Contacts of the strand formed by residues 38 - 44 (chain A) in PDB entry 1YLA
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 GLU 38 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A VAL* 3.0 47.8 + - + +
33A ASP* 3.1 20.1 + - + +
36A PHE 3.2 0.6 - - - -
37A THR* 1.3 83.6 + - - +
39A LEU* 1.3 68.5 + - - +
40A ARG* 4.5 8.5 + - - -
59A GLU* 4.1 15.6 - - + +
60A ILE 3.1 14.1 - - - +
61A LYS* 3.9 28.6 - - + -
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Residues in contact with LEU 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A ILE* 4.6 4.9 - - + -
13A PHE* 5.0 4.0 - - + -
29A VAL* 3.6 18.4 - - + -
30A ASP 3.1 10.1 - - - +
31A LEU* 3.1 35.4 - - + -
32A VAL* 3.9 4.2 - - - +
36A PHE* 3.8 13.5 - - + +
38A GLU* 1.3 86.8 - - - +
40A ARG* 1.3 62.7 + - - +
59A GLU* 4.1 1.6 - - - -
60A ILE* 2.8 41.2 + - + +
62A ILE* 3.2 41.5 - - + -
106A LEU* 4.3 12.8 - - + -
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Residues in contact with ARG 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A VAL* 3.1 5.3 - - - -
30A ASP* 2.7 52.0 + - + +
32A VAL* 3.5 42.2 - - + +
38A GLU* 4.5 10.1 + - - -
39A LEU* 1.3 74.7 - - - +
41A GLY* 1.3 68.2 + - - +
57A GLN* 3.9 25.7 - - + +
58A LEU 3.3 19.3 - - - +
59A GLU* 5.0 3.0 - - - +
76A ILE* 4.6 14.5 - - - +
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Residues in contact with GLY 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A LYS 3.3 10.8 - - - -
29A VAL* 4.1 5.8 - - - -
40A ARG* 1.3 80.2 - - - +
42A GLU* 1.3 65.0 + - - +
57A GLN* 3.3 6.6 - - - +
58A LEU* 2.8 40.8 + - - +
60A ILE* 4.0 6.3 - - - +
110A LEU* 4.5 8.1 - - - -
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Residues in contact with GLU 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A GLN 4.6 0.2 - - - -
27A ILE* 3.4 4.5 - - - -
28A LYS* 3.0 61.6 + - + +
41A GLY* 1.3 76.9 - - - +
43A ILE* 1.3 67.2 + - - +
55A ARG* 3.6 32.6 + - - +
56A TYR 3.0 24.5 - - - +
57A GLN* 3.7 20.7 - - + +
58A LEU* 4.4 3.2 - - - +
110A LEU* 4.5 0.8 - - - +
154B GLY* 5.7 2.8 - - - -
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Residues in contact with ILE 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A GLN 3.5 6.3 - - - +
27A ILE* 4.3 7.4 - - + -
42A GLU* 1.3 79.9 - - - +
44A ALA* 1.3 63.5 + - - +
55A ARG* 3.5 2.0 - - - -
56A TYR* 2.7 49.0 + - + +
58A LEU* 4.0 7.8 - - + +
75A PHE* 4.0 18.8 - - + -
110A LEU* 3.5 42.6 - - + +
113A LEU* 3.9 36.1 - - + +
114A GLN* 4.0 8.3 - - + +
117A LEU* 4.3 7.6 - - + -
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Residues in contact with ALA 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ASN 3.7 23.3 - - - +
26A GLN* 3.1 20.8 + - - +
43A ILE* 1.3 76.1 - - - +
45A GLY* 1.3 69.6 + - - +
46A PRO* 3.3 4.3 - - - +
54A GLY 3.5 7.4 - - - +
55A ARG* 4.5 6.7 - - + +
56A TYR* 4.8 0.9 - - - -
114A GLN* 2.9 23.9 + - - +
117A LEU* 4.9 0.5 - - - +
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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