Contacts of the strand formed by residues 116 - 119 (chain A) in PDB entry 1T0H
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 GLY 116 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A LEU* 3.8 11.2 - - - -
83A MSE 3.3 17.3 - - - -
85A ILE* 3.6 9.2 - - - +
105A ILE* 3.3 7.4 - - - +
106A GLY 2.8 32.5 + - - +
114A GLU 3.6 0.6 + - - -
115A ILE* 1.3 75.7 - - - +
117A PHE* 1.3 64.4 + - - -
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Residues in contact with PHE 117 (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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48A ALA* 3.8 22.2 - - + -
52A LEU* 3.8 20.6 - - + -
78A VAL* 4.0 10.8 - - + -
79A PRO* 3.8 22.9 - - + -
80A VAL* 3.8 32.1 - - + -
83A MSE 2.8 23.2 + - + -
84A ALA* 3.4 3.6 - - - -
85A ILE* 2.8 27.7 + - - +
99A PHE* 3.9 20.2 - + + -
103A TRP* 3.7 26.8 - - + -
104A TRP 3.2 10.8 - - - -
105A ILE* 3.8 20.2 - - + -
116A GLY* 1.3 72.3 - - - -
118A ILE* 1.3 60.0 + - - +
119A PRO* 4.2 0.5 - - - +
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Residues in contact with ILE 118 (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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85A ILE* 4.0 22.0 - - + -
87A PHE* 4.5 0.9 - - + -
93A LEU* 3.9 29.8 - - + -
94A HIS 4.2 5.2 - - - +
95A VAL* 4.3 9.9 - - + -
103A TRP* 3.4 4.3 - - - -
104A TRP* 2.7 50.7 + - + +
105A ILE 4.4 1.1 - - - -
106A GLY* 3.6 36.1 - - - +
107A ARG* 3.9 4.3 - - - +
117A PHE* 1.3 74.6 - - - +
119A PRO* 1.3 68.5 - - + +
220B TYR* 3.3 26.2 - - + +
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Residues in contact with PRO 119 (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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70A TYR* 3.5 38.1 - - + -
85A ILE 4.2 3.8 - - - +
87A PHE* 4.2 3.1 - - + -
102A ASP 3.6 7.4 - - - +
103A TRP* 3.5 12.0 - - + -
104A TRP* 4.8 0.2 - - - -
117A PHE 4.2 0.9 - - - +
118A ILE* 1.3 89.6 - - + +
120A SER* 1.3 63.0 + - - +
123A LYS* 3.9 19.3 - - + -
124A LEU* 3.7 25.6 - - + -
127A MSE 4.2 4.5 - - + -
220B TYR* 2.6 34.7 + - - +
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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