Contacts of the strand formed by residues 121 - 126 (chain B) 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 121 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B LEU* 3.5 22.1 - - + +
86B GLY* 3.1 34.5 + - - +
88B VAL* 4.0 7.0 - - + -
117B LEU* 3.9 27.8 - - + -
119B GLU* 4.2 8.1 - - + +
120B LYS* 1.3 77.0 + - - +
122B VAL* 1.3 64.0 + - - +
123B GLN 3.4 20.2 - - - +
124B VAL* 3.8 11.7 - - + -
133B ALA* 3.9 10.1 - - + -
134B LEU 3.3 15.9 - - - +
135B THR* 4.2 2.2 - - + +
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Residues in contact with VAL 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B VAL* 4.6 4.5 - - + +
30B HIS* 3.9 39.8 - - + +
31B SER 4.6 10.2 + - - +
71B GLN* 4.5 1.2 - - - +
82B LEU* 3.3 14.5 - - - +
120B LYS* 4.3 13.2 - - - +
121B VAL* 1.3 77.6 - - - +
123B GLN* 1.3 62.9 + - - +
134B LEU* 2.8 24.7 + - + +
135B THR 3.9 12.6 - - - +
136B ASP* 3.7 27.4 - - + -
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Residues in contact with GLN 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B SER* 2.9 43.6 + - - -
30B HIS* 3.8 14.8 - - + +
71B GLN* 3.4 16.5 + - - +
82B LEU* 3.5 3.8 - - - +
121B VAL* 3.4 4.0 - - - +
122B VAL* 1.3 84.3 - - - +
124B VAL* 1.3 72.9 + - - +
133B ALA* 3.5 0.2 - - - -
134B LEU* 2.7 41.8 + - + +
175B VAL 4.1 0.2 - - - +
176B LYS* 3.2 15.8 - - - +
177B VAL* 3.0 37.9 + - + +
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Residues in contact with VAL 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B GLN* 2.9 40.9 + - + +
73B GLU* 3.7 10.8 - - + +
80B VAL* 4.1 31.6 - - + +
82B LEU* 4.5 14.4 - - + -
88B VAL* 4.1 18.2 - - + -
121B VAL* 3.8 16.8 - - + -
123B GLN* 1.3 85.0 - - - +
125B SER* 1.3 62.7 + - - +
131B THR* 5.6 0.4 - - + -
132B ALA 3.2 13.5 - - - +
133B ALA* 4.2 3.4 - - + -
177B VAL* 4.2 3.6 - - - +
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Residues in contact with SER 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B GLU* 4.6 8.7 - - - -
80B VAL* 5.8 0.2 - - - -
124B VAL* 1.3 78.1 - - - +
126B ALA* 1.3 60.5 + - - +
131B THR* 3.5 5.4 - - - +
132B ALA* 2.9 46.7 + - - +
177B VAL* 4.0 17.7 - - - +
178B ALA* 4.0 1.1 - - - -
179B SER* 2.7 36.2 + - - -
184B LEU* 3.7 5.0 - - - +
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Residues in contact with ALA 126 (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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73B GLU* 4.7 10.9 + - + +
74B ALA 4.2 8.1 - - - +
75B GLY* 3.6 29.4 - - - +
78B HIS* 3.8 16.8 - - - +
80B VAL* 4.2 13.2 - - + -
125B SER* 1.3 78.9 - - - +
127B GLY* 1.3 58.9 + - - +
130B HIS 3.6 3.8 - - - -
131B THR* 4.6 0.2 - - - +
179B SER* 3.7 17.1 + - - +
180B GLY 5.2 0.2 - - - -
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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