Contacts of the strand formed by residues 142 - 147 (chain B) in PDB entry 5I2Y
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 ALA 142 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B GLN* 3.3 14.4 - - - +
123B ASP 4.1 10.1 - - - -
124B ALA* 4.3 5.8 - - + +
141B GLY* 1.3 74.6 - - - +
143B THR* 1.3 62.8 + - - +
144B LEU* 4.7 2.7 - - + -
155B CYS 3.6 0.2 - - - +
156B LEU* 3.2 7.2 - - - +
157B VAL* 2.7 43.7 + - + +
162B LEU* 4.5 2.4 - - + +
174B PHE* 4.1 29.2 - - + -
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Residues in contact with THR 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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121B LEU* 3.0 45.0 + - + -
122B GLN* 2.9 31.7 + - - +
142B ALA* 1.3 75.2 + - - +
144B LEU* 1.3 66.2 + - - +
154B ARG* 4.5 24.9 - - + +
155B CYS 3.4 8.7 - - - +
156B LEU* 4.3 12.0 - - + +
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Residues in contact with LEU 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B LEU* 3.9 19.1 - - + -
119B GLU 3.6 3.1 - - - -
120B VAL* 3.9 18.4 - - + -
121B LEU* 4.6 4.0 - - - -
142B ALA* 4.7 0.9 - - + -
143B THR* 1.3 87.9 - - - +
145B LEU* 1.3 58.6 + - - +
146B VAL* 4.0 8.5 - - + -
153B VAL 3.5 0.3 - - - +
154B ARG* 3.3 5.5 - - - +
155B CYS* 2.7 42.3 + - + +
157B VAL* 3.8 23.6 - - + -
174B PHE* 3.8 38.4 - - + -
182B LEU* 3.6 30.1 - - + -
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Residues in contact with LEU 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B LEU* 3.8 1.7 - - - +
118B LEU* 2.8 47.1 + - + +
119B GLU* 2.8 47.5 + - + +
121B LEU* 4.4 13.8 - - + +
144B LEU* 1.3 71.0 - - - +
146B VAL* 1.3 54.9 + - - +
152B SER* 3.7 28.5 - - - +
153B VAL* 3.6 20.4 - - - +
154B ARG* 4.1 11.0 - - + +
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Residues in contact with VAL 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B TRP* 4.6 13.5 - - + -
99B ILE* 3.9 4.8 - - + +
115B GLY* 4.0 15.0 - - - -
116B GLN 3.2 11.4 - - - +
117B LEU* 4.8 1.6 - - - -
118B LEU* 4.6 0.4 - - - -
144B LEU* 4.2 15.3 - - + -
145B LEU* 1.3 79.0 - - - +
147B SER* 1.3 70.4 + - - +
152B SER* 3.1 5.7 - - - -
153B VAL* 3.0 32.1 + - + +
155B CYS* 3.6 30.7 - - + -
182B LEU* 4.2 19.5 - - + -
184B LEU* 4.7 6.1 - - + -
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Residues in contact with SER 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A LEU* 3.5 5.8 - - - +
99B ILE* 4.3 0.4 - - - -
115B GLY* 3.1 6.9 - - - -
116B GLN* 2.7 42.6 + - - -
118B LEU* 3.8 32.1 - - - +
146B VAL* 1.3 75.5 - - - +
148B ASP* 1.3 57.7 + - - +
149B GLY* 2.7 31.2 + - - -
151B HIS 3.3 10.7 + - - -
152B SER* 4.3 0.4 - - - +
219B LEU 5.3 1.4 + - - -
221B VAL* 4.0 9.9 - - - +
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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