Contacts of the strand formed by residues 142 - 150 (chain C) in PDB entry 3RBQ
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 GLN 142 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95C ASP* 3.8 5.4 + - - +
96C MET* 3.0 49.3 + - + +
97C ASP* 4.6 1.6 + - - -
140C LEU* 3.7 0.6 - - - +
141C ARG* 1.3 118.4 + - - +
143C VAL* 1.3 69.3 + - - +
193C ILE* 3.4 32.6 - - + +
194C TYR 3.4 5.2 - - - +
195C ASP* 2.7 26.2 + - - +
196C PHE* 4.6 0.2 - - - -
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Residues in contact with VAL 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C ILE* 3.8 33.4 - - + -
94C ARG 3.3 9.4 - - - +
95C ASP* 4.6 0.2 - - - -
96C MET* 3.9 3.4 - - - -
102C LEU* 3.8 12.3 - - + -
137C PHE* 4.7 2.7 - - + -
140C LEU* 3.7 23.3 - - + -
142C GLN* 1.3 78.1 - - - +
144C GLY* 1.3 62.0 + - - +
193C ILE* 3.6 1.7 - - - +
194C TYR* 2.7 48.3 + - + +
196C PHE* 3.5 29.8 - - + -
500I DAO 4.7 5.8 - - + -
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Residues in contact with GLY 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C LYS* 3.5 1.4 - - - +
93C ILE* 3.2 3.8 - - - -
94C ARG* 2.8 40.6 + - - +
96C MET* 3.5 23.6 - - - +
143C VAL* 1.3 72.6 - - - +
145C ALA* 1.3 60.6 + - - -
146C THR* 5.1 1.8 + - - -
192C HIS 3.6 6.3 - - - -
193C ILE* 4.2 7.0 - - - -
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Residues in contact with ALA 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C PHE* 4.0 14.6 - - + -
92C LYS 3.2 4.3 - - - -
93C ILE* 3.8 11.9 - - + -
143C VAL 4.0 1.2 + - - -
144C GLY* 1.3 73.7 - - - -
146C THR* 1.3 62.9 + - - +
147C VAL* 4.1 4.5 - - + -
190C CYS 3.8 0.3 - - - +
191C GLU* 3.2 6.8 - - - +
192C HIS* 2.8 39.7 + - + +
194C TYR* 3.7 27.6 - - + -
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Residues in contact with THR 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C ARG* 3.9 18.9 - - - +
91C PHE* 3.4 5.5 - - - -
92C LYS* 2.8 57.2 + - - +
94C ARG* 5.7 2.3 - - - +
144C GLY 4.1 2.1 + - - -
145C ALA* 1.3 75.9 + - - +
147C VAL* 1.3 65.1 + - - +
148C GLU* 5.2 0.9 - - + -
189C THR* 3.7 25.8 - - + -
190C CYS 3.4 3.8 - - - +
191C GLU* 3.7 23.7 + - - +
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Residues in contact with VAL 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C PHE* 4.6 10.1 - - + -
90C ARG* 3.4 5.6 - - - +
91C PHE* 3.6 30.5 - - + -
145C ALA* 4.1 3.6 - - + -
146C THR* 1.3 74.8 - - - +
148C GLU* 1.3 62.0 + - - +
149C PHE* 4.3 7.6 - - + -
179C PHE* 4.0 22.4 - - + -
189C THR* 3.1 9.7 - - - +
190C CYS* 2.9 58.9 + - + +
192C HIS* 5.1 3.6 - - - +
502I ALA* 4.2 12.1 - - + -
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Residues in contact with GLU 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C PHE* 3.5 4.9 - - - +
89C VAL* 2.8 35.6 + - + +
90C ARG* 2.9 57.9 + - + +
106C LYS* 4.4 9.7 + - - -
146C THR* 5.2 0.7 - - + -
147C VAL* 1.3 75.5 - - - +
149C PHE* 1.3 64.7 + - - +
187C LYS* 3.6 24.3 + - + +
188C ASN 3.1 6.5 - - - +
189C THR* 3.5 26.4 + - + +
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Residues in contact with PHE 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C ILE* 4.1 3.1 - - + -
87C ASP 3.2 14.6 - - - +
88C PHE* 3.7 22.7 - + + -
89C VAL* 4.1 3.5 - - - +
147C VAL* 4.3 12.3 - - + -
148C GLU* 1.3 77.8 - - - +
150C THR* 1.3 71.9 + - - +
151C VAL* 4.1 7.0 - - + -
159C PHE* 3.7 20.9 - + - -
179C PHE* 4.1 12.6 - + + -
182C CYS* 3.6 31.2 - - - -
187C LYS* 3.4 0.8 - - - +
188C ASN* 2.7 74.0 + - + +
190C CYS* 3.8 23.6 - - - -
130F ARG* 5.3 0.7 - - - -
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Residues in contact with THR 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C LYS 3.9 2.8 + - - -
86C ILE* 3.2 6.4 - - - +
87C ASP* 3.0 46.6 + - - +
89C VAL* 4.5 14.6 - - + -
149C PHE* 1.3 79.8 - - - +
151C VAL* 1.3 67.4 + - - +
185C SER 5.9 0.2 - - - -
186C SER* 3.2 15.9 - - - +
187C LYS* 4.1 20.6 - - + -
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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