Contacts of the helix formed by residues 48 - 54 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25B ASN* 3.9 12.1 - - - -
26B LEU* 4.2 9.6 - - - +
46B GLY 3.5 1.4 + - - -
47B SER* 1.3 80.0 - - - +
49B LYS* 1.3 66.9 + - - +
50B SER 3.3 2.9 - - - -
51B SER* 3.1 10.8 + - - -
52B LEU* 3.2 16.3 + - - +
453B VAL* 4.2 6.9 - - - +
902B ADP 3.0 19.1 + - - -
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Residues in contact with LYS 49 (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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41B PHE* 3.2 32.0 - - - +
42B THR* 3.5 31.4 - - - +
43B GLY 3.0 2.2 + - - +
44B VAL 2.7 20.0 + - - -
45B SER* 4.1 0.8 - - - +
47B SER* 3.8 6.1 + - - +
48B GLY* 1.3 75.9 - - - +
50B SER* 1.3 57.0 + - - +
52B LEU* 3.9 3.0 - - - +
53B ALA* 3.1 30.0 + - - +
437B VAL* 3.9 20.2 - - + -
438B GLU 4.7 1.1 - - - +
439B HIS* 3.0 36.4 + - - +
453B VAL* 4.3 12.3 - - + +
902B ADP 2.7 31.0 + - - +
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Residues in contact with SER 50 (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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49B LYS* 1.3 70.9 - - - +
51B SER* 1.3 64.0 + - - +
52B LEU 3.2 1.6 - - - -
53B ALA* 4.0 2.0 - - - +
54B PHE* 3.1 30.1 + - - +
55B GLY* 3.0 18.4 + - - -
101B ARG* 3.6 15.2 + - - -
406B ASP* 5.4 4.3 - - - -
437B VAL* 5.0 6.3 - - - -
902B ADP 2.8 47.1 + - - -
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Residues in contact with SER 51 (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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23B GLN* 3.8 18.8 - - - +
24B HIS* 3.0 36.7 + - - +
25B ASN* 3.9 0.2 + - - -
26B LEU* 3.9 8.7 - - - -
48B GLY* 3.1 8.2 + - - -
50B SER* 1.3 77.1 - - - +
52B LEU* 1.3 50.9 + - - +
55B GLY* 3.1 6.7 - - - +
56B THR* 2.8 36.2 + - - -
902B ADP 2.6 27.5 + - - -
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Residues in contact with LEU 52 (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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18B VAL* 4.9 4.0 - - + -
26B LEU* 4.1 11.9 - - + -
29B ILE* 4.3 11.7 - - + -
31B VAL* 4.2 24.9 - - + -
41B PHE* 3.9 27.8 - - + -
48B GLY 3.2 11.0 + - - +
49B LYS 3.9 2.0 - - - +
50B SER 3.2 0.2 - - - -
51B SER* 1.3 78.9 - - - +
53B ALA* 1.3 58.9 + - - +
56B THR* 3.3 16.6 - - + +
57B LEU* 2.9 49.8 + - + +
451B VAL* 4.1 15.5 - - + -
453B VAL* 4.5 11.9 - - + -
464B ILE* 4.6 8.3 - - + -
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Residues in contact with ALA 53 (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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41B PHE* 4.4 21.3 - - + -
49B LYS 3.1 18.2 + - - +
52B LEU* 1.3 78.9 - - - +
54B PHE* 1.3 73.0 + - + +
57B LEU* 3.6 12.6 - - - +
58B TYR* 3.0 24.3 + - - +
404B VAL* 3.9 14.4 - - + +
435B PHE* 5.2 3.8 - - + +
436B VAL 6.0 0.2 - - - -
437B VAL* 4.3 13.0 - - + +
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Residues in contact with PHE 54 (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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50B SER* 3.1 24.3 + - - +
53B ALA* 1.3 82.1 - - + +
55B GLY* 1.3 62.4 + - - +
56B THR 3.3 2.2 - - - -
58B TYR* 3.5 20.9 - + + +
59B ALA* 3.1 27.4 + - - +
96B ALA* 4.6 6.5 - - + -
98B GLN* 4.5 19.1 - - + -
404B VAL* 3.8 32.5 - - + -
405B LEU 3.9 9.2 - - - -
406B ASP* 3.7 26.2 - - + -
437B VAL* 3.5 26.5 - - + -
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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