Contacts of the strand formed by residues 26 - 32 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23G ALA 3.6 22.2 - - - -
24G GLY* 5.7 1.1 - - - -
26G PHE* 4.0 26.5 - + - -
28G PHE* 3.7 14.1 - + - -
26H PHE* 4.1 17.9 - + - -
21I ILE 3.9 0.5 - - - +
22I LYS* 3.5 6.2 - - - +
23I ALA 2.9 32.2 + - - +
25I ASN* 1.3 88.2 - - + +
27I LEU* 1.3 61.0 + - - +
28I PHE* 3.7 22.5 + + + -
67I TYR* 3.9 1.6 - - - -
73I ILE* 3.5 33.0 - - + -
122I ILE* 4.1 8.5 - - + -
123I ALA 3.1 8.1 - - - -
124I TYR* 3.7 22.2 - + - -
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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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5I ILE* 4.5 2.2 - - + -
20I ALA* 4.4 10.5 - - + -
21I ILE 3.5 16.2 - - - +
22I LYS* 4.0 17.0 - - + -
26I PHE* 1.3 74.4 - - - +
28I PHE* 1.3 61.3 + - - +
29I ILE* 3.7 28.8 + - + +
61I ILE 4.6 2.7 - - - +
62I LEU* 4.2 13.5 - - + -
65I ALA* 4.0 23.6 - - + -
67I TYR* 3.7 40.6 - - + -
122I ILE* 3.2 6.6 - - - +
123I ALA* 2.7 35.8 + - + +
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Residues in contact with PHE 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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28G PHE* 5.9 3.8 - + - -
26H PHE* 3.6 24.7 - + - -
28H PHE* 5.6 3.4 - + - -
73H ILE* 3.5 28.0 - - + -
74H LYS* 3.6 33.7 - - + -
102H ALA* 4.0 4.7 - - + +
122H ILE* 3.8 22.4 - - + -
20I ALA* 3.2 4.6 - - - -
21I ILE* 2.9 45.3 + - + +
23I ALA* 5.0 2.9 - - + -
26I PHE* 3.7 26.7 - + + -
27I LEU* 1.3 73.9 - - - +
29I ILE* 1.3 62.4 + - - +
121I ALA 4.0 2.0 - - - -
122I ILE* 3.6 32.1 - - + -
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Residues in contact with ILE 29 (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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74H LYS* 5.2 4.7 - - - +
102H ALA* 4.5 1.6 - - - -
104H VAL* 4.9 0.7 - - - +
19I GLN 3.7 11.4 - - - +
20I ALA* 4.2 5.4 - - + -
27I LEU* 4.1 20.4 - - + +
28I PHE* 1.3 76.2 - - - +
30I ALA* 1.3 77.8 + - - +
31I GLY 3.7 0.5 + - - -
32I GLN* 4.3 4.3 - - + +
58I ILE* 3.8 31.6 - - + +
61I ILE* 4.0 17.5 - - + -
62I LEU* 3.9 28.5 - - + +
72I VAL* 6.2 0.2 - - + -
119I ILE 5.7 0.4 - - - +
120I GLU* 3.9 6.4 - - - +
121I ALA* 2.9 43.1 + - + +
123I ALA* 5.7 2.0 - - + -
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Residues in contact with ALA 30 (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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74H LYS* 6.4 0.4 - - - -
102H ALA* 3.8 9.8 - - + +
103H ARG 3.3 31.2 - - - +
104H VAL* 4.7 1.3 - - - -
18I SER 3.5 20.2 - - - +
19I GLN* 3.1 12.2 + - - +
29I ILE* 1.3 80.1 - - - +
31I GLY* 1.3 67.2 + - - +
32I GLN* 2.9 22.0 + - - +
119I ILE 3.9 1.7 - - - +
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Residues in contact with GLY 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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103H ARG 3.1 14.1 + - - +
104H VAL* 3.4 15.7 - - - +
30I ALA* 1.3 71.7 - - - +
32I GLN* 1.3 66.0 + - - -
33I ILE* 4.3 2.3 + - - +
118I GLU* 3.8 24.2 - - - +
119I ILE 3.2 15.5 - - - -
120I GLU* 4.0 0.7 - - - -
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Residues in contact with GLN 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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10I ALA* 4.6 0.5 - - - +
11I PRO* 4.1 27.9 - - - +
19I GLN* 4.0 11.7 + - - +
29I ILE* 4.6 1.6 - - + -
30I ALA* 2.9 29.7 + - - +
31I GLY* 1.3 75.8 + - - -
33I ILE* 1.3 61.8 + - - +
54I VAL* 4.0 13.2 - - + +
57I ASN* 4.2 16.1 - - + +
58I ILE* 4.0 18.4 - - + -
61I ILE* 3.4 32.2 - - + +
117I ILE 4.0 0.2 - - - +
118I GLU* 3.2 10.6 - - - +
119I ILE 2.8 30.3 + - - +
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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