Contacts of the strand formed by residues 38 - 45 (chain B) in PDB entry 1YRP
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B LYS* 3.2 39.2 + - - +
30B CYS 3.5 10.7 - - - +
31B ARG* 4.4 16.9 + - + +
36B GLY 4.3 6.1 - - - +
37B LYS* 1.3 84.0 - - - +
39B TYR* 1.3 64.9 + - - +
95B LEU* 3.7 24.3 + - + +
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Residues in contact with TYR 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B TYR* 4.0 12.1 - + - -
29B LYS* 3.9 2.4 - - - -
30B CYS* 2.9 45.1 + - - +
32B GLN* 3.5 31.2 + - - -
37B LYS* 3.5 42.1 + - + +
38B GLU* 1.3 78.6 - - - +
40B ALA* 1.3 59.4 + - - +
80B HIS* 3.6 38.7 + + + -
92B ILE* 3.9 18.8 - - + -
93B LEU 3.4 20.4 - - - +
94B GLU* 4.7 5.4 - - - -
95B LEU* 3.9 13.2 - - - +
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Residues in contact with ALA 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B LEU* 4.7 3.1 - - + -
27B VAL* 4.7 14.4 - - + -
28B ARG 3.8 5.4 - - - +
29B LYS* 4.9 0.2 - - - +
30B CYS* 4.6 1.1 - - - -
39B TYR* 1.3 73.4 - - - +
41B ALA* 1.3 58.9 + - - +
42B LYS 3.9 0.2 + - - -
91B LEU 3.6 0.7 - - - +
93B LEU* 2.7 48.4 + - + +
94B GLU 3.7 19.7 - - - +
95B LEU* 4.0 17.6 - - + +
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Residues in contact with ALA 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B MET* 3.2 34.5 - - + -
26B ILE 3.7 1.4 - - - +
27B VAL* 3.4 4.1 - - - -
28B ARG 2.9 41.8 + - - +
30B CYS* 4.0 3.1 - - - -
39B TYR 4.1 1.0 - - - -
40B ALA* 1.3 71.4 - - - +
42B LYS* 1.3 61.0 + - - +
43B PHE* 3.8 4.4 + - + -
90B VAL* 4.2 6.7 - - + -
91B LEU 3.4 4.7 - - - -
92B ILE* 3.8 17.9 - - + -
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Residues in contact with LYS 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B ALA* 4.1 25.6 - - + -
26B ILE 3.7 2.9 - - - -
27B VAL* 4.5 16.2 - - + +
40B ALA 3.9 0.8 + - - -
41B ALA* 1.3 70.1 - - - +
43B PHE* 1.3 61.4 + - - +
44B ILE* 3.4 24.4 - - + +
64B GLU* 2.5 34.5 + - - +
90B VAL* 3.4 2.9 - - - -
91B LEU* 2.8 47.0 + - + +
93B LEU* 3.7 26.4 - - + +
161B ASP* 3.3 31.5 + - - +
163B GLY* 4.3 1.4 - - - +
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Residues in contact with PHE 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B VAL* 4.4 10.8 - - + -
10B GLU* 4.7 5.8 - - - -
15B MET* 3.6 37.2 - - + -
24B PHE 3.6 2.6 - - - +
25B ALA* 3.4 7.1 - - - -
26B ILE* 2.8 53.8 + - + +
28B ARG* 4.3 29.6 - - + -
41B ALA* 4.1 7.6 - - + -
42B LYS* 1.3 69.6 - - - +
44B ILE* 1.3 61.0 + - - +
45B LYS 4.0 0.4 - - - -
85B ASN* 6.2 1.1 - - - -
88B ASP* 4.3 20.6 - - + +
89B VAL 3.7 3.1 - - - -
90B VAL* 3.9 29.4 - - + +
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Residues in contact with ILE 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B PHE 4.1 3.6 - - - +
25B ALA* 4.9 4.5 - - + -
42B LYS* 3.4 37.7 - - + +
43B PHE* 1.3 72.8 - - - +
45B LYS* 1.3 69.6 + - - +
46B LYS* 3.5 1.9 + - - +
56B VAL* 3.8 17.5 - - + -
61B ILE* 3.5 37.5 - - + -
64B GLU* 4.8 8.1 - - - +
88B ASP* 3.4 3.1 + - - -
89B VAL* 2.8 45.6 + - + +
91B LEU* 3.6 32.1 - - + -
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Residues in contact with LYS 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B PHE* 3.5 20.1 + - + +
26B ILE* 6.4 2.9 - - + -
43B PHE 3.9 0.4 + - - -
44B ILE* 1.3 77.5 - - - +
46B LYS* 1.3 66.3 + - - +
48B ARG* 5.5 8.3 - - + +
54B ARG* 4.6 6.1 - - + +
55B GLY* 4.0 14.1 - - - -
56B VAL* 2.8 26.0 + - - +
87B THR* 3.7 30.6 + - - +
88B ASP* 3.3 24.9 + - - +
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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