Contacts of the helix formed by residues 128 - 138 (chain A) in PDB entry 2XGZ
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 128 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A ASN 4.8 0.9 - - - +
127A VAL* 1.3 91.2 - - + +
129A LEU* 1.3 67.3 + - - +
130A TYR* 3.3 42.2 - - + +
131A LYS* 3.0 31.7 + - + +
132A HIS 3.3 6.8 + - - -
385A ASP* 5.2 0.2 - - - +
418A GLU* 3.7 13.5 - - - +
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Residues in contact with LEU 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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118A SER* 3.7 35.9 - - - +
119A ARG* 4.1 20.4 - - + +
122A ALA* 3.8 13.1 - - + +
127A VAL 3.7 0.8 + - - -
128A PRO* 1.3 72.6 - - - +
130A TYR* 1.3 58.5 + - - +
132A HIS* 3.0 6.2 + - + +
133A LEU* 2.8 47.2 + - + +
382A PHE* 3.7 31.0 - - + +
385A ASP* 3.4 31.4 + - + +
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Residues in contact with TYR 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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128A PRO* 3.4 20.1 - - + +
129A LEU* 1.3 75.0 - - - +
131A LYS* 1.3 78.9 + - + +
133A LEU* 4.4 1.3 - - - -
134A ALA* 3.0 28.6 + - - +
144A TYR* 4.1 7.5 - + - -
385A ASP* 3.1 46.9 + - - +
388A VAL* 4.0 25.1 - - + -
389A GLY* 3.5 4.9 - - - -
411A GLN* 5.9 0.2 - - - -
415A ILE* 3.7 30.5 - - + -
418A GLU* 2.8 43.1 + - - +
419A LEU* 3.9 28.1 - - + +
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Residues in contact with LYS 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 VAL* 4.0 16.8 - - + -
128A PRO* 3.0 32.8 + - + +
130A TYR* 1.3 102.3 - - + +
132A HIS* 1.3 62.1 + - - +
134A ALA* 3.4 3.9 + - - +
135A ASP* 3.1 30.2 + - - +
144A TYR* 3.3 31.4 - - - +
419A LEU* 5.0 4.5 - - - -
1441A MG 4.1 0.7 - - - -
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Residues in contact with HIS 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A VAL 4.8 1.4 + - - -
84A LYS* 4.0 9.6 + - + -
86A GLN* 4.9 0.4 + - - -
118A SER* 3.4 29.5 + - - -
121A ALA* 3.5 23.7 - - + +
122A ALA* 3.8 22.0 - - + -
125A LYS* 2.9 33.0 + - + +
127A VAL* 3.8 8.8 - - + +
128A PRO 3.3 2.2 + - - -
129A LEU* 3.0 8.4 + - + +
131A LYS* 1.3 81.1 - - - +
133A LEU* 1.3 59.8 + - + +
135A ASP* 3.1 10.4 + - - +
136A LEU* 2.9 65.9 + - + +
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Residues in contact with LEU 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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118A SER* 4.2 2.9 - - - +
129A LEU* 2.8 39.9 + - + +
130A TYR* 3.9 4.7 - - - +
132A HIS* 1.3 74.4 - - + +
134A ALA* 1.3 58.6 + - - +
136A LEU* 3.4 14.0 + - + +
137A SER* 3.0 30.4 + - - -
352A LEU* 3.8 32.1 - - + -
356A ILE* 4.9 3.7 - - + +
382A PHE* 3.8 18.6 - - + -
385A ASP* 3.7 5.8 - - + -
386A LEU* 3.6 39.9 - - + +
389A GLY* 4.0 12.2 - - - -
390A LEU* 5.3 0.7 - - + +
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Residues in contact with ALA 134 (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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130A TYR 3.0 18.9 + - - +
131A LYS* 3.6 5.2 - - - +
132A HIS 3.3 0.2 - - - -
133A LEU* 1.3 74.2 - - - +
135A ASP* 1.3 57.7 + - - +
137A SER* 3.4 0.4 + - - -
138A LYS* 2.9 25.1 + - - -
139A SER* 3.1 26.6 + - - +
141A THR* 3.8 23.1 - - + -
144A TYR* 4.0 10.3 - - + -
389A GLY* 3.2 16.4 - - - +
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Residues in contact with ASP 135 (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 LYS* 2.7 34.9 + - - +
127A VAL* 5.2 2.1 - - - +
131A LYS* 3.1 13.3 + - - +
132A HIS* 3.1 10.0 + - + +
134A ALA* 1.3 73.2 - - - +
136A LEU* 1.3 65.3 + - + +
138A LYS* 3.2 18.3 + - - +
1441A MG 2.2 31.9 - - - -
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Residues in contact with LEU 136 (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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84A LYS 3.8 14.4 - - - +
86A GLN* 3.6 37.0 - - + +
87A LYS* 5.8 3.6 + - - -
132A HIS* 2.9 51.5 + - + +
133A LEU* 3.4 11.9 + - + +
135A ASP* 1.3 76.5 - - + +
137A SER* 1.3 59.8 + - - +
138A LYS* 3.7 4.2 + - - +
352A LEU* 3.9 17.9 - - + -
356A ILE* 3.8 20.4 - - + +
360A GLN* 4.2 3.8 + - - -
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Residues in contact with SER 137 (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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133A LEU 3.0 18.0 + - - -
134A ALA 3.4 3.6 + - - -
136A LEU* 1.3 76.1 - - - +
138A LYS* 1.3 66.0 + - - +
139A SER* 3.3 7.2 + - - -
356A ILE* 3.9 11.2 - - - -
360A GLN* 3.0 27.1 + - - +
389A GLY 3.2 18.4 + - - -
390A LEU* 3.6 25.9 - - - +
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Residues in contact with LYS 138 (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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87A LYS* 6.2 2.0 - - - +
134A ALA 2.9 7.6 + - - -
135A ASP* 3.2 12.4 + - - +
136A LEU 4.4 4.5 - - - +
137A SER* 1.3 80.0 - - - +
139A SER* 1.3 64.6 + - - +
140A LYS 3.9 0.7 + - - -
360A GLN* 4.5 13.0 - - - +
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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