Contacts of the strand formed by residues 38 - 42 (chain D) in PDB entry 1Y8R
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 ARG 38 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36D ALA 5.5 0.2 - - - +
37D SER* 1.3 75.3 - - - +
39D VAL* 1.3 63.4 + - - +
61D LYS* 3.5 44.3 - - + +
62D GLY* 3.2 17.9 - - - +
64D THR* 5.1 4.1 + - - +
107D ASP* 3.4 29.1 + - - +
109D LYS* 3.7 22.1 - - - +
125D GLN* 3.9 28.1 + - - +
126D PHE* 3.7 22.9 - - + -
127D ASP* 2.7 47.3 + - - +
128D ALA 3.6 0.9 + - - -
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Residues in contact with VAL 39 (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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38D ARG* 1.3 78.4 - - - +
40D LEU* 1.3 74.1 + - - +
41D LEU* 4.1 2.5 - - + +
55D LEU* 3.8 24.0 - - + -
60D VAL* 4.2 15.7 - - + -
62D GLY 2.9 7.6 + - - +
63D LEU* 3.3 17.5 - - + +
64D THR 3.0 24.4 + - - -
126D PHE* 3.9 7.0 - - - -
128D ALA* 3.7 20.2 - - + +
130D CYS* 5.2 7.0 - - + +
314D ILE* 4.4 4.3 - - + -
318D LEU* 3.9 27.8 - - + -
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Residues in contact with LEU 40 (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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39D VAL* 1.3 77.5 - - - +
41D LEU* 1.3 62.5 + - - +
42D VAL* 3.5 23.3 - - + -
64D THR* 3.2 24.7 - - + +
66D LEU* 4.5 9.6 - - + -
115D ILE* 5.0 4.5 - - + -
122D PHE* 4.4 13.7 - - + -
123D PHE* 5.2 3.1 - - + -
126D PHE* 3.5 47.3 - - + -
128D ALA 3.1 9.5 + - - +
129D VAL* 3.3 27.3 - - + -
130D CYS 2.8 27.4 + - - -
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Residues in contact with LEU 41 (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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39D VAL* 4.1 2.4 + - + -
40D LEU* 1.3 73.6 - - - +
42D VAL* 1.3 70.5 + - - +
43D GLY 4.7 2.2 - - - +
44D LEU* 4.3 13.4 - - + +
48D GLY* 3.3 28.5 - - - +
51D ILE* 4.3 16.8 - - + -
52D ALA* 3.8 24.7 - - + +
55D LEU* 5.9 0.2 - - + -
63D LEU* 4.5 17.9 - - + -
64D THR 3.2 9.7 + - - +
65D MET* 3.4 5.5 - - + -
66D LEU 2.8 24.4 + - - -
130D CYS* 3.6 27.8 - - + +
132D THR* 4.2 10.8 - - - +
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Residues in contact with VAL 42 (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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40D LEU* 3.5 27.1 - - + -
41D LEU* 1.3 75.7 - - - +
43D GLY* 1.3 66.9 + - - +
66D LEU* 3.1 28.7 - - + +
67D ASP* 5.2 1.3 - - - -
115D ILE* 3.8 28.7 - - + -
130D CYS 3.0 11.9 + - - +
131D LEU* 4.3 12.1 - - + -
132D THR* 3.1 30.4 + - - +
134D CYS* 4.2 20.2 - - - -
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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