Contacts of the helix formed by residues 127 - 135 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38B TYR* 5.7 2.9 - - - +
39B SER* 5.8 1.0 + - - -
40B ASN* 3.2 25.5 + - - +
118B PHE* 4.5 0.3 - - - -
122B LEU* 4.4 2.8 - - - +
125B GLY 3.7 1.9 + - - -
126B ALA* 1.3 73.6 - - - +
128B ILE* 1.3 68.9 + - - +
129B SER* 2.6 38.0 + - - +
130B MET* 3.0 29.1 + - + +
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Residues in contact with ILE 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B ILE* 4.2 22.9 - - + -
38B TYR* 3.9 37.9 - - + -
40B ASN* 3.5 27.1 - - + +
43B ILE* 4.3 5.2 - - + -
118B PHE* 4.0 21.5 - - + -
122B LEU* 4.1 16.5 - - + +
126B ALA 3.8 2.2 + - - -
127B ASP* 1.3 78.4 + - - +
129B SER* 1.4 58.1 + - - +
130B MET 3.1 0.4 - - - -
131B ILE* 3.0 39.9 + - + +
140B SER* 5.8 0.2 - - - -
143B LEU* 3.7 28.0 - - + -
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Residues in contact with SER 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B ASN* 3.6 14.7 + - - -
43B ILE* 3.8 26.0 - - - +
46B ARG* 2.8 28.6 - - - +
127B ASP* 2.6 29.7 + - - +
128B ILE* 1.4 77.4 - - - +
130B MET* 1.3 64.3 + - - +
131B ILE* 3.2 1.6 - - - +
132B GLY 4.3 1.4 - - - -
133B GLN* 5.2 2.8 - - - -
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Residues in contact with MET 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B PHE* 3.9 11.0 - - + -
126B ALA* 4.6 8.3 - - + -
127B ASP* 3.0 28.3 + - + +
129B SER* 1.3 80.6 + - - +
131B ILE* 1.4 64.6 + - - +
132B GLY 3.3 0.7 - - - -
133B GLN* 3.0 56.6 + - + +
134B PHE* 3.4 24.6 - - + -
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Residues in contact with ILE 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B LEU* 4.5 1.3 - - + -
33B ILE* 3.7 26.2 - - + -
43B ILE* 3.9 20.4 - - + -
47B GLU* 4.0 13.7 - - + +
118B PHE* 3.5 35.2 - - + -
128B ILE* 3.0 23.6 + - + +
129B SER 3.2 0.9 - - - +
130B MET* 1.4 76.8 - - - +
132B GLY* 1.3 65.0 + - - +
134B PHE* 3.1 14.9 + - - +
135B GLY 3.6 6.1 + - - -
136B VAL* 3.4 37.4 + - + +
137B GLY* 4.1 1.8 - - - -
140B SER* 4.0 15.3 - - - +
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Residues in contact with GLY 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B GLU* 3.2 30.7 + - - -
129B SER 4.3 1.2 - - - -
130B MET 3.2 1.0 + - - -
131B ILE* 1.3 83.2 - - - +
133B GLN* 1.4 60.5 + - - +
135B GLY* 3.2 13.9 + - - -
137B GLY* 4.2 6.5 - - - -
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Residues in contact with GLN 133 (chain B).
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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129B SER 5.2 2.7 - - - -
130B MET* 3.0 52.6 + - + +
132B GLY* 1.4 75.0 - - - +
134B PHE* 1.3 65.7 + - + +
135B GLY 3.4 0.6 + - - -
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Residues in contact with PHE 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B LYS* 5.7 0.5 - - - +
114B GLY* 3.5 34.3 + - - +
117B ALA* 3.8 17.0 - - + -
118B PHE* 3.5 55.9 - + + -
121B ALA* 4.0 19.3 - - + -
130B MET* 3.4 39.3 - - + -
131B ILE 3.1 8.8 + - - +
133B GLN* 1.3 82.1 - - + +
135B GLY* 1.3 59.3 + - - +
136B VAL* 3.3 6.0 + - + +
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Residues in contact with GLY 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B LYS* 3.6 18.9 + - - -
132B GLY 3.2 14.3 + - - -
133B GLN 3.4 1.8 + - - -
134B PHE* 1.3 76.4 - - - +
136B VAL* 1.4 59.7 + - - +
137B GLY 3.6 2.5 - - - -
1224B GOL 3.3 16.8 + - - -
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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