Contacts of the strand formed by residues 42 - 47 (chain C) in PDB entry 1QDV
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 LEU 42 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B LEU* 5.5 6.1 - - + -
37C ILE 3.6 0.3 - - - +
39C ILE 2.9 34.9 + - - +
41C GLY* 1.3 74.3 - - - +
43C ARG* 1.3 64.8 + - - +
44C PHE* 3.4 36.8 - - + -
82C ARG* 2.8 55.0 - - + +
83C PRO* 5.8 0.2 - - + -
42D LEU* 5.5 5.2 - - + -
82D ARG* 3.9 18.2 - - - +
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Residues in contact with ARG 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B GLU* 3.6 10.5 + - - -
36C VAL* 4.6 11.0 - - + +
37C ILE 3.7 2.9 - - - -
38C ASN* 2.5 33.8 + - - -
41C GLY 3.5 14.7 + - - +
42C LEU* 1.3 75.2 - - - +
44C PHE* 1.3 63.1 + - - +
45C GLU* 5.7 3.1 - - + +
73C ARG* 3.2 28.9 + - - +
75C GLU* 2.5 28.5 + - - -
41D GLY* 3.7 17.9 - - - +
42D LEU* 5.1 0.2 - - - -
82D ARG* 3.5 21.1 + - - -
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Residues in contact with PHE 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C VAL* 3.4 6.9 - - - +
37C ILE* 2.8 42.4 + - + +
39C ILE* 3.8 11.0 - - + -
42C LEU* 3.4 46.9 - - + -
43C ARG* 1.3 74.7 - - - +
45C GLU* 1.3 65.1 + - - +
82C ARG 4.6 0.9 - - - -
85C PHE* 3.5 41.1 - + + -
86C ASP* 3.7 27.8 - - + -
89C LEU* 4.1 16.6 - - + -
40D SER 3.4 3.8 - - - +
82D ARG* 3.4 36.8 - - - -
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Residues in contact with GLU 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C ARG* 2.6 39.2 + - - -
35C VAL 3.3 6.5 - - - +
36C VAL* 4.0 18.6 - - + -
37C ILE* 6.2 0.2 - - - -
43C ARG* 5.4 3.7 - - + +
44C PHE* 1.3 81.8 - - - +
46C THR* 1.3 65.3 - - - +
89C LEU* 4.2 1.4 - - - +
38D ASN* 3.4 14.5 - - - +
40D SER* 3.0 30.7 + - - +
41D GLY* 3.7 19.4 - - - +
43D ARG* 3.5 11.6 + - - -
73D ARG* 2.9 19.0 + - - -
77D PHE* 3.9 10.7 - - + -
79D ASP* 4.1 0.3 - - - +
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Residues in contact with THR 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C ARG* 3.4 8.8 - - - -
35C VAL* 2.9 47.9 + - + +
37C ILE* 4.4 8.3 - - + -
45C GLU* 1.3 77.0 - - - +
47C GLN* 1.3 67.6 + - - +
50C THR* 3.3 15.1 - - - +
51C LEU* 4.0 17.0 - - + -
89C LEU* 3.8 25.5 - - + +
77D PHE* 4.4 4.0 - - - -
79D ASP* 2.6 27.4 + - - -
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Residues in contact with GLN 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C GLU 3.2 14.6 + - - +
34C ARG* 5.4 2.0 - - - +
35C VAL* 4.0 2.9 - - - -
46C THR* 1.3 83.3 + - - +
48C LEU* 1.3 66.8 + - - +
49C LYS* 3.3 40.3 + - + +
50C THR* 2.9 20.7 + - - +
51C LEU* 3.3 8.7 + - - +
77D PHE* 4.5 13.8 - - + -
79D ASP* 2.8 34.1 + - - +
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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