Contacts of the strand formed by residues 17 - 23 (chain D) in PDB entry 2IY1
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 17 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16D TYR* 1.3 78.8 - - - +
18D LYS* 1.3 60.3 + - - +
19D LEU* 3.8 14.7 + - + -
31D PHE 3.8 0.7 - - - +
32D LYS* 3.6 3.9 - - - -
33D VAL* 2.9 36.5 + - + +
35D MET* 3.5 29.2 - - + -
72D PRO* 4.5 4.0 - - + -
77D MET* 3.6 35.2 - - + +
78D GLU* 3.6 14.6 - - - +
79D GLU* 3.2 32.8 - - + +
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Residues in contact with LYS 18 (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 ILE* 1.3 71.5 - - - +
19D LEU* 1.3 60.8 + - - +
30D HIS* 5.9 5.2 - - + -
31D PHE 3.3 8.7 - - - +
32D LYS* 4.6 22.4 - - + +
78D GLU 4.3 0.3 - - - +
79D GLU* 2.9 33.3 + - - +
80D GLU* 2.8 34.9 + - - +
81D ASP 4.1 0.3 + - - -
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Residues in contact with LEU 19 (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 ILE* 3.8 18.8 + - + -
18D LYS* 1.3 74.0 - - - +
20D LYS* 1.3 64.4 + - - +
21D VAL* 4.0 2.4 + - + -
30D HIS* 3.4 6.9 - - - +
31D PHE* 2.8 36.9 + - + +
33D VAL* 3.8 27.1 - - + -
39D LEU* 4.7 1.3 - - + -
42D LEU* 4.2 10.3 - - + -
72D PRO* 4.9 0.4 - - + -
77D MET* 3.6 33.0 - - + -
78D GLU 4.4 0.9 - - - +
80D GLU* 5.4 0.7 - - - -
81D ASP* 3.5 28.0 - - + +
82D VAL 4.8 0.4 - - - +
83D ILE* 3.9 26.7 - - + -
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Residues in contact with LYS 20 (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 LEU* 1.3 74.3 - - - +
21D VAL* 1.3 56.2 + - - +
22D ILE* 3.7 18.2 + - + -
28D GLU* 4.0 17.0 - - + +
29D ILE 4.0 2.2 - - - -
30D HIS* 3.4 35.4 - - + +
80D GLU* 3.5 36.2 + - - +
81D ASP 2.8 13.2 + - - +
82D VAL* 3.3 10.8 - - + +
83D ILE 2.7 32.6 + - - +
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Residues in contact with VAL 21 (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 LEU* 5.1 2.5 - - + +
20D LYS* 1.3 72.6 - - - +
22D ILE* 1.3 59.1 + - - +
23D GLY 4.0 0.6 + - - -
27D SER 3.6 1.7 - - - +
28D GLU* 3.3 3.5 - - - -
29D ILE 2.9 37.9 + - - +
31D PHE* 3.6 29.2 - - + -
42D LEU* 4.0 18.4 - - + -
46D TYR* 3.3 35.4 - - + -
59D PHE* 4.4 2.9 - - + -
83D ILE* 3.2 26.7 - - + +
85D VAL* 3.5 16.4 - - + -
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Residues in contact with ILE 22 (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 LYS* 4.2 14.4 - - + -
21D VAL* 1.3 75.7 - - - +
23D GLY* 1.3 74.4 + - - +
26D SER* 4.3 13.0 - - - +
27D SER 3.4 6.7 - - - +
28D GLU* 3.8 27.8 - - + +
46D TYR* 4.6 0.9 - - - -
82D VAL* 3.6 39.0 - - + -
83D ILE 2.8 9.3 + - - -
84D GLU* 3.5 10.0 - - + +
85D VAL* 3.1 22.5 + - - -
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Residues in contact with GLY 23 (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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22D ILE* 1.3 86.8 - - - +
24D GLN* 1.3 57.9 + - - -
25D ASP* 3.1 17.9 - - - -
26D SER* 2.9 17.0 + - - -
27D SER 2.8 12.3 + - - -
46D TYR* 3.7 17.8 + - - -
85D VAL* 4.1 10.1 - - - -
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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