Contacts of the strand formed by residues 44 - 47 (chain O) in PDB entry 2V10
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 O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24O ILE* 4.9 6.7 - - + -
26O ILE* 5.7 1.8 - - + -
42O SER 5.5 0.9 - - - +
43O ASN* 1.3 82.5 - - - +
45O TRP* 1.3 69.4 + - - +
46O VAL* 5.7 0.9 - - + -
79O LEU* 5.5 0.9 - - - +
81O LEU* 5.2 0.7 - - - +
97O ILE* 4.3 14.4 - - + -
106O GLN* 3.7 22.9 - - + +
107O MET 4.6 3.1 + - - +
108O PHE* 3.6 24.7 - - + -
109O GLY* 2.9 21.8 + - - -
127O VAL 3.4 9.0 - - - +
128O VAL* 4.3 17.9 - - + -
129O GLY 4.4 2.0 - - - +
142O PRO* 5.8 0.7 - - + -
143O ILE* 4.3 23.1 - - + +
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Residues in contact with TRP 45 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35O VAL* 6.1 0.2 - - - +
43O ASN 4.7 1.8 - - - -
44O VAL* 1.3 80.6 - - - +
46O VAL* 1.4 66.7 - - - +
47O PRO* 4.2 5.2 - - + -
81O LEU* 3.6 17.3 - - + -
83O TYR* 2.7 31.8 + + - -
88O VAL* 4.0 13.1 - - + +
108O PHE* 4.9 0.9 - - - -
109O GLY* 3.7 18.6 - - - +
111O VAL* 3.0 35.4 - - + -
114O MET* 4.3 9.0 - - - -
119O PHE* 3.2 46.7 - + - -
124O PHE* 5.8 0.2 - + - -
125O ASP 3.5 21.1 - - - -
126O GLY* 3.2 9.8 - - - -
127O VAL* 2.7 61.0 + - + +
1341O C61 4.8 0.2 - - + -
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Residues in contact with VAL 46 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24O ILE* 5.0 6.3 - - + -
26O ILE* 3.1 29.2 - - + -
33O PHE* 3.8 25.4 - - + -
35O VAL* 5.6 2.5 - - + -
44O VAL* 5.7 1.6 - - + -
45O TRP* 1.4 78.3 - - - +
47O PRO* 1.4 69.2 - - + +
64O PHE* 3.9 18.6 - - + -
108O PHE* 3.8 29.2 - - + -
109O GLY 3.2 2.4 - - - +
110O GLU* 3.7 1.1 - - + -
111O VAL 3.1 20.4 + - - -
125O ASP 4.2 1.3 - - - -
126O GLY* 5.1 4.3 - - - -
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Residues in contact with PRO 47 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45O TRP* 4.2 2.5 - - + -
46O VAL* 1.4 81.8 - - + +
48O SER* 1.4 51.6 + - - +
61O HIS* 4.3 11.9 - - + -
62O LYS 2.9 24.4 - - - +
63O LEU* 3.2 16.7 - - + -
64O PHE* 2.5 35.7 + - - +
111O VAL* 4.0 11.7 - - + +
114O MET* 4.3 20.2 - - + -
125O ASP* 2.8 39.7 - - + +
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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