Contacts of the strand formed by residues 18 - 23 (chain D) in PDB entry 1YCY
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 LYS 18 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16D GLY 4.0 1.2 + - - -
17D HIS* 1.3 73.4 - - - +
19D VAL* 1.3 63.0 + - - +
30D THR* 4.0 30.6 - - - +
31D GLY* 3.9 13.7 - - - +
32D THR* 4.0 10.7 + - - +
69D LEU* 3.6 2.8 - - - +
70D LEU* 3.1 52.1 + - + +
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Residues in contact with VAL 19 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14D TRP* 4.5 17.0 - - + +
17D HIS 3.3 12.1 - - - +
18D LYS* 1.3 80.7 - - - +
20D ALA* 1.3 57.6 + - - +
21D VAL* 4.0 19.5 - - + +
30D THR* 2.6 23.2 + - - -
31D GLY 3.0 25.6 + - - +
33D LEU* 4.4 22.0 - - + -
41D ILE* 5.8 0.7 - - + -
43D LEU* 4.8 6.1 - - + -
67D ILE* 4.1 9.4 - - + -
68D MSE 3.2 15.5 - - - +
69D LEU* 4.3 12.1 - - + -
70D LEU* 4.3 2.5 - - - -
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Residues in contact with ALA 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 VAL* 1.3 72.4 - - - +
21D VAL* 1.3 66.6 + - - +
29D PHE 3.8 6.3 - - - +
30D THR* 3.8 11.9 - - - +
66D TRP* 4.2 4.7 - - + -
67D ILE* 3.5 2.9 - - - +
68D MSE 2.8 61.4 + - + +
70D LEU* 4.3 9.2 - - + +
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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 VAL* 4.0 18.2 - - + -
20D ALA* 1.3 82.1 - - - +
22D SER* 1.3 64.4 + - - +
23D VAL* 4.0 2.8 + - + +
29D PHE* 3.3 28.1 + - + +
41D ILE* 4.4 13.2 - - + -
43D LEU* 4.1 20.2 - - + -
57D MSE 6.0 0.7 - - + -
59D ILE* 4.7 10.8 - - + -
64D ILE* 3.8 35.0 - - + -
66D TRP* 3.6 10.6 - - - +
67D ILE* 4.1 11.0 - - + -
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Residues in contact with SER 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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21D VAL* 1.3 74.4 - - - +
23D VAL* 1.3 56.4 + - - +
24D GLY 3.9 6.2 + - - -
64D ILE* 3.3 6.3 - - - +
65D ASN* 2.6 50.3 + - - +
66D TRP* 3.0 46.3 + - - -
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Residues in contact with VAL 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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21D VAL* 4.0 3.6 + - + -
22D SER* 1.3 71.7 + - - +
24D GLY* 1.3 63.7 + - - +
57D MSE 5.9 4.5 - - + -
59D ILE* 4.4 21.8 - - + -
63D ASP* 3.1 18.4 - - + +
64D ILE* 5.0 1.3 - - + -
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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