2 - - + -
138C VAL* 1.3 74.7 - - - +
140C VAL* 1.3 68.4 + - - +
141C TRP* 4.1 30.7 - - + +
162C ILE* 3.4 22.7 - - + +
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Residues in contact with VAL 140 (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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62C MSE 5.1 4.2 - - - +
77C ILE* 3.6 17.9 - - + +
139C VAL* 1.3 76.1 - - - +
141C TRP* 1.3 68.9 + - - +
142C ALA* 3.4 20.6 - - + +
148C LEU* 3.9 11.0 - - + -
161C MSE 3.4 33.4 - - + -
162C ILE 3.0 8.9 + - - +
163C LEU* 3.6 21.1 - - + -
164C PRO* 3.6 15.6 - - - +
193C PHE* 4.8 1.0 - - - -
196C ILE* 3.8 25.4 - - + -
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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