Contacts of the strand formed by residues 145 - 152 (chain C) in PDB entry 3VU7
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 145 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C VAL* 4.2 4.9 - - - -
87C ILE* 3.5 6.6 - - - +
88C LEU* 2.8 48.7 + - + +
89C ASP 3.6 16.2 - - - +
90C LYS* 5.1 2.0 - - - -
92C HIS* 4.7 12.8 - - + +
143C GLY 4.5 3.6 - - - +
144C CYS* 1.3 76.3 - - - +
146C PHE* 1.3 71.9 + - - +
1884Z PRO* 4.9 4.0 - - - +
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Residues in contact with PHE 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C VAL* 4.7 6.5 - - + -
31C LEU* 3.6 42.2 - - + -
36C VAL* 4.2 2.8 - - + +
37C TYR* 4.3 10.5 + + - -
60C LEU* 4.2 6.7 - - + -
63C TYR* 3.9 22.0 - + - -
64C ILE* 4.4 9.4 - - + -
85C VAL* 3.7 14.6 - - + -
86C VAL 3.1 11.9 - - - +
87C ILE* 4.3 11.0 - - + -
88C LEU* 4.5 1.1 - - - +
145C THR* 1.3 82.9 + - - +
147C THR* 1.3 83.8 + - - +
148C VAL* 3.8 23.6 - - + -
1884Z PRO* 3.1 47.0 - - + +
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Residues in contact with THR 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C TYR* 4.9 7.5 + - - -
85C VAL* 3.6 4.0 - - - -
86C VAL* 2.8 59.2 + - + +
88C LEU* 4.3 17.0 - - + -
146C PHE* 1.3 86.9 - - - +
148C VAL* 1.3 77.8 + - - +
149C LEU* 4.7 6.5 - - + +
178C ASP* 5.7 4.5 - - + +
1879Z LYS* 4.6 18.4 + - - +
1880Z PRO* 4.8 2.9 - - - +
1884Z PRO* 5.5 1.8 - - - -
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Residues in contact with VAL 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C VAL* 5.4 6.7 - - + -
63C TYR* 5.0 7.1 + - + -
64C ILE* 6.5 0.7 - - - -
67C THR* 3.8 34.3 - - + +
68C LEU* 5.9 3.6 - - + -
71C VAL* 5.7 0.9 - - + -
83C VAL* 4.3 16.8 - - + -
84C VAL 3.5 8.7 - - - +
85C VAL* 5.1 9.0 - - + -
146C PHE* 3.8 19.7 - - + -
147C THR* 1.3 84.3 + - - +
149C LEU* 1.3 79.8 + - - +
150C VAL* 4.7 6.5 - - + -
171C TRP* 4.5 1.0 - - + -
1878Z LEU 4.0 0.2 - - - +
1879Z LYS* 4.0 0.3 - - - -
1880Z PRO* 3.3 26.9 - - + +
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Residues in contact with LEU 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C VAL* 3.6 2.4 - - - -
84C VAL* 2.9 44.1 + - + +
86C VAL* 3.9 26.2 - - + -
97C LYS* 5.1 2.2 - - - +
147C THR* 4.7 6.5 - - + +
148C VAL* 1.3 84.8 - - - +
150C VAL* 1.3 64.1 + - - +
151C HIS* 4.0 10.4 + - + -
174C ALA* 4.5 5.6 - - + -
178C ASP* 4.0 13.7 - - + +
179C VAL* 3.8 29.2 - - + -
1877Z ILE* 4.2 16.4 - - + -
1878Z LEU 3.4 3.4 - - - +
1879Z LYS* 4.0 26.5 - - + -
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Residues in contact with VAL 150 (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 VAL* 3.8 21.8 - - + -
74C LEU* 4.8 6.3 - - + -
80C VAL* 3.8 36.6 - - + -
82C LYS 3.7 2.5 - - - -
83C VAL* 4.7 4.9 - - + +
148C VAL* 4.7 4.9 - - + -
149C LEU* 1.3 77.2 - - - +
151C HIS* 1.3 64.2 + - - +
152C THR* 3.4 10.0 + - + +
163C ILE* 4.6 2.5 - - + -
171C TRP* 3.5 33.2 - - + -
1876Z ASN 3.6 0.3 - - - +
1877Z ILE* 4.5 0.7 - - - -
1878Z LEU* 2.9 39.8 + - + +
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Residues in contact with HIS 151 (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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80C VAL* 3.7 1.2 - - - -
81C GLU* 2.7 40.9 + - - +
82C LYS* 2.8 50.7 + - + +
84C VAL* 3.8 24.4 - - + +
97C LYS* 5.6 2.7 - - - -
149C LEU* 4.4 13.9 - - + +
150C VAL* 1.3 73.0 - - - +
152C THR* 1.3 54.6 + - - +
179C VAL* 4.7 13.8 - - + +
1876Z ASN* 3.5 12.3 - - - +
1877Z ILE* 4.0 33.3 - - + +
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Residues in contact with THR 152 (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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74C LEU* 4.1 20.2 - - + -
79C ASP 3.3 9.4 - - - +
80C VAL* 4.3 0.2 - - - +
81C GLU* 3.6 5.5 - - - +
150C VAL* 3.4 6.7 + - + +
151C HIS* 1.3 74.7 - - - +
153C ARG* 1.3 64.1 + - - +
154C GLU 2.9 15.1 + - - -
155C ALA* 4.7 0.2 - - - -
156C ALA 5.0 0.2 + - - -
159C ASN* 3.3 36.3 + - + +
1876Z ASN* 2.6 62.4 + - - +
1878Z LEU* 4.4 11.1 - - + +
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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