Contacts of the helix formed by residues 130 - 141 (chain X) in PDB entry 1XDM
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 LEU 130 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108X LEU* 3.6 39.9 - - + +
131X SER* 1.3 66.0 + - - +
132X GLU* 2.4 32.2 + - - -
133X ARG* 2.6 50.0 + - - +
134X CYS* 3.1 8.4 + - - -
147X TRP* 4.7 9.2 - - + -
173X TYR* 4.3 28.5 - - + -
176X ILE* 3.4 34.5 - - + -
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Residues in contact with SER 131 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130X LEU* 1.3 78.8 - - - +
132X GLU* 1.3 72.3 + - - +
134X CYS* 3.7 0.4 - - - -
135X ALA* 3.0 24.3 + - - +
176X ILE* 3.7 20.0 - - - +
179X GLN* 5.6 2.1 - - - +
180X ASN* 3.1 32.4 + - - +
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Residues in contact with GLU 132 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130X LEU 2.4 38.5 + - - +
131X SER* 1.3 87.0 + - - +
133X ARG* 1.3 65.8 + - + +
135X ALA* 4.0 3.5 - - - +
136X GLN* 3.2 21.4 + - - +
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Residues in contact with ARG 133 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108X LEU* 3.3 38.0 + - + +
109X ASP* 3.6 9.1 - - - +
130X LEU* 2.6 43.2 + - + +
132X GLU* 1.3 79.1 - - + +
134X CYS* 1.3 55.0 + - - +
136X GLN* 3.6 6.6 - - - +
137X TYR* 2.9 58.3 + - + +
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Residues in contact with CYS 134 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108X LEU* 3.0 37.7 - - - -
130X LEU* 3.1 11.3 + - - -
131X SER 3.5 2.0 - - - +
133X ARG* 1.3 72.1 - - - +
135X ALA* 1.3 61.6 + - - +
136X GLN 2.8 0.9 - - - -
137X TYR* 2.5 34.2 + - - +
138X LYS* 2.9 11.1 + - - -
176X ILE* 4.2 12.1 - - - -
177X CYS* 4.3 6.5 - - - -
180X ASN* 3.2 31.4 - - + +
182X LEU* 4.2 14.5 - - + +
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Residues in contact with ALA 135 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131X SER* 3.0 10.7 + - - +
132X GLU* 4.0 4.0 - - - +
134X CYS* 1.3 76.2 - - - +
136X GLN* 1.3 63.3 + - - +
138X LYS* 3.5 8.3 - - - +
139X LYS* 3.4 27.1 + - - +
180X ASN* 3.0 29.0 + - - +
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Residues in contact with GLN 136 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84X TYR* 4.2 7.5 + - - +
132X GLU 3.2 15.6 + - - +
133X ARG* 3.6 7.9 - - - +
134X CYS 2.6 4.0 + - - -
135X ALA* 1.3 74.9 - - - +
137X TYR* 1.3 62.4 + - + +
139X LYS* 2.7 49.3 + - - +
140X ASP* 2.7 44.0 + - - +
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Residues in contact with TYR 137 (chain X).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80X HIS* 3.7 31.2 + + - +
83X LEU* 3.8 13.9 - - + -
84X TYR* 3.5 29.8 - + - -
106X ILE* 3.6 33.7 - - + +
107X LYS 4.5 3.7 + - - -
108X LEU* 3.3 36.7 - - + -
133X ARG* 2.9 36.9 + - + +
134X CYS* 2.5 12.0 + - - +
136X GLN* 1.3 78.6 - - + +
138X LYS* 1.3 61.8 + - - +
140X ASP* 3.2 8.4 + - - +
141X GLY 3.0 17.8 + - - -
142X VAL* 3.0 13.0 + - + +
182X LEU* 5.0 2.0 - - + -
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Residues in contact with LYS 138 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14X GLU* 3.3 30.8 + - - -
18X ILE* 3.5 9.7 - - - +
134X CYS 2.9 8.1 + - - +
135X ALA 3.5 10.1 - - - +
137X TYR* 1.3 75.5 - - - +
139X LYS* 1.3 66.4 + - - +
141X GLY* 3.1 12.1 + - - -
142X VAL* 2.8 23.0 - - - +
143X ASP* 2.7 29.6 + - - +
180X ASN 3.6 19.7 - - - +
181X GLY* 3.3 14.0 + - - +
182X LEU* 3.5 14.5 - - + +
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Residues in contact with LYS 139 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135X ALA* 3.4 20.0 + - - +
136X GLN* 2.7 30.9 + - - +
138X LYS* 1.3 75.9 - - - +
140X ASP* 1.3 67.7 + - - +
141X GLY* 2.9 3.3 + - - -
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Residues in contact with ASP 140 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83X LEU* 4.5 5.6 - - + -
84X TYR* 2.6 42.0 + - + +
94X ARG* 2.8 40.9 + - - +
98X LYS* 4.6 0.2 + - - -
136X GLN* 2.7 35.7 + - - +
137X TYR* 3.2 12.3 + - - +
139X LYS* 1.3 76.1 - - - +
141X GLY* 1.3 56.7 + - - +
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Residues in contact with GLY 141 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94X ARG* 4.1 4.0 - - - -
98X LYS* 2.6 42.1 + - - -
104X VAL* 3.9 4.2 - - - +
137X TYR 3.0 1.0 + - - -
138X LYS 3.1 5.1 + - - -
139X LYS 2.9 7.6 + - - -
140X ASP* 1.3 80.0 - - - +
142X VAL* 1.3 67.9 + - - +
143X ASP* 3.8 6.0 - - - +
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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