Contacts of the strand formed by residues 48 - 51 (chain F) in PDB entry 1VQN
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 48 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36F THR* 4.0 7.6 - - + -
40F ILE* 3.8 34.5 - - + -
45F ALA* 4.3 3.1 - - + -
47F LEU* 1.3 76.5 - - - +
49F PHE* 1.3 63.4 + - - +
50F VAL* 5.2 0.7 - - + -
63F ILE* 4.3 9.6 - - + -
67F ALA* 4.9 1.6 - - + -
72F VAL* 4.1 11.7 - - + -
73F PRO 3.1 7.4 + - - +
74F PHE* 3.1 25.1 - - + +
75F ILE* 2.9 27.7 + - - +
96F ALA 3.1 6.7 - - - +
97F ALA* 3.4 24.7 - - + -
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Residues in contact with PHE 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F ALA* 3.6 43.5 - - + -
17F LEU* 4.2 2.7 - - + -
19F ALA* 5.7 1.3 - - + -
20F LEU* 3.7 22.4 - - + -
47F LEU* 4.0 22.0 - - + -
48F VAL* 1.3 78.0 - - - +
50F VAL* 1.3 67.5 + - - +
75F ILE* 3.4 15.7 - - + +
77F VAL* 4.0 10.1 - - + -
83F LEU* 3.4 37.0 - - + -
95F ALA* 3.1 5.5 - - - +
96F ALA* 2.4 47.9 + - + +
98F VAL* 3.2 31.0 - - + -
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Residues in contact with VAL 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3F TYR* 3.7 12.1 - - + -
48F VAL* 5.2 3.1 - - + +
49F PHE* 1.3 81.1 - - - +
51F ALA* 1.3 77.2 + - - +
60F VAL* 3.2 27.6 - - + -
63F ILE* 3.3 39.9 - - + -
64F PRO* 5.8 0.4 - - + -
74F PHE* 5.5 2.7 - - + -
75F ILE 3.0 9.1 + - - +
76F PHE* 3.3 24.2 - - + -
77F VAL 3.1 18.9 + - - +
83F LEU* 4.3 1.1 - - - -
94F ALA 3.6 3.6 - - - +
95F ALA* 4.2 3.6 - - + -
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Residues in contact with ALA 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3F TYR* 3.0 15.2 + - - -
50F VAL* 1.3 87.4 - - - +
52F GLU* 1.3 59.7 + - - +
53F ASP* 3.5 18.2 - - - +
54F VAL* 3.7 11.4 - - + +
77F VAL* 3.4 10.8 - - - +
79F GLN 4.0 3.8 - - - +
80F GLN* 3.7 20.4 - - + -
83F LEU* 3.8 5.4 - - + +
93F SER 4.1 4.9 - - - +
94F ALA 2.8 18.9 + - - +
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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