Contacts of the strand formed by residues 141 - 146 (chain B) in PDB entry 4I6J
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 THR 141 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B GLN 3.1 5.7 + - - +
112B TYR* 3.6 30.0 - - + -
113B VAL* 3.3 26.7 + - - +
139B LEU* 3.4 5.9 - - - +
140B LYS* 1.3 81.4 + - - +
142B LEU* 1.3 70.2 + - - +
143B GLY* 4.7 0.9 - - - +
174B LEU* 4.4 2.2 - - - -
175B SER* 4.8 2.1 - - - -
176B SER* 3.7 25.5 + - - -
178B LYS* 5.8 6.1 - - + +
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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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113B VAL* 3.4 30.1 - - + +
115B PHE* 4.3 15.5 - - + -
131B LEU* 4.5 7.9 - - + -
139B LEU* 4.1 12.6 - - + -
141B THR* 1.3 78.7 - - - +
143B GLY* 1.3 58.4 + - - +
144B LEU* 4.3 11.7 - - + -
164B LEU* 4.1 18.8 - - + -
167B VAL* 3.7 34.3 - - + -
174B LEU* 4.4 8.3 - - + -
176B SER 3.1 8.5 + - - +
177B LEU* 3.4 20.9 + - + +
178B LYS* 3.0 24.9 + - - +
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Residues in contact with GLY 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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113B VAL 3.0 11.2 + - - -
114B SER* 3.2 5.6 - - - -
115B PHE* 2.8 27.7 + - - -
141B THR* 4.7 2.0 - - - +
142B LEU* 1.3 75.7 - - - +
144B LEU* 1.3 66.7 + - - +
145B ILE* 3.7 12.3 - - - -
178B LYS* 3.7 16.8 - - - -
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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
----------------------------------------------------------
115B PHE* 3.7 29.6 - - + -
127B ALA* 5.8 0.2 - - + -
131B LEU* 4.4 18.8 - - + -
142B LEU* 4.5 10.8 - - + -
143B GLY* 1.3 80.6 - - - +
145B ILE* 1.3 61.5 + - - +
146B SER 4.0 2.1 + - - -
152B PHE* 4.2 22.4 - - + -
160B PHE* 3.6 37.5 - - + -
164B LEU* 4.8 4.7 - - + -
178B LYS* 2.8 19.0 + - - +
179B ILE* 3.7 21.1 - - + -
180B ASP* 4.1 18.0 + - - +
182B THR* 4.3 6.3 - - - +
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Residues in contact with ILE 145 (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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501A ARG* 6.5 0.4 - - + -
504A GLN* 4.0 32.8 - - - +
80B GLU* 5.3 2.9 - - - +
114B SER* 4.2 12.6 - - - +
115B PHE 2.7 18.8 + - - +
116B LYS* 4.2 23.6 - - + -
117B VAL* 2.7 34.8 + - - +
143B GLY* 3.7 21.8 - - - +
144B LEU* 1.3 76.0 - - - +
146B SER* 1.3 61.8 + - - +
147B THR* 3.5 12.3 + - - +
152B PHE* 4.8 2.0 - - - -
178B LYS* 5.2 8.5 - - + +
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Residues in contact with SER 146 (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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497A LEU* 5.1 0.6 - - - +
501A ARG* 3.1 18.5 + - - +
117B VAL* 3.5 9.0 - - - +
144B LEU 4.0 1.7 + - - -
145B ILE* 1.3 73.6 - - - +
147B THR* 1.3 65.8 + - - +
148B ALA 3.0 4.1 + - - -
149B ARG 4.5 2.9 - - - -
150B PRO* 4.3 21.1 - - - +
151B SER* 4.9 1.3 + - - -
152B PHE* 3.7 23.5 - - - -
180B ASP 4.3 2.5 + - - -
181B ASP* 3.9 28.6 + - - +
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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