Contacts of the helix formed by residues 129 - 140 (chain Y) 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 GLY 129 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128Y ASP* 1.3 79.6 + - - +
130Y LEU* 1.3 54.4 + - - +
131Y SER* 2.6 19.6 + - - -
132Y GLU* 2.8 41.6 + - - +
133Y ARG* 3.9 5.4 + - - +
176Y ILE* 5.9 3.6 - - - +
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Residues in contact with LEU 130 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108Y LEU* 4.3 21.0 - - + +
128Y ASP 3.0 14.0 - - - +
129Y GLY* 1.3 76.9 - - - +
131Y SER* 1.3 56.8 + - - +
132Y GLU 3.3 0.4 - - - -
133Y ARG* 3.3 31.5 + - - +
134Y CYS* 3.0 41.1 + - - -
147Y TRP* 3.4 40.6 - - + -
173Y TYR* 4.4 9.0 - - + -
176Y ILE* 3.3 39.4 - - + +
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Residues in contact with SER 131 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129Y GLY* 2.6 5.7 - - - -
130Y LEU* 1.3 79.8 - - - +
132Y GLU* 1.3 80.0 + - - +
134Y CYS 3.3 4.9 + - - -
135Y ALA* 3.4 0.9 + - - +
176Y ILE* 3.4 27.1 - - - +
179Y GLN* 5.7 1.6 - - - +
180Y ASN* 3.0 37.7 + - - +
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Residues in contact with GLU 132 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128Y ASP 4.6 0.2 - - - +
129Y GLY* 2.8 32.8 + - - +
131Y SER* 1.3 95.1 + - - +
133Y ARG* 1.3 65.1 + - + +
135Y ALA* 3.6 7.1 + - - +
136Y GLN* 3.5 15.2 + - - +
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Residues in contact with ARG 133 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80Y HIS* 4.6 11.9 + - - -
107Y LYS 5.4 0.4 + - - -
108Y LEU* 3.0 30.2 + - + -
109Y ASP* 4.9 8.1 + - - +
128Y ASP 5.5 1.6 - - - -
129Y GLY 3.9 4.0 - - - +
130Y LEU* 3.3 33.2 - - - +
132Y GLU* 1.3 76.4 - - + +
134Y CYS* 1.3 67.0 + - - +
136Y GLN* 2.8 19.6 + - - +
137Y TYR* 2.8 49.6 + - + -
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Residues in contact with CYS 134 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108Y LEU* 3.5 31.4 - - - -
130Y LEU* 3.0 31.8 + - - -
131Y SER 3.5 5.2 - - - +
132Y GLU 3.3 0.2 - - - -
133Y ARG* 1.3 75.0 - - - +
135Y ALA* 1.3 66.8 + - - +
136Y GLN 2.7 1.9 + - - -
137Y TYR* 2.7 20.3 + - - +
138Y LYS* 2.7 12.6 + - - +
176Y ILE* 4.6 0.2 - - - -
177Y CYS* 4.4 10.5 - - - -
180Y ASN* 3.4 24.9 - - + +
182Y LEU* 4.1 17.6 - - + +
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Residues in contact with ALA 135 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131Y SER 3.4 3.9 + - - +
132Y GLU* 3.8 10.1 - - - +
134Y CYS* 1.3 78.6 - - - +
136Y GLN* 1.3 57.3 + - - +
138Y LYS* 3.2 10.8 - - - +
139Y LYS* 3.0 38.7 + - - +
180Y ASN* 3.5 23.1 - - + +
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Residues in contact with GLN 136 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84Y TYR* 5.5 3.6 - - - +
132Y GLU 3.5 6.7 + - - +
133Y ARG* 2.8 18.4 + - - +
134Y CYS 2.7 4.2 + - - -
135Y ALA* 1.3 72.7 - - - +
137Y TYR* 1.3 53.6 + - + +
138Y LYS 2.9 4.7 - - - -
139Y LYS* 2.8 47.3 + - - +
140Y ASP* 3.0 31.0 - - - +
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Residues in contact with TYR 137 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80Y HIS* 3.5 29.1 + + - +
83Y LEU* 3.5 19.3 - - + -
84Y TYR* 4.1 12.6 - - - -
106Y ILE* 3.3 41.6 - - + +
107Y LYS 4.5 3.9 + - - -
108Y LEU* 3.8 26.0 - - + -
133Y ARG* 2.8 62.1 + - + -
134Y CYS* 2.7 10.0 + - - +
136Y GLN* 1.3 73.4 - - + +
138Y LYS* 1.3 56.9 + - - +
140Y ASP* 3.5 6.8 + - - +
141Y GLY 3.5 3.1 + - - -
142Y VAL* 2.9 40.7 + - + +
182Y LEU* 4.9 2.7 - - + -
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Residues in contact with LYS 138 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14Y GLU* 2.8 30.3 + - - -
18Y ILE* 4.3 0.6 - - - +
134Y CYS 2.7 9.9 + - - +
135Y ALA* 3.2 14.1 - - - +
137Y TYR* 1.3 77.0 - - - +
139Y LYS* 1.3 65.1 + - + +
140Y ASP 3.1 0.2 - - - -
141Y GLY* 3.3 12.5 + - - -
142Y VAL 3.5 6.1 - - - +
143Y ASP* 2.8 29.6 + - - +
180Y ASN 3.9 14.6 - - - +
181Y GLY* 2.8 31.0 + - - +
182Y LEU* 3.7 6.9 - - + +
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Residues in contact with LYS 139 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135Y ALA* 3.0 21.3 + - - +
136Y GLN* 2.8 35.4 + - - +
138Y LYS* 1.3 79.5 - - + +
140Y ASP* 1.3 64.3 + - - +
141Y GLY 3.5 0.5 + - - -
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Residues in contact with ASP 140 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83Y LEU* 4.4 10.1 - - + -
84Y TYR* 3.0 36.6 + - - -
94Y ARG* 2.5 55.0 + - - +
98Y LYS* 5.2 1.1 + - - -
136Y GLN* 3.0 28.2 + - - +
137Y TYR* 3.9 9.4 - - - +
138Y LYS 3.1 0.8 - - - -
139Y LYS* 1.3 85.9 - - - +
141Y GLY* 1.3 51.8 + - - +
142Y VAL* 4.9 0.4 - - - -
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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