Contacts of the strand formed by residues 38 - 41 (chain O) in PDB entry 2V16
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 38 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18O ILE* 5.0 3.8 - - + -
20O ILE* 6.1 1.6 - - + -
36O SER 5.3 1.3 - - - +
37O ASN* 1.4 76.4 - - - +
39O TRP* 1.3 66.3 + - - +
40O VAL* 6.2 0.9 - - + -
71O LEU* 5.4 1.6 - - - +
89O ILE* 4.1 17.3 - - + -
99O GLN* 3.9 20.4 - - + +
100O MET 4.4 3.7 + - - +
101O PHE* 3.6 22.6 - - + -
102O GLY* 3.0 21.9 + - - -
120O VAL 3.4 9.2 - - - +
121O VAL* 4.2 21.1 - - + -
122O GLY* 4.3 2.7 - - - +
135O PRO* 5.8 0.7 - - + -
136O ILE* 4.0 23.8 - - + +
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Residues in contact with TRP 39 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29O VAL* 5.7 0.2 - - - +
37O ASN 4.5 1.3 - - - -
38O VAL* 1.3 79.0 - - - +
40O VAL* 1.3 68.4 - - - +
41O PRO* 4.2 5.8 - - + -
71O LEU* 6.0 0.9 - - + -
73O LEU* 3.8 15.7 - - + +
75O TYR* 2.7 31.9 + + - -
80O VAL* 4.2 9.1 - - + +
101O PHE* 5.1 0.7 - - - -
102O GLY* 3.7 17.5 - - - +
104O VAL* 3.2 33.9 - - + -
107O MET* 4.6 7.6 - - - -
112O PHE* 3.3 44.2 - + - -
118O ASP 3.4 22.0 - - - -
119O GLY* 3.1 6.9 - - - -
120O VAL* 2.7 56.7 + - + +
1327O C47 6.0 0.2 - - + -
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Residues in contact with VAL 40 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18O ILE* 5.2 5.8 - - + -
20O ILE* 3.5 27.8 - - + -
27O PHE* 3.7 27.6 - - + -
29O VAL* 5.5 3.1 - - + -
38O VAL* 6.2 1.3 - - + -
39O TRP* 1.3 77.4 - - - +
41O PRO* 1.5 76.7 - - + +
56O PHE* 4.0 9.0 - - + -
101O PHE* 3.7 28.9 - - + -
102O GLY 3.1 4.2 + - - +
103O GLU* 3.5 0.9 - - - -
104O VAL* 3.1 20.8 + - - +
118O ASP 4.3 1.1 - - - -
119O GLY* 5.0 4.7 - - - +
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Residues in contact with PRO 41 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39O TRP* 4.2 1.8 - - + -
40O VAL* 1.5 67.9 - - + +
42O SER* 1.5 52.4 + - - +
50O CYS* 5.0 0.2 - - - -
53O HIS* 4.1 14.1 - - + -
54O LYS 3.0 24.4 - - - +
55O LEU* 3.4 15.7 - - + -
56O PHE* 2.5 38.7 + - - +
104O VAL* 3.9 11.7 - - + +
107O MET* 4.2 17.3 - - + -
118O ASP* 2.9 39.5 - - + +
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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
------------------------------------------------------------
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