Contacts of the strand formed by residues 140 - 144 (chain D) in PDB entry 1I2M
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 140 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D ALA* 4.6 2.5 - - + -
133D ALA 3.4 5.6 - - - +
134D LEU* 3.8 8.7 - - + -
139D ARG* 1.3 77.7 - - - +
141D PHE* 1.3 68.6 + - - +
167D GLN* 3.4 6.1 - - - +
168D VAL* 2.7 59.8 + - + +
170D LEU* 5.2 1.6 - - + -
174D VAL* 3.7 34.5 - - + -
177D VAL* 3.9 20.4 - - + -
184D LEU* 4.6 9.2 - - + -
186D MET* 4.0 13.9 - - - -
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Residues in contact with PHE 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D LEU* 3.7 37.0 - - + -
119D GLU* 4.0 12.3 - - + -
132D ALA* 3.3 3.5 - - - -
133D ALA 2.7 35.8 + - - +
135D THR* 3.7 31.2 - - + -
139D ARG* 3.9 20.4 - - + -
140D VAL* 1.3 79.2 - - - +
142D LEU* 1.3 62.1 + - - +
143D TRP* 4.2 8.6 - - + -
165D PRO* 4.2 9.2 - - + -
166D VAL* 3.4 7.0 - - - -
167D GLN* 3.7 48.5 - - + -
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Residues in contact with LEU 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D HIS* 3.7 26.9 - - + -
131D THR 3.2 22.0 - - - +
132D ALA* 3.8 6.1 - - + -
141D PHE* 1.3 75.7 - - - +
143D TRP* 1.3 65.6 + - - +
146D PHE* 4.1 13.5 - - + -
155D LEU* 3.8 24.9 - - + -
156D LEU* 3.8 26.7 - - + -
166D VAL* 2.8 42.1 + - + +
168D VAL* 4.1 13.9 - - + -
184D LEU* 3.8 21.1 - - + -
196D LEU* 4.4 2.0 - - + -
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Residues in contact with TRP 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D VAL* 5.1 1.3 - - + +
88D VAL* 4.3 15.9 - - + -
90D SER* 5.8 0.4 - - - -
97D GLY 3.4 6.7 - - - +
98D ALA 2.8 29.2 + - - -
99D LEU 3.5 2.0 - - - -
100D GLY* 3.2 29.0 - - - +
115D VAL* 4.2 23.6 - - + -
117D LEU* 4.5 3.8 - - + -
124D VAL* 5.8 0.2 - - + -
130D HIS* 3.3 7.1 - - - +
131D THR* 3.1 56.2 + - + -
133D ALA* 3.9 31.0 - - + -
141D PHE* 4.2 7.4 - - + -
142D LEU* 1.3 92.7 - - - +
144D GLY* 1.3 60.7 - - - +
155D LEU* 3.6 9.8 - - - +
162D SER 3.8 4.0 - - - +
164D VAL 3.7 20.2 - - - +
165D PRO* 3.5 27.4 - - + -
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Residues in contact with GLY 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D GLU 3.3 16.4 - - - -
97D GLY 3.6 9.6 + - - -
98D ALA 3.9 0.2 - - - -
129D SER 3.3 10.5 - - - -
143D TRP* 1.3 73.7 - - - +
145D SER* 1.3 65.3 + - - -
155D LEU* 3.5 7.6 - - - +
161D LYS* 3.4 1.6 - - - +
162D SER 2.7 39.4 + - - -
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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