Contacts of the helix formed by residues 122 - 133 (chain A) in PDB entry 2CAS
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 ASN 122 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A PHE* 1.3 74.5 - - - +
123A PRO* 1.3 79.7 - - + -
124A GLY* 2.7 18.9 + - - -
125A ASP* 2.8 30.1 + - - +
126A TRP* 2.8 22.3 + - - +
464A TYR* 3.2 5.6 - - - -
571A ILE* 6.0 1.1 - - + -
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Residues in contact with PRO 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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122A ASN* 1.3 92.2 - - + +
124A GLY* 1.3 57.4 + - - +
126A TRP* 3.8 5.5 - - + +
127A GLN* 3.0 25.5 + - - +
464A TYR* 3.3 18.1 - - + +
551A MET* 3.4 14.6 - - + +
561A TYR* 3.7 41.3 - - + +
571A ILE* 4.9 15.9 - - + -
572A VAL 6.0 0.7 - - - +
574A GLU* 4.5 4.5 - - - +
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Residues in contact with GLY 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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122A ASN* 2.7 16.0 + - - -
123A PRO* 1.3 75.9 - - - +
125A ASP* 1.3 61.1 + - - -
127A GLN* 3.3 18.2 + - - +
128A LEU* 3.4 11.6 + - - +
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Residues in contact with ASP 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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49A THR* 3.6 26.6 + - - +
51A PHE* 4.4 12.3 - - + -
121A PHE* 3.6 25.0 - - + -
122A ASN* 2.8 40.1 + - - +
124A GLY* 1.3 69.1 - - - -
126A TRP* 1.3 68.4 - - - +
128A LEU* 3.1 19.8 + - - +
129A ILE* 3.1 18.3 + - - +
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Residues in contact with TRP 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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117A TRP* 3.3 47.3 - + - -
121A PHE* 4.1 16.5 - + + +
122A ASN 2.8 14.7 + - - +
123A PRO* 3.8 6.3 - - + +
125A ASP* 1.3 78.9 - - - +
127A GLN* 1.3 65.6 + - - +
129A ILE* 3.1 15.7 + - + +
130A VAL* 3.0 52.2 + - + +
136A LEU* 5.3 4.3 - - + -
275A LEU* 5.7 1.8 - - + -
462A PRO* 4.1 15.0 - - + -
464A TYR* 3.4 49.4 - + + +
551A MET* 4.5 3.4 - - + -
574A GLU* 4.0 18.4 - - + +
575A LYS 3.6 12.1 + - - -
576A SER* 3.8 21.5 - - - -
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Residues in contact with GLN 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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123A PRO 3.0 15.0 + - - +
124A GLY* 3.5 12.4 - - - +
126A TRP* 1.3 75.2 - - - +
128A LEU* 1.3 54.5 + - - +
130A VAL* 4.7 0.9 - - - -
131A ASN* 2.7 58.3 + - - +
551A MET* 2.8 45.5 + - + +
552A SER* 3.6 16.2 - - - +
553A ILE* 4.4 2.0 - - - +
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Residues in contact with LEU 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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51A PHE* 3.9 39.3 - - + -
53A PHE* 5.9 6.5 - - + -
124A GLY 3.4 8.7 + - - +
125A ASP* 3.1 11.1 + - - +
127A GLN* 1.3 76.2 - - - +
129A ILE* 1.3 61.7 + - - +
132A THR* 2.8 53.5 + - + +
133A MET* 4.2 2.4 - - + +
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Residues in contact with ILE 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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51A PHE* 4.0 17.3 - - + -
61A ILE* 4.5 14.8 - - + -
121A PHE* 3.8 43.1 - - + -
125A ASP 3.1 13.6 + - - +
126A TRP* 3.7 17.3 - - + +
128A LEU* 1.3 75.8 - - - +
130A VAL* 1.3 66.9 + - + +
133A MET* 2.8 45.8 + - + +
136A LEU* 4.4 20.6 - - + -
275A LEU* 3.6 23.4 - - + +
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Residues in contact with VAL 130 (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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126A TRP* 3.1 50.7 - - + +
127A GLN 4.2 1.1 - - - +
129A ILE* 1.3 86.4 - - + +
131A ASN* 1.3 64.0 + - - +
133A MET 4.3 6.8 - - - +
275A LEU* 4.6 10.9 - - + +
540A ARG* 5.7 0.2 - - - -
550A GLN* 5.1 0.2 - - - +
551A MET* 4.5 8.1 - - + -
575A LYS 3.9 10.1 - - - +
576A SER* 3.5 30.4 - - - +
578A LEU* 3.7 31.5 + - + +
579A ALA 5.7 0.9 + - - -
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Residues in contact with ASN 131 (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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127A GLN* 2.7 36.3 + - - +
130A VAL* 1.3 74.5 - - - +
132A THR* 1.3 66.8 - - + +
540A ARG* 3.0 25.3 + - - -
550A GLN* 3.4 33.1 + - - +
551A MET* 2.6 52.1 + - - +
578A LEU* 3.3 12.5 - - - +
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Residues in contact with THR 132 (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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128A LEU* 2.8 40.9 + - + +
131A ASN* 1.3 90.4 - - + +
133A MET* 1.3 73.0 + - - +
539A LEU* 3.7 12.7 - - - +
540A ARG* 3.0 31.9 + - - +
550A GLN* 5.5 1.6 - - - +
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Residues in contact with MET 133 (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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51A PHE* 4.0 29.2 - - + -
53A PHE* 5.1 2.9 - - + -
59A VAL* 3.6 30.3 - - + -
61A ILE* 4.3 4.5 - - + -
128A LEU* 4.4 6.7 - - + +
129A ILE* 2.8 33.4 + - + +
130A VAL 4.3 5.7 - - - +
132A THR* 1.3 83.7 - - - +
134A SER* 1.3 62.2 + - - +
135A GLU 4.3 1.1 - - - +
275A LEU* 3.7 25.3 - - + +
276A THR* 5.5 0.9 - - - +
537A ALA* 3.8 13.9 - - + -
538A LYS 3.2 11.9 - - - +
539A LEU* 3.4 27.8 - - + -
540A ARG* 4.3 6.4 - - - +
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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