Contacts of the strand formed by residues 128 - 131 (chain B) in PDB entry 2I7D
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 ILE 128 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A LEU 3.9 6.2 - - - +
131A THR* 4.0 8.8 + - - -
132A ARG* 4.5 4.3 + - - +
11B MET* 5.9 1.1 - - - -
97B ILE* 3.4 15.9 - - + +
99B THR* 4.4 13.9 - - + -
112B LYS* 4.6 2.0 - - + +
113B TYR* 3.7 58.4 + - + +
116B VAL* 3.9 31.2 - - + -
124B PHE 3.9 7.6 - - - +
125B VAL* 3.2 27.3 + - - +
126B GLU 3.5 2.5 - - - +
127B ARG* 1.3 78.0 - - - +
129B ILE* 1.3 73.9 + - - +
130B LEU* 4.3 1.6 - - + +
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Residues in contact with ILE 129 (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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129A ILE* 4.2 19.5 - - + -
130A LEU 3.3 9.9 - - - +
131A THR* 3.7 15.5 - - - +
136A VAL* 3.9 23.1 - - + -
137A VAL* 5.7 1.8 - - + -
8B LEU* 4.9 1.6 - - + -
96B PHE* 3.7 37.0 - - + -
97B ILE 2.8 12.1 + - - +
98B CYS* 3.4 8.1 - - + -
99B THR* 3.0 27.5 + - - +
128B ILE* 1.3 80.0 - - - +
130B LEU* 1.3 61.2 + - - +
131B THR* 3.9 5.6 + - + -
137B VAL* 4.0 31.4 - - + -
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Residues in contact with LEU 130 (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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113A TYR* 3.2 30.0 + - + +
128A ILE 3.8 0.9 - - - +
129A ILE* 3.3 5.5 - - - +
130A LEU* 3.0 42.7 + - + +
99B THR* 3.1 36.1 - - + +
100B SER 4.2 0.7 - - - -
101B PRO* 3.8 17.5 - - + -
109B VAL* 3.6 32.3 - - + +
112B LYS* 4.6 9.2 - - + -
113B TYR* 4.5 19.1 - - + +
128B ILE* 4.2 4.7 - - + +
129B ILE* 1.3 70.6 - - - +
131B THR* 1.3 63.0 + - - +
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Residues in contact with THR 131 (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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96A PHE* 5.3 0.7 - - - -
128A ILE 4.0 7.1 + - - -
129A ILE* 3.8 24.3 - - - +
98B CYS* 3.9 27.8 - - - -
99B THR 3.1 7.1 + - - +
100B SER* 2.7 31.0 + - - -
101B PRO* 4.2 5.2 - - - -
129B ILE* 4.3 2.9 - - + -
130B LEU* 1.3 78.8 - - - +
132B ARG* 1.3 53.3 + - - +
133B ASP* 2.9 37.7 + - - +
134B LYS* 4.1 3.8 - - + +
137B VAL* 4.3 7.9 - - + -
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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