Contacts of the strand formed by residues 45 - 52 (chain B) in PDB entry 3VTW
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 LYS 45 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B ARG* 3.2 20.1 + - - -
42B HIS* 3.2 42.3 + - + +
44B THR* 1.3 87.1 - - - +
46B ILE* 1.3 63.2 + - - +
47B PRO* 4.1 3.1 - - - +
68B LEU* 3.4 36.6 - - + +
69B VAL 3.1 10.3 - - - +
70B PRO* 4.1 26.9 - - + -
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Residues in contact with ILE 46 (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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39B ARG* 3.5 23.8 - - - +
45B LYS* 1.3 73.1 - - - +
47B PRO* 1.4 66.3 - - + +
48B VAL* 3.4 20.9 - - + +
67B PHE 3.4 3.6 - - - +
68B LEU* 3.6 2.9 - - - +
69B VAL* 2.5 35.2 + - + +
71B ASP* 4.1 25.1 - - + -
110B ILE* 4.1 14.6 - - + -
111B SER* 4.2 14.6 - - - +
114B TYR* 3.7 46.0 - - + -
124B LEU* 4.4 8.7 - - + -
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Residues in contact with PRO 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B VAL* 4.2 6.3 - - + -
38B ILE* 4.0 23.1 - - + -
39B ARG* 3.8 31.9 - - + -
45B LYS 4.1 1.1 - - - +
46B ILE* 1.4 86.6 - - + +
48B VAL* 1.3 60.0 + - - +
67B PHE 3.4 5.6 - - - +
68B LEU* 4.0 3.8 - - + -
114B TYR* 4.0 9.2 - - + -
122B GLY 4.0 11.7 - - - +
123B PHE* 3.6 24.8 - - + -
124B LEU* 3.0 24.6 + - - +
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Residues in contact with VAL 48 (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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46B ILE* 3.4 27.1 - - + +
47B PRO* 1.3 78.6 - - - +
49B ILE* 1.3 67.4 + - - +
50B ILE* 4.0 11.2 - - + -
65B THR 3.4 1.9 - - - +
66B LYS* 3.4 2.8 - - - +
67B PHE* 2.6 50.3 + - + +
69B VAL* 3.8 16.4 - - + -
78B LEU* 5.2 0.7 - - + -
110B ILE* 4.1 5.8 - - + -
123B PHE* 4.0 1.6 - - - -
124B LEU* 3.4 11.7 - - + +
126B MET* 3.2 39.7 - - + -
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Residues in contact with ILE 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B PHE* 3.8 19.7 - - + -
48B VAL* 1.3 74.7 - - - +
50B ILE* 1.3 56.5 + - - +
51B GLU* 3.8 13.7 - - - +
65B THR* 3.3 20.6 - - + +
66B LYS* 3.4 32.8 - - + -
123B PHE* 3.6 32.5 - - + -
124B LEU 3.0 5.7 + - - +
125B TYR* 3.5 37.0 - - + -
126B MET* 2.8 34.3 + - - +
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Residues in contact with ILE 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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48B VAL* 4.0 19.1 - - + -
49B ILE* 1.3 76.8 - - - +
51B GLU* 1.3 69.0 + - - +
62B LEU* 3.6 29.3 - - + +
64B LYS 4.4 0.3 - - - +
65B THR* 3.1 18.8 + - - +
67B PHE* 3.9 24.2 - - + -
69B VAL* 6.0 0.2 - - + -
78B LEU* 4.6 11.9 - - + -
82B ILE* 3.8 32.8 - - + -
96B LEU* 4.3 14.8 - - + -
126B MET* 3.6 17.5 - - + +
128B TYR* 3.8 15.5 - - + -
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Residues in contact with GLU 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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21B THR* 3.4 16.8 - - - +
22B PHE* 2.8 33.2 + - - +
23B LYS 5.6 0.2 + - - -
25B ARG* 4.7 1.4 + - - -
49B ILE* 3.8 18.9 - - + +
50B ILE* 1.3 81.1 - - - +
52B ARG* 1.3 66.4 + - - +
62B LEU* 5.2 0.9 - - - -
65B THR* 3.6 14.1 - - + +
125B TYR* 4.4 9.5 - - - -
126B MET 3.0 11.7 + - - +
127B VAL* 3.3 10.8 - - + +
128B TYR* 3.1 31.1 + - - -
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Residues in contact with ARG 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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19B GLU* 2.6 42.4 + - - +
51B GLU* 1.3 76.8 - - - +
53B TYR* 1.3 71.2 + - - +
54B LYS* 3.1 6.1 + - - -
56B GLU* 3.6 32.9 + - + +
59B LEU 3.2 28.7 + - - -
60B PRO* 3.8 6.3 - - - +
61B VAL* 3.5 31.9 - - + +
62B LEU* 5.9 0.6 - - - +
127B VAL* 4.1 1.5 - - - +
128B TYR* 3.5 32.6 - - + +
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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