Contacts of the strand formed by residues 44 - 49 (chain L) in PDB entry 2VDP
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 PHE 44 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39H GLN* 3.5 21.1 - - - -
45H LEU* 3.6 24.5 - - + -
95H TYR* 3.7 17.3 - + - -
109H TRP* 3.5 56.1 + + + +
36L LEU* 4.0 22.9 - - + -
37L GLN 3.4 3.6 - - - -
38L GLN* 3.3 42.8 - - + -
43L SER* 1.3 85.8 + - - +
45L MET* 1.3 68.8 + - - +
87L TYR* 3.7 27.1 - + - -
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Residues in contact with MET 45 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107H ASP 4.7 1.6 - - - -
36L LEU* 3.6 5.0 - - - -
37L GLN* 3.0 50.6 + - + +
39L LYS* 6.0 6.3 - - + -
43L SER 4.9 3.4 - - - +
44L PHE* 1.3 80.3 - - - +
46L GLY* 1.3 65.2 + - - +
47L LEU* 3.6 3.7 + - + +
58L VAL* 6.5 1.1 - - + -
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Residues in contact with GLY 46 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107H ASP* 3.2 29.5 + - - -
35L TRP 3.9 5.4 - - - -
36L LEU* 4.0 11.3 - - - +
45L MET* 1.3 76.2 - - - +
47L LEU* 1.3 62.1 + - - +
48L ILE 5.7 0.2 - - - -
55L VAL* 3.5 19.3 - - - +
58L VAL* 3.4 16.3 - - - +
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Residues in contact with LEU 47 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35L TRP 2.8 15.9 + - - +
36L LEU 4.1 6.5 - - - -
37L GLN* 3.8 30.5 - - + +
45L MET* 4.1 4.9 - - + +
46L GLY* 1.3 79.3 - - - +
48L ILE* 1.3 68.9 + - + +
54L LEU* 3.4 7.6 - - - +
55L VAL* 2.9 23.7 + - - +
58L VAL* 3.8 28.8 - - + +
59L PRO* 5.8 0.4 - - + -
62L PHE* 4.1 20.6 - - + -
73L LEU* 4.0 15.5 - - + -
86L TYR* 3.7 33.2 - - + -
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Residues in contact with ILE 48 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107H ASP* 4.4 4.5 - - - +
34L GLY* 3.2 4.9 - - - -
35L TRP* 3.2 37.8 + - + +
46L GLY* 5.7 0.3 - - - -
47L LEU* 1.3 84.7 + - + +
49L TYR* 1.3 65.8 + - - +
51L GLY* 3.4 36.6 - - - +
52L THR 3.5 5.6 - - - +
53L ASN 3.2 9.4 - - - +
54L LEU* 3.4 33.4 - - + -
55L VAL* 4.5 2.2 - - - -
62L PHE* 4.9 2.5 - - + -
63L SER* 4.2 4.0 - - - +
64L GLY 3.9 18.2 - - - +
73L LEU* 4.0 24.2 - - + -
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Residues in contact with TYR 49 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A ARG* 3.4 33.2 + - + +
211A ILE* 4.3 8.3 - - + -
100H LEU* 4.8 4.5 - - + -
101H TYR* 3.3 38.8 - + + -
102H ASP* 4.2 16.8 - - + -
105H ALA* 4.2 3.6 - - + -
107H ASP* 3.6 24.7 - - - +
33L ILE 4.2 1.3 - - - -
34L GLY* 4.6 0.9 - - - -
48L ILE* 1.3 73.7 - - - +
50L TYR* 1.3 74.8 + - + +
51L GLY 3.1 3.5 + - - -
53L ASN* 2.7 56.9 + - + +
54L LEU 3.6 20.2 - - - -
55L VAL* 4.0 18.8 - - + -
56L ASP* 5.5 0.2 + - - -
91L TYR* 3.8 9.9 - - - +
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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