Contacts of the strand formed by residues 36 - 42 (chain G) in PDB entry 1YI5
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 36 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B LYS* 6.1 0.8 - - - +
183B VAL* 3.4 32.4 - - + +
184B THR 3.1 21.3 - - - +
185B TYR* 3.7 29.1 + - + -
24G THR* 3.3 5.9 - - - -
25G TRP* 2.8 83.5 + - + +
27G ASP* 5.2 1.7 + - - +
34G GLY 3.6 2.4 + - - -
35G LYS* 1.3 73.1 - - - +
37G VAL* 1.3 59.0 + - - +
38G ASP* 5.5 7.9 + - - +
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Residues in contact with VAL 37 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184B THR* 3.3 31.2 + - + +
185B TYR 4.4 0.9 - - - -
186B SER* 3.2 39.7 - - - +
6G THR* 4.1 1.1 + - - +
22G THR* 5.2 1.6 - - + -
23G LYS 3.4 13.5 - - - +
24G THR* 4.0 13.9 - - + -
36G ARG* 1.3 74.8 - - - +
38G ASP* 1.3 58.0 + - - +
39G LEU* 3.9 29.7 + - + -
65G PHE* 4.0 21.8 - - + -
66G PRO* 5.4 9.6 - - + -
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Residues in contact with ASP 38 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6G THR* 3.2 23.3 - - - +
21G TYR* 3.4 35.3 + - - -
23G LYS* 3.6 42.5 + - + +
25G TRP* 4.8 13.6 - - + -
36G ARG* 5.5 6.0 + - - +
37G VAL* 1.3 71.4 - - - +
39G LEU* 1.3 65.3 + - - +
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Residues in contact with LEU 39 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4G PHE* 3.3 20.2 - - + +
5G ILE* 4.8 2.5 - - - +
6G THR* 3.4 36.3 + - - +
8G ASP 5.8 1.8 - - - +
21G TYR* 3.6 7.2 + - - +
22G THR* 3.4 31.0 - - + +
37G VAL* 3.9 14.6 - - + -
38G ASP* 1.3 84.2 - - - +
40G GLY* 1.3 59.3 + - - +
63G ASN* 3.4 33.9 - - - +
64G PRO 4.5 6.3 - - - +
65G PHE* 4.1 25.4 - - + +
66G PRO* 6.1 0.7 - - + -
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Residues in contact with GLY 40 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3G CYS* 4.1 5.1 - - - +
4G PHE 3.3 12.3 + - - -
5G ILE* 4.1 11.9 - - - -
20G CYS* 3.6 5.2 - - - +
21G TYR* 2.9 40.5 + - - +
39G LEU* 1.3 79.2 - - - +
41G CYS* 1.3 60.2 + - - -
63G ASN* 4.3 1.0 - - - +
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Residues in contact with CYS 41 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3G CYS* 3.6 15.3 - - + -
5G ILE* 4.4 12.2 - - + +
14G CYS* 2.0 51.1 - - + -
17G GLY* 4.8 4.5 - - - +
19G VAL 3.2 14.4 - - - +
21G TYR* 3.7 7.7 - - - -
40G GLY* 1.3 74.5 - - - -
42G ALA* 1.3 67.6 + - - +
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Residues in contact with ALA 42 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17G GLY* 2.8 27.7 - - - -
18G HIS 2.9 2.4 + - - -
19G VAL* 3.1 15.8 + - + +
21G TYR* 4.0 16.4 - - + -
41G CYS* 1.3 82.6 - - - +
43G ALA* 1.3 63.6 + - - +
44G THR 3.5 16.2 - - - +
46G PRO* 5.8 1.1 - - + -
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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