Contacts of the helix formed by residues 72 - 77 (chain B) in PDB entry 2VF8
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 72 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A GLN* 4.9 5.9 + - - -
105A THR* 4.8 11.8 - - + +
106A ALA* 4.3 22.0 - - + -
108A SER* 3.4 36.6 - - - -
112A SER* 4.9 6.7 - - - +
113A VAL* 3.9 23.8 - - + +
377A THR* 4.7 2.7 + - - -
385A LEU* 5.1 7.3 - - - +
389A ARG* 5.0 10.3 - - - -
70B SER* 2.5 9.6 + - - -
71B PRO* 1.3 106.7 - - + +
73B ALA* 1.3 66.7 + - + +
74B ARG 3.8 0.2 - - - -
75B ARG* 4.0 5.7 + - - +
76B LEU* 3.9 22.5 + - - +
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Residues in contact with ALA 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B SER* 2.5 30.2 + - - +
72B TYR* 1.3 77.5 - - - +
74B ARG* 1.3 67.8 + - - +
75B ARG 3.2 0.2 + - - -
76B LEU* 3.6 9.2 + - - +
77B PHE* 3.8 15.5 + - - -
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Residues in contact with ARG 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B ALA 5.7 0.6 + - - -
62B GLN* 5.7 0.6 - - - +
63B ARG* 3.6 32.0 - - - +
66B LEU* 3.6 45.0 - - + +
67B GLU* 3.7 19.9 + - + +
70B SER* 3.4 14.5 + - - +
73B ALA* 1.3 78.0 - - - +
75B ARG* 1.3 55.6 + - - +
77B PHE* 2.6 43.5 + - + -
78B ASN* 2.9 44.9 - - - +
81B GLY* 4.2 12.7 - - - +
655B LEU* 6.0 10.2 - - + +
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Residues in contact with ARG 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A SER 4.4 6.3 - - - -
113A VAL 5.3 0.2 - - - -
115A THR* 3.4 39.6 - - - +
118A ASN* 5.8 6.5 - - - +
63B ARG* 4.3 7.5 - - - +
67B GLU* 3.0 51.5 + - + +
71B PRO* 3.1 43.5 - - + +
72B TYR* 4.0 6.1 - - - +
73B ALA 3.2 0.6 + - - -
74B ARG* 1.3 73.7 - - - +
76B LEU* 1.3 65.9 + - - +
78B ASN* 2.9 32.4 + - - +
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Residues in contact with LEU 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A ARG* 5.6 0.2 - - - +
140A GLU* 3.4 41.0 - - - +
145A ASN* 5.4 9.0 - - + +
146A THR* 4.6 12.1 - - + -
1847A SO4 4.3 26.7 - - - +
72B TYR 3.9 11.4 + - - +
73B ALA* 3.6 7.4 + - - +
74B ARG 3.4 0.6 - - - -
75B ARG* 1.3 76.8 - - - +
77B PHE* 1.3 66.5 + - + +
78B ASN* 2.8 15.5 + - - +
79B GLN* 3.5 8.3 + - - +
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Residues in contact with PHE 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B ALA 4.1 12.6 - - - -
74B ARG* 2.6 36.8 + - - +
76B LEU* 1.3 76.7 - - + +
78B ASN* 1.3 54.0 + - - -
79B GLN* 3.0 31.9 + - + +
80B ALA* 4.2 5.0 + - - +
81B GLY 4.8 0.7 + - - -
652B VAL* 5.0 5.4 - - + -
654B LEU* 2.7 56.3 - - + -
655B LEU* 4.0 29.6 - - + +
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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