Contacts of the strand formed by residues 51 - 56 (chain I) in PDB entry 6D6Q
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 PRO 51 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19I GLU* 3.2 31.2 - - - +
20I GLY* 3.2 6.7 - - - -
21I SER 2.9 22.7 + - - -
43I LYS* 4.3 24.7 - - + -
44I SER 3.2 14.8 - - - +
45I SER* 4.6 6.5 - - - -
49I ALA 3.5 9.2 - - - +
50I LEU* 1.3 95.0 - - + +
52I VAL* 1.3 59.8 + - - +
53I VAL 3.9 0.7 - - - +
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Residues in contact with VAL 52 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21I SER* 3.5 20.9 - - - +
22I PRO 4.5 0.7 - - - +
23I GLY* 3.8 26.9 - - - +
42I MET 3.6 0.9 - - - +
43I LYS* 3.3 1.9 - - - -
44I SER* 2.9 51.6 + - - +
46I GLU* 5.9 7.4 - - + +
50I LEU* 4.3 8.5 - - + +
51I PRO* 1.3 72.9 - - - +
53I VAL* 1.3 63.6 + - - +
54I SER* 4.9 3.4 + - - -
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Residues in contact with VAL 53 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14I LEU* 4.3 24.5 - - + -
15I CYS* 4.1 23.8 - - - -
20I GLY* 5.6 1.3 - - - -
21I SER 2.9 25.2 + - - +
22I PRO* 4.2 3.1 - - + -
23I GLY* 2.7 33.1 + - - -
24I SER 4.7 0.2 - - - +
26I THR* 4.9 4.1 - - + +
33I ILE* 4.1 13.0 - - + -
41I LEU* 4.9 9.6 - - + -
42I MET 3.5 9.6 - - - +
43I LYS* 4.0 14.4 - - + +
51I PRO* 3.9 2.4 - - + -
52I VAL* 1.3 73.1 - - - +
54I SER* 1.3 68.1 + - - +
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Residues in contact with SER 54 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23I GLY* 4.5 4.3 - - - -
24I SER* 3.6 24.2 - - - -
26I THR* 4.7 1.1 - - - -
41I LEU* 3.2 5.4 - - - +
42I MET* 2.9 57.1 + - - +
52I VAL* 4.9 3.2 + - - -
53I VAL* 1.3 77.9 - - - +
55I VAL* 1.3 67.2 + - - +
56I VAL* 4.7 5.0 - - - +
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Residues in contact with VAL 55 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8I CYS* 3.3 35.0 - - - -
14I LEU* 4.1 7.6 - - + -
24I SER* 3.2 14.6 + - - +
25I GLY* 3.8 16.5 - - - +
26I THR* 4.0 16.8 - - + -
35I SER* 3.9 10.8 - - - +
37I LEU* 4.2 28.5 - - + +
39I GLY* 4.4 5.2 - - - -
40I CYS 3.5 6.7 - - - +
41I LEU* 4.1 7.9 - - + -
54I SER* 1.3 82.2 - - - +
56I VAL* 1.3 70.9 + - - +
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Residues in contact with VAL 56 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24I SER* 6.5 0.4 - - - -
37I LEU* 5.5 2.7 - - - -
39I GLY* 3.4 3.9 - - - -
40I CYS* 2.9 46.5 + - + +
42I MET* 3.4 31.9 - - + -
54I SER* 4.7 6.7 - - - +
55I VAL* 1.3 84.4 - - - +
57I ARG* 1.3 59.8 + - - +
58I GLU* 3.7 25.6 + - + +
61I SER* 4.9 14.6 - - - +
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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