Contacts of the strand formed by residues 26 - 32 (chain D) in PDB entry 2DYY
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 PHE 26 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21D ILE 4.0 0.3 - - - +
22D LYS* 3.4 6.4 - - - +
23D ALA 2.9 36.0 + - - +
25D ASN* 1.3 88.4 - - + +
27D LEU* 1.3 60.0 + - - +
28D PHE* 3.8 21.1 - + + -
67D TYR* 3.6 1.8 - - - -
73D ILE* 4.0 21.3 - - + -
122D ILE* 4.4 8.3 - - + -
123D ALA 3.4 11.0 - - - -
124D TYR* 3.4 33.2 - + + -
23E ALA* 3.8 17.7 - - + -
24E GLY* 5.7 1.1 - - - -
26E PHE* 3.9 22.4 - + - -
28E PHE* 4.0 12.8 - + - -
26F PHE* 4.0 22.0 - + + -
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Residues in contact with LEU 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D ILE* 4.9 2.0 - - + -
20D ALA* 4.0 14.8 - - + -
21D ILE 3.7 17.9 - - - +
22D LYS* 4.1 9.4 - - + +
26D PHE* 1.3 74.8 - - - +
28D PHE* 1.3 63.7 + - - +
29D ILE* 4.0 17.7 - - + -
61D ILE 4.8 0.7 - - - +
62D LEU* 4.0 24.2 - - + -
65D ALA* 3.4 35.0 - - + -
67D TYR* 3.6 26.2 + - + -
121D ALA 3.9 0.5 - - - +
122D ILE* 3.3 9.2 - - - +
123D ALA* 2.9 36.0 + - + +
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Residues in contact with PHE 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D ALA* 3.1 4.4 - - - -
21D ILE* 3.0 43.2 + - + +
23D ALA* 4.5 2.2 - - + -
26D PHE* 3.8 22.9 - + + -
27D LEU* 1.3 75.4 - - - +
29D ILE* 1.3 62.7 + - - +
121D ALA 4.1 2.0 - - - -
122D ILE* 3.8 31.9 - - + -
28E PHE* 6.0 2.2 - + - -
26F PHE* 3.8 20.4 - + - -
28F PHE* 5.8 3.1 - + - -
73F ILE* 3.3 35.2 - - + +
74F LYS* 3.6 35.0 - - + -
102F ALA* 3.6 8.9 - - + +
122F ILE* 4.1 21.5 - - + -
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Residues in contact with ILE 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D GLN 3.6 11.2 - - - +
20D ALA* 3.9 3.4 - - + -
27D LEU* 4.0 16.2 - - + +
28D PHE* 1.3 74.3 - - - +
30D ALA* 1.3 74.9 + - - +
31D GLY 3.8 0.5 + - - -
32D GLN* 4.2 6.3 - - + -
58D ILE* 4.2 20.9 - - + +
61D ILE* 4.0 28.5 - - + -
62D LEU* 3.8 35.7 - - + -
119D ILE 5.7 0.2 - - - +
120D GLU* 3.9 7.6 - - - +
121D ALA* 3.0 40.7 + - + +
122D ILE* 5.6 0.2 - - - -
123D ALA* 5.8 1.3 - - + +
74F LYS* 5.4 4.3 + - - -
102F ALA* 4.3 1.5 - - - +
104F VAL* 5.0 0.7 - - - +
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Residues in contact with ALA 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D TYR* 3.9 11.7 - - + -
18D SER 3.1 26.9 - - - +
19D GLN* 2.8 13.5 + - - +
28D PHE 3.8 2.6 + - - -
29D ILE* 1.3 78.1 - - - +
31D GLY* 1.3 67.0 + - - +
32D GLN* 3.2 18.7 + - - +
119D ILE 4.0 2.1 - - - +
102F ALA* 3.8 8.2 - - - +
103F ARG 3.4 22.4 - - - +
104F VAL* 4.8 1.3 - - - -
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Residues in contact with GLY 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D TYR* 5.0 8.8 + - - -
30D ALA* 1.3 74.2 - - - +
32D GLN* 1.3 63.8 + - - +
33D ILE* 4.1 3.6 + - - +
118D GLU* 3.6 26.4 - - - +
119D ILE 3.7 7.4 - - - -
120D GLU* 4.1 4.9 - - - -
103F ARG 2.8 18.6 + - - +
104F VAL* 3.6 12.3 - - - +
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Residues in contact with GLN 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D PRO* 3.4 37.7 + - - +
17D TYR* 5.7 1.6 - - - -
19D GLN* 4.2 10.4 - - - +
29D ILE* 4.2 0.9 - - + -
30D ALA* 3.4 22.0 - - - +
31D GLY* 1.3 76.5 - - - +
33D ILE* 1.3 62.9 + - - +
54D VAL* 3.5 16.3 - - + +
57D ASN* 3.6 11.1 - - + +
58D ILE* 3.9 26.7 - - + -
61D ILE* 3.4 25.9 - - + +
118D GLU* 3.4 5.6 - - - +
119D ILE 2.9 32.5 + - - +
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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