Contacts of the strand formed by residues 81 - 88 (chain Q) in PDB entry 5GAH
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 VAL 81 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14Q LYS* 2.7 38.8 + - - +
28Q VAL* 3.7 29.8 - - + -
29Q LYS 4.0 2.2 - - - -
30Q VAL* 4.4 4.9 - - + +
59Q PHE* 5.7 0.9 - - + -
74Q PHE* 4.4 23.6 - - + -
75Q GLN 4.2 17.5 - - - +
76Q THR* 4.6 3.4 - - - +
78Q SER* 3.4 2.3 + - - +
79Q PRO 3.2 6.5 - - - +
80Q VAL* 1.3 79.3 - - + +
82Q ASP* 1.3 63.7 + - - +
83Q SER* 3.9 9.6 - - - +
84Q ILE* 3.9 21.3 - - + -
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Residues in contact with ASP 82 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14Q LYS* 4.9 3.5 + - - +
29Q LYS 2.8 15.0 + - - +
31Q TRP* 3.0 41.4 + - + +
40Q LEU* 4.0 23.8 - - + +
79Q PRO 4.8 0.2 - - - -
80Q VAL 3.4 4.2 + - - -
81Q VAL* 1.3 76.2 - - - +
83Q SER* 1.3 71.2 + - - +
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Residues in contact with SER 83 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27Q GLU 3.9 0.7 - - - +
28Q VAL* 3.4 4.7 - - - +
29Q LYS* 2.9 54.2 + - - +
81Q VAL* 3.6 2.3 - - - -
82Q ASP* 1.3 89.8 + - - +
84Q ILE* 1.3 66.1 + - - +
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Residues in contact with ILE 84 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17Q VAL* 4.2 22.7 - - + -
18Q PRO* 3.4 35.2 - - + +
20Q PHE* 4.4 15.5 - - + -
26Q VAL* 4.5 9.9 - - + -
27Q GLU 3.8 2.2 - - - -
28Q VAL* 4.2 16.2 - - + +
59Q PHE* 3.5 31.9 - - + -
76Q THR* 4.6 7.0 - - + +
81Q VAL* 3.9 18.2 - - + -
83Q SER* 1.3 80.2 - - - +
85Q SER* 1.3 71.7 + - - +
86Q VAL* 5.7 0.4 - - + -
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Residues in contact with SER 85 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18Q PRO* 5.0 2.7 - - - -
26Q VAL* 3.4 6.8 - - - +
27Q GLU* 2.9 44.0 + - - +
84Q ILE* 1.3 76.6 - - - +
86Q VAL* 1.3 64.8 + - - +
87Q LYS* 4.0 23.4 + - - +
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Residues in contact with VAL 86 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18Q PRO* 5.4 7.9 - - + -
19Q SER 4.3 8.1 - - - +
20Q PHE* 3.8 28.9 - - + -
24Q ASP* 4.2 12.1 - - + -
25Q THR 3.3 9.2 - - - +
26Q VAL* 3.9 4.3 - - + -
84Q ILE* 5.7 0.7 - - + -
85Q SER* 1.3 78.0 - - - +
87Q LYS* 1.3 65.9 + - - +
88Q ARG* 3.3 30.5 - - - +
89Q ARG* 4.2 14.4 - - + -
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Residues in contact with LYS 87 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25Q THR* 2.9 21.5 + - + +
26Q VAL 4.3 1.6 - - - -
27Q GLU* 3.2 49.6 + - - +
44Q GLU* 4.0 22.2 - - - +
85Q SER* 4.0 11.1 + - - +
86Q VAL* 1.3 78.9 - - - +
88Q ARG* 1.3 62.3 + - + +
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Residues in contact with ARG 88 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23Q GLY 5.2 1.2 + - - +
24Q ASP* 3.8 0.2 - - - -
25Q THR* 3.1 47.1 + - - +
86Q VAL* 3.3 11.2 - - - +
87Q LYS* 1.3 80.9 - - + +
89Q ARG* 1.3 64.5 + - - +
90Q GLY* 4.8 3.2 - - - +
110Q ILE* 3.1 40.0 + - - +
112Q GLU* 3.2 49.4 + - - +
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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