Contacts of the helix formed by residues 48 - 54 (chain A) in PDB entry 2VF7
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 GLY 48 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A ASN* 3.8 13.5 - - - -
26A LEU* 3.6 16.6 - - - +
46A GLY 3.4 1.0 - - - -
47A SER* 1.3 78.2 - - - +
49A LYS* 1.3 66.8 + - - +
50A SER 3.4 2.7 - - - -
51A SER* 3.5 1.0 + - - -
52A LEU* 3.2 21.1 + - - +
453A VAL* 4.0 5.7 - - - +
902A ADP 2.9 18.5 + - - -
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Residues in contact with LYS 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A PHE* 3.4 22.7 - - + +
42A THR* 3.4 34.5 - - - +
43A GLY 2.8 20.2 + - - -
44A VAL 3.0 7.1 + - - -
45A SER* 4.0 2.4 - - - +
47A SER* 3.7 10.7 + - - +
48A GLY* 1.3 76.8 - - - +
50A SER* 1.3 58.1 + - - +
52A LEU* 3.5 3.2 + - - +
53A ALA* 3.0 28.6 + - - +
437A VAL* 3.9 24.2 - - + +
438A GLU 4.9 1.1 - - - -
439A HIS* 3.3 29.3 + - - -
453A VAL* 4.2 10.5 - - + +
902A ADP 2.6 32.4 + - - +
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Residues in contact with SER 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A LYS* 1.3 68.2 - - - +
51A SER* 1.3 67.5 + - - +
52A LEU 3.0 2.2 - - - -
53A ALA* 5.0 0.2 - - - -
54A PHE* 2.9 44.0 + - - +
55A GLY 2.9 6.6 + - - -
101A ARG* 3.8 25.5 + - - -
406A ASP* 4.3 11.4 + - - -
437A VAL* 4.6 5.5 - - - +
902A ADP 2.9 29.3 + - - -
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Residues in contact with SER 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A GLN* 3.9 7.3 - - - +
24A HIS* 2.5 36.9 + - - +
25A ASN* 4.6 0.4 - - - -
26A LEU* 3.7 20.7 - - - +
48A GLY* 3.5 8.9 + - - -
50A SER* 1.3 74.5 - - - +
52A LEU* 1.3 51.0 + - - +
55A GLY* 3.3 7.9 - - - +
56A THR* 2.8 35.3 + - - -
902A ADP 2.8 30.3 + - - -
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Residues in contact with LEU 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A VAL* 4.8 3.6 - - + -
21A ALA* 4.8 2.5 - - + -
26A LEU* 4.0 14.1 - - + +
29A ILE* 4.4 17.9 - - + -
31A VAL* 4.6 11.7 - - + -
41A PHE* 4.2 23.3 - - + -
48A GLY 3.2 15.4 + - - +
49A LYS* 3.7 4.0 - - - +
50A SER 3.0 1.4 + - - -
51A SER* 1.3 74.3 - - - +
53A ALA* 1.3 60.8 + - - +
56A THR* 3.3 20.4 + - + -
57A LEU* 2.9 38.0 + - + +
451A VAL* 4.4 4.3 - - + -
453A VAL* 4.2 13.2 - - + -
464A ILE* 4.1 26.2 - - + -
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Residues in contact with ALA 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A PHE* 4.1 28.0 - - + -
49A LYS 3.0 18.4 + - - +
52A LEU* 1.3 73.8 - - - +
54A PHE* 1.3 62.7 + - + +
57A LEU* 3.5 12.9 - - - +
58A TYR* 3.0 26.3 + - - +
404A VAL* 3.8 15.3 - - + +
435A PHE* 4.8 3.0 - - + +
437A VAL* 4.2 17.0 - - + -
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Residues in contact with PHE 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A SER* 2.9 31.1 + - - +
53A ALA* 1.3 79.9 - - + +
55A GLY* 1.3 64.2 + - - +
56A THR 3.2 2.2 - - - -
58A TYR* 3.7 21.2 - + + +
59A ALA* 3.2 26.0 + - - +
96A ALA* 4.1 14.4 - - + -
98A GLN* 4.9 10.8 - - + -
404A VAL* 3.7 39.3 - - + -
405A LEU 3.9 2.7 - - - -
406A ASP* 3.8 26.2 - - + -
437A VAL* 3.8 22.9 - - + -
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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