Contacts of the strand formed by residues 123 - 129 (chain B) in PDB entry 3R9X
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 LEU 123 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25B GLU 4.4 2.5 - - - +
26B LEU* 3.5 38.4 - - + +
97B LYS* 3.5 29.7 - - + +
98B VAL 3.4 18.7 + - - -
121B VAL* 3.3 8.2 + - - +
122B PRO* 1.3 84.7 - - + +
124B ALA* 1.3 64.9 + - - +
125B VAL* 4.6 1.6 - - + -
153B TYR* 4.5 1.3 - - - -
178B LYS* 3.6 30.5 - - + +
179B LEU 3.0 9.2 - - - +
180B VAL* 4.0 20.6 - - + -
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Residues in contact with ALA 124 (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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98B VAL* 3.1 20.9 - - + +
114B THR* 4.8 4.5 - - + -
121B VAL* 4.7 6.1 - - + -
123B LEU* 1.3 75.5 - - - +
125B VAL* 1.3 64.9 + - - +
126B PHE* 3.7 25.7 - - + -
153B TYR* 5.5 1.5 - - + -
177B ILE 4.1 0.3 - - - +
178B LYS* 3.5 3.6 - - - +
179B LEU* 2.7 48.7 + - + +
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Residues in contact with VAL 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ILE* 3.8 30.5 - - + +
25B GLU* 3.9 26.9 - - + +
26B LEU* 3.5 29.4 - - + -
98B VAL 3.0 6.7 + - - -
99B VAL* 3.0 11.1 - - + +
100B GLY 3.0 24.4 + - - +
123B LEU* 4.6 1.6 - - + -
124B ALA* 1.3 76.2 - - - +
126B PHE* 1.3 65.6 + - - +
176B VAL* 4.0 21.1 - - + -
177B ILE 3.5 4.0 - - - +
178B LYS* 4.2 10.8 - - + -
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Residues in contact with PHE 126 (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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22B ILE* 5.5 1.1 - - - -
37B VAL* 4.9 1.6 - - + -
98B VAL* 3.5 29.6 - - + -
99B VAL 4.2 1.6 - - - -
100B GLY 3.3 22.4 - - - +
102B LEU* 3.4 33.0 - - + -
110B ILE* 4.3 9.0 - - + -
111B ILE* 4.4 12.8 - - + -
114B THR* 4.0 17.5 - - + -
124B ALA* 3.7 21.1 - - + -
125B VAL* 1.3 78.1 - - - +
127B MET* 1.3 58.6 + - - +
128B VAL* 4.2 11.2 - - + -
176B VAL* 3.3 8.1 - - - +
177B ILE* 2.7 53.8 + - + +
179B LEU* 4.3 19.7 - - + -
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Residues in contact with MET 127 (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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14B VAL* 3.9 18.2 - - + -
18B VAL* 3.7 29.2 - - + -
19B LEU* 6.0 0.4 - - + -
22B ILE* 4.3 17.4 - - + +
100B GLY 3.1 5.5 + - - -
101B ASN* 3.0 42.9 + - + +
102B LEU* 2.9 25.1 + - - +
126B PHE* 1.3 71.8 - - - +
128B VAL* 1.3 71.8 + - - +
161B VAL* 3.9 30.3 - - + -
166B PHE* 4.4 3.4 - - + -
174B SER* 4.1 16.8 - - - +
175B ALA 3.3 7.4 - - - +
176B VAL* 4.4 3.4 - - + +
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Residues in contact with VAL 128 (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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101B ASN* 5.0 0.2 - - - +
102B LEU* 4.0 33.4 - - + -
107B ALA* 4.4 6.3 - - + -
111B ILE* 4.6 2.9 - - + -
126B PHE* 4.2 8.3 - - + -
127B MET* 1.3 86.5 - - - +
129B GLN* 1.3 72.3 + - - +
132B VAL* 4.0 19.7 - - + -
133B ALA* 3.9 13.5 - - + -
174B SER* 3.1 9.0 - - - -
175B ALA 2.7 37.4 + - - +
177B ILE* 3.8 27.1 - - + -
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Residues in contact with GLN 129 (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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102B LEU 5.3 1.0 + - - -
104B TYR* 3.1 55.6 + - + +
128B VAL* 1.3 78.5 - - - +
130B LYS* 1.3 72.2 + - - +
131B GLU* 2.9 36.7 - - - +
132B VAL* 3.0 16.5 + - + +
133B ALA 3.1 9.4 + - - -
171B LYS* 6.4 0.9 - - - -
172B VAL* 3.1 38.6 - - + +
173B GLN 3.1 17.9 + - - +
174B SER* 3.8 9.4 + - - +
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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