Contacts of the strand formed by residues 143 - 149 (chain C) in PDB entry 6VVT
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 VAL 143 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98C PHE* 5.4 2.2 - - + -
125C PHE* 3.4 5.4 - - - +
126C VAL* 2.9 38.3 + - + +
141C GLN* 4.0 10.3 + - + +
142C THR* 1.3 81.9 - - - +
144C PHE* 1.3 58.4 + - - +
145C MET* 3.4 28.8 + - - -
405C PRO* 4.4 12.6 - - + +
406C GLN* 4.5 5.2 - - + +
409C ILE* 3.6 30.1 - - + -
411C ILE* 4.1 4.3 - - + -
326F GLN* 2.9 30.1 - - - +
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Residues in contact with PHE 144 (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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123C PRO* 3.3 22.7 - - + -
124C LEU 3.5 7.2 - - - -
125C PHE* 3.2 35.2 - + + -
143C VAL* 1.3 68.0 - - - +
145C MET* 1.3 58.7 + - - +
146C GLY* 3.2 34.5 - - - -
147C ASP* 3.6 10.5 - - - -
411C ILE* 2.9 22.1 - - + +
325F LEU* 3.2 38.4 - - + -
326F GLN* 2.4 39.3 + - - +
327F ASP 6.0 0.2 - - - +
329F GLY* 3.0 38.6 - - - -
330F ARG* 4.9 0.4 - - - -
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Residues in contact with MET 145 (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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98C PHE* 6.1 4.9 - - + -
124C LEU* 3.2 31.3 + - + -
126C VAL* 3.4 34.3 - - + -
143C VAL* 3.4 27.6 - - - +
144C PHE* 1.3 73.6 - - - +
146C GLY* 1.3 56.5 + - - +
384C LEU* 4.6 11.9 - - + -
409C ILE* 4.8 6.1 - - + -
411C ILE* 3.1 44.6 - - + +
414C VAL* 4.0 30.3 - - + +
415C VAL* 4.1 13.7 + - - +
418C ILE* 5.8 0.9 - - - +
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Residues in contact with GLY 146 (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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124C LEU* 2.9 31.4 + - - +
144C PHE* 3.2 26.7 - - - -
145C MET* 1.3 80.2 - - - +
147C ASP* 1.3 66.5 + - - -
411C ILE* 4.8 0.9 - - - -
415C VAL* 4.8 11.2 - - - -
418C ILE* 5.8 2.5 - - - -
325F LEU* 5.7 0.2 - - - -
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Residues in contact with ASP 147 (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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107C LYS* 2.9 32.8 + - + -
119C THR* 5.7 5.2 - - + -
121C ALA* 3.9 17.1 - - + +
123C PRO* 3.9 11.5 - - + +
144C PHE* 4.2 10.5 - - - -
146C GLY* 1.3 71.9 - - - -
148C PHE* 1.3 59.5 + - - +
149C PRO* 3.6 9.2 - - - +
415C VAL* 5.2 10.1 - - - +
418C ILE* 4.2 10.7 - - - +
325F LEU* 5.8 1.4 - - - +
329F GLY 4.5 1.6 - - - +
330F ARG* 5.1 3.5 - - - -
331F GLU 5.7 2.0 + - - -
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Residues in contact with PHE 148 (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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52C PHE* 4.5 2.7 - + - -
55C LEU* 4.3 18.6 - - + -
56C VAL* 4.3 17.0 - - + -
77C LEU* 4.8 7.2 - - + -
103C PHE* 3.2 34.3 - + + -
121C ALA* 3.3 3.4 - - - -
122C ALA 2.6 45.7 + - - +
124C LEU* 4.6 14.8 - - + -
146C GLY 3.3 4.9 + - - +
147C ASP* 1.3 71.8 - - - +
149C PRO* 1.3 91.2 - - + +
150C MET* 3.3 7.7 - - + +
376C ILE* 4.8 4.9 - - + -
380C ILE* 3.6 33.4 - - + -
418C ILE* 4.5 18.8 - - + -
422C PHE* 6.5 0.9 - + - -
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Residues in contact with PRO 149 (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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52C PHE* 3.4 8.3 - - - -
119C THR* 4.6 5.6 - - - +
120C TYR 3.3 12.6 - - - +
121C ALA* 3.6 3.3 - - + -
147C ASP 3.6 8.3 - - - +
148C PHE* 1.3 107.3 - - + +
150C MET* 1.3 68.1 + - - +
157C PHE* 4.2 2.7 - - + -
159C ILE* 4.0 16.6 - - + -
418C ILE* 4.7 11.9 - - + -
422C PHE* 3.4 42.8 - - + -
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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