Contacts of the strand formed by residues 121 - 127 (chain A) in PDB entry 3JTC
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 SER 121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A ALA* 3.2 5.0 - - - -
118A VAL* 2.8 34.9 + - - +
119A ASN 3.3 4.9 + - - -
120A GLY* 1.3 81.4 + - - +
122A SER* 1.3 67.8 - - - +
123A PHE* 4.1 0.5 - - - +
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Residues in contact with SER 122 (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 VAL 4.3 0.9 - - - -
117A ALA* 4.2 7.7 - - - +
120A GLY 4.3 1.0 + - - -
121A SER* 1.3 76.5 - - - +
123A PHE* 1.4 61.8 + - - +
136A ASP* 3.7 28.4 + - - +
137A THR* 3.6 17.4 - - - +
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Residues in contact with PHE 123 (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 VAL* 3.0 22.5 + - + +
118A VAL* 3.6 34.5 - - + +
121A SER 4.1 0.2 - - - +
122A SER* 1.4 75.5 - - - +
124A VAL* 1.3 91.4 + - + +
135A ALA* 3.5 2.4 - - - -
136A ASP* 2.8 22.4 + - - +
137A THR* 3.5 14.0 + - + +
143A VAL* 4.2 11.2 - - + -
144A VAL* 3.4 33.0 - - + -
147A THR* 3.9 33.9 - - + -
606A PTY 4.1 25.4 - - + -
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Residues in contact with VAL 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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116A VAL* 2.8 45.9 + - + +
123A PHE* 1.3 110.4 - - + +
125A SER* 1.3 64.5 + - - +
133A TRP* 4.0 16.6 - - + -
134A GLN 3.2 10.8 - - - +
135A ALA* 4.3 2.9 - - - -
136A ASP* 3.4 6.4 - - - +
144A VAL* 4.4 5.6 - - + -
147A THR* 4.8 4.0 - - + -
148A LEU* 3.7 30.7 - - + -
151A LEU* 4.3 11.2 - - + -
606A PTY 5.3 0.7 - - + -
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Residues in contact with SER 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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114A PHE 3.4 12.3 - - - -
115A GLU* 3.9 12.6 - - - -
124A VAL* 1.3 73.2 - - - +
126A PHE* 1.3 61.7 + - - +
127A ARG* 2.6 35.7 + - - -
133A TRP* 3.3 7.8 - - - -
134A GLN* 2.9 33.4 + - - +
136A ASP* 2.8 28.6 + - - -
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Residues in contact with PHE 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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112A VAL* 5.3 0.6 - - + +
113A PHE* 5.1 3.6 - - - -
114A PHE* 3.0 32.4 + - + +
125A SER* 1.3 72.6 - - - +
127A ARG* 1.3 78.7 + - - +
128A PRO* 3.7 31.6 - - + +
131A ALA* 3.6 35.4 - - + -
132A LEU 3.8 2.2 - - - -
133A TRP* 3.4 39.5 - + + -
157A THR 4.1 1.3 - - - -
158A ARG 3.4 24.5 - - - -
161A LEU* 3.7 20.0 - - + -
162A ARG* 3.9 16.6 - - + -
165A LEU* 4.0 13.2 - - + -
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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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113A PHE* 6.3 0.8 - - - +
115A GLU* 4.7 12.1 + - - +
125A SER* 2.6 35.3 + - - -
126A PHE* 1.3 87.1 + - - +
128A PRO* 1.3 65.3 - - - +
129A GLU* 3.2 12.6 + - - +
130A ARG 3.8 2.2 + - - +
131A ALA 3.0 19.6 + - - -
132A LEU* 2.8 28.9 + - + +
134A GLN* 3.1 44.7 + - + +
136A ASP* 4.4 1.6 + - - -
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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