Contacts of the strand formed by residues 24 - 28 (chain I) in PDB entry 1AVG
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 THR 24 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23I GLY* 1.3 76.4 + - - -
25I TRP* 1.3 65.4 + - - +
26I TYR* 3.8 22.4 - - + -
52I GLN* 3.0 34.5 + - + +
54I VAL* 4.4 2.5 - - + -
129I ARG* 3.2 32.4 + - - +
138I ALA* 3.6 26.8 - - + +
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Residues in contact with TRP 25 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20I PHE* 3.0 59.8 + + - -
24I THR* 1.3 74.5 - - - +
26I TYR* 1.3 63.5 + - - +
51I THR* 3.7 20.6 - - + -
52I GLN 2.9 6.5 + - - +
53I ILE* 3.3 16.5 - - + +
54I VAL* 2.9 24.1 + - - -
102I SER 3.8 13.9 - - - -
103I TYR* 3.6 15.9 - - - -
105I ASN 3.9 4.9 - - - -
106I PHE* 4.1 4.9 - - - -
107I ALA* 4.4 4.7 - - + -
127I PHE* 3.6 31.2 - - + -
128I GLU 3.3 24.5 - - - -
129I ARG* 3.2 55.4 - - + +
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Residues in contact with TYR 26 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77H ARG* 4.9 3.1 - - - +
24I THR* 3.8 15.2 - - + +
25I TRP* 1.3 78.1 - - - +
27I LEU* 1.3 60.3 + - - +
28I ALA 4.2 1.1 + - - -
54I VAL* 3.5 29.6 - - + +
56I ILE* 4.8 0.7 - - + -
126I VAL 4.2 0.7 - - - +
127I PHE* 3.7 0.6 - - - -
128I GLU* 2.8 43.4 + - + +
129I ARG 4.5 7.0 - - - -
130I THR 4.5 6.3 - - - +
131I LYS* 3.8 36.1 + - + +
135I ASP* 4.1 28.3 - - + +
136I PRO 3.2 21.3 - - - -
137I ASP* 3.6 9.0 + - - -
138I ALA* 2.9 31.1 + - + +
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Residues in contact with LEU 27 (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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26I TYR* 1.3 76.4 - - - +
28I ALA* 1.3 63.3 + - - +
29I HIS* 4.6 3.1 - - - +
53I ILE* 4.3 7.2 - - + -
54I VAL 2.8 13.2 + - - +
55I GLU* 3.3 27.1 - - + +
56I ILE* 2.7 35.8 + - - +
111I ARG* 5.0 2.0 - - - +
125I LEU* 3.7 39.7 - - + -
126I VAL 3.7 21.3 - - - +
127I PHE* 3.6 37.7 - - + +
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Residues in contact with ALA 28 (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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77H ARG* 3.1 48.7 + - + +
26I TYR 4.2 1.0 + - - -
27I LEU* 1.3 85.0 - - - +
29I HIS* 1.3 63.0 + - - +
30I GLY 3.3 13.6 + - - +
33I VAL 5.0 0.7 - - - +
56I ILE* 3.5 15.9 - - + -
125I LEU* 5.8 0.9 - - - +
126I VAL 4.8 4.0 + - - +
128I GLU* 5.4 1.6 + - - -
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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