Contacts of the strand formed by residues 141 - 148 (chain A) in PDB entry 3B3T
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 ARG 141 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A PRO* 5.0 2.6 - - - +
84A GLY* 3.2 9.1 - - - -
87A ALA 3.5 7.0 - - - +
90A GLU* 2.8 41.9 + - + +
92A ILE* 3.7 17.0 - - + +
139A PRO* 3.2 23.9 - - - +
140A LYS* 1.3 75.2 - - - +
142A SER* 1.3 66.6 + - - +
143A ILE* 4.1 0.3 - - - +
173A VAL* 3.9 18.6 - - - +
286A MET* 3.0 43.5 + - - +
287A GLY* 3.0 9.9 + - - +
289A ALA* 3.1 33.2 + - - +
290A THR* 3.6 5.1 - - + +
291A GLY* 2.9 30.5 + - - +
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Residues in contact with SER 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A ILE 3.2 9.6 - - - -
83A THR* 3.6 6.1 - - - +
84A GLY* 3.0 16.2 + - - +
87A ALA 3.8 1.2 + - - -
88A PRO* 2.7 28.5 + - - +
90A GLU 3.0 8.5 + - - +
91A TRP* 3.4 32.6 - - - -
92A ILE* 2.9 25.5 + - - +
141A ARG* 1.3 74.7 - - - +
143A ILE* 1.3 63.0 + - - +
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Residues in contact with ILE 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A MET 3.8 0.5 - - - +
81A THR* 3.2 5.0 - - - -
82A ILE* 2.9 36.4 + - + +
91A TRP* 3.7 4.6 - - - -
92A ILE* 3.2 23.6 - - + +
94A ILE* 4.7 5.8 - - + -
137A PHE* 3.7 31.4 - - + -
139A PRO* 3.9 12.1 - - + -
141A ARG 4.1 7.4 - - - +
142A SER* 1.3 79.9 - - - +
144A ALA* 1.3 67.2 + - - +
145A PHE* 3.6 36.2 - - + -
283A ALA* 3.9 23.6 - - + +
287A GLY* 4.4 3.4 - - - -
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Residues in contact with ALA 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A VAL* 4.4 3.1 - - + -
80A MET 3.3 7.0 - - - +
81A THR* 4.3 4.5 - - + -
91A TRP* 4.0 20.3 - - + -
92A ILE 2.8 11.1 + - - +
93A VAL* 3.3 8.4 - - + +
94A ILE* 2.9 28.2 + - - +
143A ILE* 1.3 75.1 - - - +
145A PHE* 1.3 61.0 + - - +
146A MET* 3.8 27.3 + - + -
165A TYR* 4.2 4.0 - - - +
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Residues in contact with PHE 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A TRP* 3.4 6.9 - - + -
79A VAL* 3.3 4.7 - - - -
80A MET* 2.8 61.4 + - + +
82A ILE* 3.7 27.4 - - + -
94A ILE* 3.2 30.5 - - + -
125A VAL* 4.0 11.4 - - + -
128A VAL* 4.0 19.3 - - + -
129A ILE* 3.5 37.7 - - + -
132A LEU* 3.8 19.3 - - + -
143A ILE* 3.6 24.5 - - + -
144A ALA* 1.3 72.9 - - - +
146A MET* 1.3 59.4 + - - +
283A ALA* 5.2 1.3 - - + -
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Residues in contact with MET 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A TRP* 3.9 6.4 - - - -
78A VAL 3.3 4.5 - - - +
79A VAL* 4.1 18.6 - - + -
93A VAL* 4.2 5.4 - - + -
94A ILE 2.9 11.0 + - - +
95A GLY* 3.0 22.7 - - - -
96A GLY 3.0 6.8 + - - -
122A ILE* 4.9 1.0 - - - +
125A VAL* 4.8 1.8 - - - +
144A ALA* 3.8 16.6 - - + +
145A PHE* 1.3 82.9 - - - +
147A ALA* 1.3 60.1 + - - +
148A TYR* 3.6 37.7 - - + +
161A LEU* 4.0 13.0 - - + -
165A TYR* 3.3 41.1 - - + +
233A TRP* 3.8 21.1 - - + -
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Residues in contact with ALA 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ILE* 4.2 6.7 - - + -
53A TRP* 3.8 15.9 - - + -
77A SER* 3.2 6.8 - - - -
78A VAL* 2.8 42.3 + - + -
96A GLY 3.2 6.1 - - - -
98A LEU* 3.6 20.1 - - + +
122A ILE* 3.7 20.2 - - + -
146A MET* 1.3 72.0 - - - +
148A TYR* 1.3 62.2 + - - +
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Residues in contact with TYR 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A SER* 3.6 3.6 - - - -
93A VAL* 3.8 16.6 - - - +
95A GLY* 4.2 4.6 + - - -
96A GLY 3.0 31.5 + - - -
97A HIS* 3.4 7.6 - - + +
98A LEU* 2.9 28.0 + - - +
99A ASP* 4.0 0.3 - - - +
146A MET* 3.6 31.6 - - + +
147A ALA* 1.3 71.2 - - - +
149A ALA* 1.3 66.4 + - - +
150A ALA 3.9 0.3 + - - -
158A SER* 3.6 28.3 - - - +
161A LEU* 4.0 14.8 - - + -
176A LEU 5.1 1.0 + - - -
177A GLN* 3.3 23.0 + - - -
229A ASP* 3.3 31.9 - - + +
233A TRP* 2.9 29.1 + + - -
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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