Contacts of the strand formed by residues 27 - 33 (chain I) in PDB entry 5DPW
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 ILE 27 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25I ASN 4.7 1.1 - - - +
26I LYS* 1.3 78.0 - - - +
28I PRO* 1.3 79.7 - - + +
29I VAL* 3.7 12.4 + - + -
48I PHE 3.5 0.5 - - - +
49I LEU* 3.4 7.6 - - - -
50I VAL* 2.8 52.6 + - + +
51I PRO 3.8 2.9 - - - +
52I GLN* 3.6 29.4 - - + +
91I MET* 4.2 21.1 - - + +
92I ALA* 4.3 8.5 - - + +
95I TYR* 3.8 32.5 - - + -
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Residues in contact with PRO 28 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16I VAL* 4.6 25.6 - - + -
19I ILE* 4.3 25.6 - - + -
20I ARG* 4.9 9.6 - - + +
26I LYS 4.0 5.8 - - - +
27I ILE* 1.3 91.3 - - + +
29I VAL* 1.3 63.2 + - - +
30I VAL* 4.4 0.6 + - - -
48I PHE 3.4 6.3 - - - +
49I LEU* 4.4 5.1 - - + -
95I TYR* 4.8 13.7 - - + -
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Residues in contact with VAL 29 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27I ILE* 4.0 17.0 - - + +
28I PRO* 1.3 78.4 - - - +
30I VAL* 1.3 66.8 + - - +
31I VAL* 3.8 12.3 - - + -
46I THR 3.7 0.9 - - - +
47I LYS* 3.6 1.7 - - - -
48I PHE* 2.7 50.4 + - + +
50I VAL* 4.0 20.9 - - + -
59I PHE* 3.7 24.7 - - + -
91I MET* 4.7 13.5 - - + -
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Residues in contact with VAL 30 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3I PHE* 4.1 52.3 - - + -
28I PRO 4.3 1.1 + - - -
29I VAL* 1.3 79.4 - - - +
31I VAL* 1.3 66.5 + - - +
32I GLU* 4.1 23.0 + - + +
46I THR* 3.3 13.7 - - - +
47I LYS* 4.4 8.7 - - + -
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Residues in contact with VAL 31 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29I VAL* 3.8 19.5 - - + -
30I VAL* 1.3 78.4 - - - +
32I GLU* 1.3 71.6 + - - +
43I LEU* 4.0 19.0 - - + +
45I LYS 4.6 2.6 - - - +
46I THR* 2.9 30.0 + - - +
48I PHE* 4.1 14.1 - - + -
59I PHE* 4.0 6.5 - - + -
63I ILE* 3.8 33.9 - - + -
77I LEU* 4.2 19.5 - - + -
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Residues in contact with GLU 32 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2I PRO* 4.0 11.5 - - - +
3I PHE* 3.6 26.6 + - - +
4I LYS* 5.5 4.7 + - - +
30I VAL* 4.1 20.8 - - + +
31I VAL* 1.3 86.9 - - - +
33I ARG* 1.3 69.5 + - - +
34I TYR 3.7 2.1 + - - -
43I LEU* 5.9 3.1 - - - -
46I THR* 5.8 6.2 - - + +
77I LEU* 5.8 1.6 - - - +
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Residues in contact with ARG 33 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1I ARG* 5.9 3.0 - - - +
32I GLU* 1.3 78.3 - - - +
34I TYR* 1.3 74.7 + - - +
35I PRO* 3.1 30.7 + - - +
36I ARG 3.7 2.6 + - - -
37I GLU* 2.5 47.9 + - + +
38I THR* 5.0 0.2 - - - +
40I LEU* 4.1 13.1 + - + -
41I PRO 4.2 11.0 - - - +
42I PRO* 4.5 19.5 - - + +
43I LEU* 5.6 3.7 - - - +
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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
------------------------------------------------------------
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