Contacts of the helix formed by residues 127 - 135 (chain A) in PDB entry 2XJJ
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 ASP 127 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A TYR* 6.0 0.4 - - - -
39A SER* 5.9 1.2 + - - -
40A ASN* 3.1 30.3 + - - +
118A PHE* 4.4 0.2 - - - -
122A LEU* 4.2 3.3 - - - +
125A GLY 3.7 2.1 + - - -
126A ALA* 1.3 76.3 - - - +
128A ILE* 1.4 64.4 + - - +
129A SER* 2.7 36.1 + - - +
130A MET* 3.1 28.0 + - + +
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Residues in contact with ILE 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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33A ILE* 4.3 14.6 - - + -
38A TYR* 3.8 41.4 - - + -
40A ASN* 3.4 29.8 - - + +
43A ILE* 4.3 2.5 - - + -
118A PHE* 3.9 20.9 - - + -
122A LEU* 4.0 21.2 - - + +
126A ALA 3.9 1.6 + - - -
127A ASP* 1.4 72.9 + - - +
129A SER* 1.4 57.0 + - - +
130A MET 3.0 5.4 - - - -
131A ILE* 3.1 39.8 + - + +
143A LEU* 3.8 29.8 - - + -
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Residues in contact with SER 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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40A ASN* 3.7 13.2 + - - -
43A ILE* 3.8 20.2 - - - +
46A ARG* 2.8 34.8 + - - +
127A ASP* 2.7 30.2 + - - +
128A ILE* 1.4 76.8 - - - +
130A MET* 1.4 71.5 + - - +
131A ILE 3.2 1.4 - - - +
132A GLY* 4.2 1.7 - - - -
133A GLN* 5.2 1.9 - - - -
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Residues in contact with MET 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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118A PHE* 3.8 11.2 - - + -
126A ALA* 4.5 9.6 - - + -
127A ASP* 3.4 26.9 - - + +
128A ILE 3.0 1.4 - - - -
129A SER* 1.4 87.5 + - - +
131A ILE* 1.4 63.4 + - - +
132A GLY 3.3 0.9 - - - -
133A GLN* 3.0 49.6 + - - +
134A PHE* 3.4 22.7 - - + -
64B LEU* 4.8 13.9 - - - +
65B THR* 4.9 7.4 - - + -
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Residues in contact with ILE 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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29A LEU* 4.8 0.7 - - + -
33A ILE* 3.7 29.6 - - + -
43A ILE* 3.9 20.2 - - + -
47A GLU* 4.0 14.1 - - + +
118A PHE* 3.5 30.7 - - + -
128A ILE* 3.1 22.8 + - + +
129A SER 3.2 1.1 - - - +
130A MET* 1.4 77.4 - - - +
132A GLY* 1.3 63.9 + - - +
134A PHE* 3.1 13.5 + - - +
135A GLY 3.5 6.8 + - - -
136A VAL* 3.4 38.1 + - + +
137A GLY* 4.1 1.8 - - - -
139A TYR* 4.6 0.2 - - + -
140A SER* 3.8 15.9 - - - +
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Residues in contact with GLY 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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47A GLU* 3.2 31.7 + - - -
129A SER 4.2 1.4 - - - -
130A MET 3.2 1.2 + - - -
131A ILE* 1.3 82.8 - - - +
133A GLN* 1.3 57.0 + - - +
135A GLY* 3.0 19.1 + - - -
137A GLY* 4.3 4.7 - - - -
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Residues in contact with GLN 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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129A SER 5.2 1.9 - - - -
130A MET* 3.0 48.0 + - - +
132A GLY* 1.3 74.1 - - - +
134A PHE* 1.3 62.3 + - + +
135A GLY 3.3 1.2 + - - -
60B ARG* 4.9 4.0 + - - -
61B TYR* 4.3 5.0 - - - -
64B LEU* 3.4 41.9 - - + +
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Residues in contact with PHE 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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112A LYS* 5.6 0.3 - - - +
114A GLY* 3.5 29.5 + - - +
117A ALA* 3.7 11.2 - - + -
118A PHE* 3.4 55.0 - + + -
121A ALA* 4.0 8.5 - - + -
130A MET* 3.4 27.4 - - + -
131A ILE 3.1 8.2 + - - +
132A GLY 3.1 0.8 - - - -
133A GLN* 1.3 77.3 - - + +
135A GLY* 1.3 61.7 + - - +
136A VAL* 3.3 6.3 + - + +
61B TYR* 3.7 47.6 + + + -
64B LEU* 3.7 24.2 - - + -
65B THR* 4.0 17.3 - - + -
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Residues in contact with GLY 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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112A LYS* 3.5 19.5 + - - -
132A GLY 3.0 14.7 + - - -
133A GLN 3.3 2.0 + - - -
134A PHE* 1.3 78.0 - - - +
136A VAL* 1.3 59.1 + - - +
137A GLY 3.7 2.0 - - - -
1224A GOL 3.2 17.4 + - - -
61B TYR* 5.8 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