Contacts of the strand formed by residues 44 - 47 (chain B) in PDB entry 3VSX
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 VAL 44 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B ILE* 5.1 4.7 - - + -
26B ILE* 5.9 0.4 - - + -
42B SER 5.1 0.7 - - - +
43B ASN* 1.3 83.6 - - - +
45B TRP* 1.3 62.9 + - - +
46B VAL* 5.5 3.1 - - + -
79B LEU* 5.3 0.5 - - - +
97B ILE* 4.1 16.6 - - + -
106B GLN* 4.6 9.9 - - + +
107B MET 4.6 2.1 + - - +
108B PHE* 3.2 23.7 - - + +
109B GLY 2.6 31.7 + - - -
127B VAL 3.6 10.8 - - - +
128B VAL* 4.3 17.5 - - + -
129B GLY 4.4 2.0 - - - +
142B PRO* 5.8 0.4 - - + -
143B ILE* 4.3 34.3 - - + +
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Residues in contact with TRP 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B ASN 5.1 1.1 - - - -
44B VAL* 1.3 81.1 - - - +
46B VAL* 1.3 77.6 + - - +
47B PRO* 3.7 2.0 - - + -
79B LEU* 5.5 0.2 - - + -
81B LEU* 3.4 26.6 - - + +
83B TYR* 2.9 23.8 + + - -
88B VAL* 4.2 10.8 - - + -
108B PHE* 4.7 1.1 - - - -
109B GLY* 3.0 24.0 - - - +
111B VAL* 3.4 25.1 - - + -
114B MET* 3.5 27.4 - - + -
119B PHE* 4.0 30.5 - + - -
124B PHE* 5.3 0.7 - + - -
125B ASP 3.4 24.9 - - - -
126B GLY* 4.0 2.0 - - - -
127B VAL* 3.2 59.6 + - + +
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Residues in contact with VAL 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ILE* 5.2 2.9 - - + -
26B ILE* 3.9 32.3 - - + -
33B PHE* 4.1 26.7 - - + -
35B VAL* 4.2 13.0 - - + -
44B VAL* 5.5 2.9 - - + -
45B TRP* 1.3 86.8 - - - +
47B PRO* 1.3 76.5 - - + +
48B SER 3.3 0.3 + - - -
64B PHE* 4.0 20.9 - - + -
108B PHE* 4.2 14.8 - - + -
109B GLY 3.3 2.5 + - - +
110B GLU* 3.8 2.9 - - + -
111B VAL 3.2 16.8 + - - -
126B GLY* 4.4 2.2 - - - +
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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
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45B TRP* 3.7 3.8 - - + -
46B VAL* 1.3 84.4 - - + +
48B SER* 1.3 59.0 + - - +
58B CYS* 4.6 5.2 - - - -
61B HIS* 3.9 13.2 - - + -
62B LYS 3.1 23.5 - - - +
63B LEU* 3.2 19.6 - - + -
64B PHE* 2.9 23.9 + - - +
111B VAL* 3.9 6.1 - - + +
114B MET* 3.3 26.2 - - + -
125B ASP* 2.8 35.2 - - + +
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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