Contacts of the strand formed by residues 107 - 112 (chain Q) in PDB entry 3HOU
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 THR 107 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26Q ARG* 4.5 4.3 - - - +
28Q TYR* 3.5 14.8 + - + +
77Q SER 3.4 3.6 + - - +
78Q LEU* 3.4 41.1 - - + -
79Q TRP* 3.1 20.8 + - - +
100Q ILE* 4.4 3.9 - - - +
105Q PHE* 4.1 6.8 - - - +
106Q GLN* 1.3 87.5 + - - +
108Q GLY* 1.3 62.0 + - - +
109Q ILE* 4.1 11.9 - - + -
131Q THR* 3.5 5.3 + - - +
133Q GLU* 4.3 14.8 - - - +
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Residues in contact with GLY 108 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79Q TRP 3.7 4.3 - - - -
96Q PHE* 3.8 3.4 - - - -
100Q ILE* 3.9 23.3 - - - +
107Q THR* 1.3 77.3 - - - +
109Q ILE* 1.3 59.3 + - - -
131Q THR 3.0 13.6 + - - -
132Q ILE* 2.9 12.7 - - - +
133Q GLU 2.7 29.6 + - - +
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Residues in contact with ILE 109 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19Q VAL* 5.3 3.1 - - + -
22Q MET* 3.3 33.4 - - + -
23Q VAL* 4.6 2.9 - - + -
26Q ARG* 4.3 4.3 - - - +
78Q LEU* 3.5 29.6 - - + -
79Q TRP 2.9 13.1 + - - +
80Q VAL* 4.2 17.9 - - + -
81Q GLU 3.0 23.8 + - - -
96Q PHE* 3.7 4.9 - - - -
107Q THR* 4.1 6.5 - - + -
108Q GLY* 1.3 74.0 - - - -
110Q PHE* 1.3 65.3 + - - +
111Q VAL* 4.2 19.1 - - + -
133Q GLU* 3.4 18.8 - - + +
135Q PHE* 4.6 12.8 - - + -
140Q LEU* 6.3 0.4 - - + -
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Residues in contact with PHE 110 (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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81Q GLU* 3.5 25.4 - - + -
82Q PHE 4.4 2.9 - - - -
83Q CYS* 4.2 15.9 - - + -
88Q VAL* 3.4 43.7 - - + -
92Q THR* 4.4 7.9 - - + -
93Q MET* 4.1 15.7 - - + -
96Q PHE* 3.3 46.4 - + + -
109Q ILE* 1.3 75.8 - - - +
111Q VAL* 1.3 62.0 + - - +
112Q TYR* 3.1 16.5 + - + -
116Q ILE* 4.3 9.9 - - + -
132Q ILE* 5.0 1.8 - - + -
133Q GLU 2.8 14.2 + - - +
134Q THR* 3.7 6.4 + - - -
135Q PHE 3.2 19.5 + - - -
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Residues in contact with VAL 111 (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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15Q ALA* 6.2 2.0 - - + -
19Q VAL* 4.5 6.1 - - + -
80Q VAL* 4.5 2.2 - - + -
81Q GLU 2.9 12.9 + - - +
82Q PHE* 4.0 44.9 - - + -
83Q CYS 4.3 3.5 + - - +
109Q ILE* 4.2 16.2 - - + -
110Q PHE* 1.3 72.6 - - - +
112Q TYR* 1.3 61.6 + - - +
135Q PHE* 3.4 11.9 - - + +
136Q ASN 4.3 2.5 - - - +
137Q GLU* 3.4 41.1 - - + +
140Q LEU* 4.5 20.9 - - + -
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Residues in contact with TYR 112 (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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83Q CYS* 5.5 1.1 - - - -
88Q VAL* 3.9 9.2 - - + -
110Q PHE* 3.1 11.5 + - - -
111Q VAL* 1.3 72.2 - - - +
113Q GLN* 1.3 63.5 + - - +
114Q ASN 4.5 0.2 - - - -
115Q ASN* 3.4 30.3 - - - +
116Q ILE* 3.6 36.3 - - + -
121Q MET* 5.6 3.8 - - + -
134Q THR* 2.9 29.6 - - + -
135Q PHE* 3.1 14.7 + - - -
136Q ASN* 3.0 50.9 + - + +
137Q GLU* 2.9 25.6 + - - +
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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