Contacts of the helix formed by residues 121 - 131 (chain A) in PDB entry 4CSC
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 PRO 121 (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 3.7 6.7 - - - +
120A LEU* 1.3 91.1 - - + +
122A SER* 1.3 56.5 + - - +
123A HIS* 3.9 15.0 - - + +
124A VAL* 2.7 33.4 + - + +
125A VAL* 3.2 11.5 + - - -
148A LEU* 3.4 34.8 - - + -
151A GLU* 3.6 31.2 - - + +
181A LYS* 5.3 0.7 - - + +
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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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120A LEU 3.8 1.4 + - - -
121A PRO* 1.3 72.9 - - - +
123A HIS* 1.3 63.2 + - - +
124A VAL 3.1 0.5 + - - -
125A VAL* 3.4 8.3 + - - +
126A THR* 3.0 30.2 + - - -
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Residues in contact with HIS 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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121A PRO* 3.9 18.1 - - + +
122A SER* 1.3 77.4 - - - +
124A VAL* 1.3 78.3 + - + +
126A THR* 3.4 8.1 - - - +
127A MET* 3.3 22.9 + - - +
147A ALA* 2.8 37.2 + - + +
148A LEU* 5.0 0.2 - - - -
150A SER* 3.4 25.4 + - - -
151A GLU* 5.1 0.8 - - - +
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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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120A LEU* 4.6 9.6 - - + -
121A PRO* 2.7 19.4 + - + +
123A HIS* 1.3 96.7 - - + +
125A VAL* 1.3 64.1 + - - +
126A THR 3.0 1.6 - - - -
127A MET* 3.1 16.3 + - - +
128A LEU* 3.1 31.3 + - + +
144A ALA* 4.1 21.3 - - + +
147A ALA* 4.2 8.5 - - + +
148A LEU* 3.5 34.3 - - + -
185A VAL* 5.0 2.2 - - + -
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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
----------------------------------------------------------
120A LEU* 4.1 28.0 - - + +
121A PRO 3.2 14.3 + - - +
122A SER* 3.9 8.1 - - - +
124A VAL* 1.3 74.8 - - - +
126A THR* 1.3 64.5 + - - +
128A LEU* 3.4 4.1 + - - +
129A ASP* 3.0 34.9 + - - +
188A LYS* 3.4 29.2 - - + +
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Residues in contact with THR 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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122A SER* 3.0 21.5 + - - -
123A HIS* 3.4 9.4 - - - +
125A VAL* 1.3 83.2 - - - +
127A MET* 1.3 63.9 + - + +
129A ASP* 3.5 5.4 + - - +
130A ASN* 3.1 34.3 + - - +
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Residues in contact with MET 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 HIS* 3.3 13.0 + - - +
124A VAL* 3.1 7.5 + - - +
126A THR* 1.3 82.6 - - + +
128A LEU* 1.3 65.5 + - + +
130A ASN* 3.1 7.1 + - - +
131A PHE* 3.0 60.8 + - + -
143A ALA* 3.6 26.0 - - + +
144A ALA* 4.3 6.3 - - - -
147A ALA* 3.8 26.7 - - + -
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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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120A LEU* 4.7 3.4 - - + -
124A VAL* 3.1 35.1 + - + +
125A VAL* 3.7 4.9 - - - +
127A MET* 1.3 75.8 - - + +
129A ASP* 1.3 62.0 + - - +
131A PHE* 3.1 34.1 + - + +
140A GLN* 4.0 14.0 + - - +
144A ALA* 3.8 21.8 - - + -
185A VAL* 4.0 23.8 - - + +
188A LYS* 4.3 24.0 - - + -
189A ILE* 3.9 23.8 - - + -
192A ASN* 3.4 18.6 - - - +
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Residues in contact with ASP 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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125A VAL* 3.0 28.4 + - - +
126A THR* 3.8 6.0 - - - +
127A MET 3.3 0.2 - - - -
128A LEU* 1.3 76.6 - - - +
130A ASN* 1.3 61.0 + - - +
131A PHE 3.7 2.8 + - - +
188A LYS* 2.6 35.7 + - - -
192A ASN* 3.1 16.2 + - - +
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Residues in contact with ASN 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 THR* 3.1 30.3 + - - +
127A MET* 3.1 7.9 + - - +
129A ASP* 1.3 78.4 + - - +
131A PHE* 1.3 67.3 + - - +
132A PRO* 3.6 4.0 - - - +
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Residues in contact with PHE 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 MET* 3.0 58.9 + - + -
128A LEU* 3.1 23.7 + - + +
129A ASP 4.5 2.8 - - - +
130A ASN* 1.3 80.7 - - + +
132A PRO* 1.3 75.1 - - + +
133A THR* 3.8 3.3 + - - +
135A LEU* 3.7 24.0 - - + -
140A GLN* 3.4 57.4 - - + +
143A ALA* 3.9 11.4 - - + -
193A LEU* 6.0 0.2 - - - +
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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