Contacts of the strand formed by residues 140 - 144 (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 140 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132B ALA* 4.6 2.0 - - + -
133B ALA 3.4 6.1 - - - +
134B LEU* 3.9 9.0 - - + -
139B ARG* 1.3 76.6 - - - +
141B PHE* 1.3 70.8 + - - +
142B LEU* 5.2 0.2 - - + -
167B GLN* 3.5 5.9 - - - +
168B VAL* 2.8 52.9 + - + +
170B LEU* 5.1 1.6 - - + -
174B VAL* 3.8 37.7 - - + -
177B VAL* 4.1 14.6 - - + -
184B LEU* 4.5 8.5 - - + -
186B MET* 3.8 22.4 - - - -
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Residues in contact with PHE 141 (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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117B LEU* 3.9 35.0 - - + -
119B GLU* 4.0 11.0 - - + -
132B ALA* 3.3 3.3 - - - -
133B ALA 2.8 35.6 + - - +
135B THR* 3.6 32.3 - - + -
139B ARG* 3.6 28.0 - - + -
140B VAL* 1.3 78.1 - - - +
142B LEU* 1.3 60.5 + - - +
143B TRP* 4.1 9.3 - - + -
165B PRO* 4.3 5.2 - - + -
166B VAL* 3.3 11.9 - - - -
167B GLN* 3.6 41.7 - - + -
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Residues in contact with LEU 142 (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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130B HIS* 3.8 28.3 - - + -
131B THR 3.2 25.4 - - - +
132B ALA* 3.9 2.2 - - + -
140B VAL* 5.2 0.2 - - + -
141B PHE* 1.3 75.5 - - - +
143B TRP* 1.3 65.6 + - - +
146B PHE* 4.1 11.7 - - + -
155B LEU* 3.6 28.5 - - + -
156B LEU* 4.0 19.7 - - + -
166B VAL* 2.8 40.0 + - + +
168B VAL* 4.0 13.0 - - + -
184B LEU* 3.9 27.1 - - + -
196B LEU* 4.3 2.2 - - + -
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Residues in contact with TRP 143 (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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80B VAL* 5.2 0.7 - - + -
88B VAL* 4.4 11.2 - - + -
90B SER* 5.8 1.1 - - - -
97B GLY 3.3 6.5 - - - -
98B ALA 2.8 29.5 + - - -
99B LEU 3.5 2.2 - - - -
100B GLY* 3.3 26.8 - - - +
115B VAL* 4.1 26.9 - - + -
117B LEU* 4.5 5.2 - - + -
130B HIS* 3.2 6.9 - - - +
131B THR* 3.0 58.6 + - + +
133B ALA* 3.9 30.3 - - + -
141B PHE* 4.1 8.7 - - + -
142B LEU* 1.3 82.9 - - - +
144B GLY* 1.3 62.4 + - - +
155B LEU* 3.6 9.2 - - - -
162B SER 3.7 4.9 - - - +
164B VAL* 3.5 20.0 - - - +
165B PRO* 3.7 26.2 - - + -
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Residues in contact with GLY 144 (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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96B GLU 3.2 19.7 - - - -
97B GLY 3.6 10.2 + - - -
98B ALA 3.9 0.2 - - - -
129B SER 3.2 9.0 - - - -
143B TRP* 1.3 74.8 - - - +
145B SER* 1.3 64.1 + - - -
155B LEU* 3.6 8.1 - - - +
161B LYS* 3.3 1.9 - - - -
162B SER 2.7 37.1 + - - -
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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