Contacts of the helix formed by residues 40 - 45 (chain K) in PDB entry 1VCB
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 GLY 40 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146C PRO* 3.6 21.6 - - - +
37K LEU 4.8 1.3 - - - -
38K THR 3.8 2.0 + - - -
39K SER* 1.3 69.8 + - - +
41K THR* 1.3 65.6 + - - +
43K LYS* 3.0 13.7 + - - +
44K ALA 3.0 17.8 + - - -
110K LEU 3.5 4.0 + - - -
111K ASP* 3.7 20.6 + - - -
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Residues in contact with THR 41 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C ILE* 3.4 28.0 - - + +
108C ARG* 3.9 8.9 - - - +
146C PRO* 4.7 4.4 - - - +
148C PHE* 4.1 0.3 - - - -
40K GLY* 1.3 74.8 - - - +
42K ILE* 1.3 52.1 + - - +
44K ALA* 2.9 9.0 + - - +
45K MET* 2.7 45.0 + - + +
109K PHE* 2.6 45.7 + - + +
110K LEU* 3.2 20.3 + - + -
111K ASP* 3.8 7.9 + - - +
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Residues in contact with ILE 42 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21K LEU* 4.1 21.3 - - + -
36K ALA* 3.9 20.9 - - + +
37K LEU* 5.5 0.2 - - + -
39K SER* 3.4 26.3 + - - +
40K GLY 3.3 0.2 - - - -
41K THR* 1.3 79.2 - - - +
43K LYS* 1.3 63.3 + - - +
44K ALA 3.0 1.3 + - - -
45K MET* 3.8 7.4 - - - +
46K LEU* 3.1 50.5 + - + +
60K VAL* 4.9 3.1 - - + -
62K PHE* 3.9 30.5 - - + -
70K LEU* 6.1 0.4 - - + -
73K VAL* 5.6 0.4 - - + -
77K PHE* 4.2 19.5 - - + -
110K LEU* 3.9 13.2 - - + -
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Residues in contact with LYS 43 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C GLY* 5.1 21.8 - - - +
37K LEU* 3.6 50.8 + - + +
39K SER 3.0 14.8 + - - +
40K GLY* 3.0 15.5 + - - +
42K ILE* 1.3 77.0 - - - +
44K ALA* 1.3 52.6 + - - +
46K LEU* 2.6 17.0 - - - +
47K SER* 3.6 14.1 - - - +
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Residues in contact with ALA 44 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C GLY 5.0 2.9 - - - +
146C PRO* 3.4 40.2 - - + +
148C PHE* 3.2 25.6 - - + -
40K GLY 3.0 2.2 + - - -
41K THR* 2.9 7.6 + - - +
43K LYS* 1.3 77.9 - - - +
45K MET* 1.3 67.0 + - - +
46K LEU 3.0 7.6 - - - +
47K SER 5.2 0.2 - - - -
48K GLY* 3.2 20.9 - - - -
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Residues in contact with MET 45 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C ILE* 5.0 0.2 - - + -
77C CYS* 3.7 30.5 - - - -
79C ARG* 4.2 19.7 + - - +
148C PHE* 3.0 25.1 - - + -
41K THR* 2.7 41.8 + - + +
42K ILE* 3.2 7.6 + - - +
44K ALA* 1.3 72.3 - - - +
46K LEU* 1.3 59.0 + - - +
48K GLY* 4.6 2.1 + - - -
60K VAL* 3.8 25.4 - - + -
61K ASN 5.4 4.3 - - - +
62K PHE* 3.6 31.9 - - + -
109K PHE* 4.5 9.0 - - + -
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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