Contacts of the strand formed by residues 123 - 129 (chain A) in PDB entry 3ARE
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 LYS 123 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119A ALA* 3.6 3.3 - - - +
120A PHE 2.8 33.6 + - - +
121A GLN 3.4 3.2 - - - +
122A GLY* 1.3 81.1 - - - +
124A TYR* 1.3 74.9 + - - +
125A VAL* 3.4 12.6 + - + +
138A GLY 4.6 14.8 + - - -
140A PRO* 5.9 5.2 - - + +
60B TRP* 4.9 0.7 - - - -
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Residues in contact with TYR 124 (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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117A HIS* 3.0 44.9 + + + -
118A VAL 3.3 21.3 - - - -
119A ALA* 3.7 5.3 - - - +
123A LYS* 1.3 79.2 - - - +
125A VAL* 1.3 64.5 + - - +
126A VAL 3.3 20.2 - - - -
127A ARG* 3.3 17.7 + - - +
136A VAL* 3.5 35.5 - - + +
139A ALA* 5.7 0.2 - - - +
60B TRP* 3.5 27.5 - + - +
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Residues in contact with VAL 125 (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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118A VAL* 3.0 8.1 + - + +
119A ALA 4.4 0.7 - - - -
120A PHE* 3.7 34.3 - - + +
123A LYS* 3.7 18.6 - - + +
124A TYR* 1.3 79.0 - - - +
126A VAL* 1.3 71.6 + - + +
135A THR* 3.4 6.9 - - - +
136A VAL* 2.8 34.2 + - - -
139A ALA* 4.3 5.7 - - + +
140A PRO* 3.8 29.2 - - + -
143A LEU* 3.7 20.0 - - + -
601A 4GH 5.5 0.9 - - + -
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Residues in contact with VAL 126 (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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118A VAL* 2.7 50.4 + - + -
124A TYR* 3.3 7.7 - - - -
125A VAL* 1.3 93.1 - - + +
127A ARG* 1.3 63.9 + - - +
133A TRP* 3.9 24.7 - - + -
134A GLN 3.4 11.0 - - - +
135A THR* 4.7 3.8 - - + -
136A VAL* 4.5 0.4 - - - -
143A LEU* 4.7 8.7 - - + -
147A ILE* 3.8 34.8 - - + -
601A 4GH 4.4 15.0 - - + -
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Residues in contact with ARG 127 (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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116A LEU 3.3 13.2 - - - +
117A HIS* 3.7 11.9 - - + +
118A VAL* 5.1 0.9 - - - -
124A TYR* 3.3 26.9 + - + +
126A VAL* 1.3 81.2 - - - +
128A PHE* 1.3 60.8 + - - +
129A TRP* 3.5 51.7 + - - +
133A TRP* 4.5 0.9 - - - -
134A GLN* 2.8 72.3 + - + +
135A THR 5.5 3.3 + - - -
136A VAL* 4.8 5.6 - - + -
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Residues in contact with PHE 128 (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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115A PHE* 5.4 1.6 - - - -
116A LEU* 3.1 32.0 + - + +
127A ARG* 1.3 72.8 - - - +
129A TRP* 1.3 69.8 + - - +
130A GLY 3.3 23.1 + - - -
132A SER 3.5 26.7 - - - -
133A TRP* 3.9 31.2 - + + +
157A SER* 3.5 41.1 - - - -
160A VAL* 3.6 31.4 - - + -
161A GLN* 3.6 14.6 - - + -
164A LEU* 3.7 16.9 - - + +
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Residues in contact with TRP 129 (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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113A GLU* 3.8 23.1 - - - -
114A SER 4.6 7.6 - - - -
115A PHE* 6.0 2.0 - - + -
127A ARG* 3.5 47.4 + - - +
128A PHE* 1.3 78.6 - - - +
130A GLY* 1.3 63.8 + - - +
131A THR 3.1 8.0 + - - -
132A SER* 3.0 19.0 + - - +
134A GLN* 3.4 34.9 + - - +
501A NAG 5.6 9.2 - - - -
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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