Contacts of the helix formed by residues 135 - 143 (chain D) in PDB entry 1XBT
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 ALA 135 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100D GLN 5.0 3.0 + - - -
102D PHE 5.4 2.5 + - - +
103D PRO* 4.8 11.4 - - + +
105D ILE* 4.4 17.6 - - + +
106D VAL* 3.9 9.4 - - + +
134D GLY* 1.3 72.1 - - - -
136D ILE* 1.3 63.6 + - - +
137D LEU 3.3 2.7 - - - -
138D ASN* 3.0 41.2 + - - +
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Residues in contact with ILE 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D VAL* 4.3 7.2 - - + -
25D LEU* 4.0 14.8 - - + -
99D GLY* 4.2 6.7 - - - +
100D GLN* 4.1 15.0 - - + +
105D ILE* 4.6 13.4 - - + +
121D VAL* 4.4 2.2 - - + -
123D ALA* 3.5 29.4 - - + -
124D LEU 3.5 19.7 - - - +
125D ASP* 4.4 4.3 - - - +
133D PHE 3.5 17.0 - - - +
134D GLY 3.4 2.6 - - - -
135D ALA* 1.3 78.2 - - - +
137D LEU* 1.3 78.8 + - + +
139D LEU* 3.2 33.2 + - + +
140D VAL* 4.3 2.1 + - - +
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Residues in contact with LEU 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B LEU* 3.1 62.5 - - + +
140B VAL* 4.1 12.1 - - + -
141B PRO* 4.0 11.7 - - + -
25D LEU* 4.4 9.6 - - + -
125D ASP* 4.0 29.6 - - + +
132D PRO* 3.8 33.4 - - + +
134D GLY 5.2 0.8 + - - -
135D ALA 3.1 1.2 + - - -
136D ILE* 1.3 82.1 - - + +
138D ASN* 1.3 57.3 + - - +
139D LEU 3.0 5.6 - - - -
140D VAL* 3.1 24.7 + - + +
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Residues in contact with ASN 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B ARG 5.2 0.7 - - - +
132B PRO* 3.5 28.0 - - + +
106D VAL* 3.5 17.3 - - + +
135D ALA* 3.0 34.8 + - - +
137D LEU* 1.3 76.7 - - - +
139D LEU* 1.3 58.9 + - - +
140D VAL 3.3 0.2 - - - -
141D PRO* 3.4 12.8 - - - +
142D LEU* 3.3 19.0 - - - +
82G ARG* 5.6 1.1 + - - +
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Residues in contact with LEU 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D ILE* 4.4 9.9 - - + -
23D VAL* 3.8 26.9 - - + -
105D ILE* 4.0 19.1 - - + -
106D VAL* 4.0 23.1 - - + +
109D CYS* 3.8 24.5 - - + -
121D VAL* 4.0 22.7 - - + -
136D ILE* 3.2 24.8 + - + +
137D LEU 3.0 0.4 - - - -
138D ASN* 1.3 79.2 - - - +
140D VAL* 1.3 58.9 + - + +
142D LEU* 2.8 31.0 + - + +
143D ALA* 3.0 14.8 + - - +
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Residues in contact with VAL 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B LEU* 4.0 26.2 - - + -
125B ASP* 4.1 12.8 - - + +
137B LEU* 4.2 8.5 - - + -
140B VAL* 5.6 3.4 - - + -
148B LYS* 2.9 24.5 + - + +
23D VAL* 5.2 4.9 - - + -
25D LEU* 4.6 13.7 - - + -
136D ILE 4.7 2.2 - - - +
137D LEU* 3.1 30.7 + - + +
139D LEU* 1.3 76.5 - - + +
141D PRO* 1.3 66.5 - - + +
142D LEU 3.2 0.9 + - - -
143D ALA* 3.3 8.1 + - - +
146D VAL* 4.2 26.0 - - + -
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Residues in contact with PRO 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B ASP* 3.6 30.5 - - - +
126B GLY* 3.9 13.1 - - - -
130B ARG* 3.5 33.8 - - - +
131B LYS 4.0 0.2 - - - -
132B PRO* 3.9 16.8 - - + -
137B LEU* 3.9 7.9 - - + -
148B LYS* 4.4 1.2 + - - -
162B TYR* 3.3 24.1 - - - -
137D LEU 3.4 12.1 - - - +
138D ASN 3.4 11.9 - - - +
140D VAL* 1.3 93.9 - - + +
142D LEU* 1.3 56.7 + - - +
143D ALA 3.5 0.4 - - - -
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Residues in contact with LEU 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B ARG* 3.4 52.8 + - + +
162B TYR* 2.6 22.6 + - - -
186B ARG* 2.8 18.5 + - - -
21D ILE* 4.0 7.9 - - + +
106D VAL* 3.7 27.4 - - + -
110D GLU* 3.7 19.3 - - + +
138D ASN 3.3 21.3 - - - +
139D LEU* 2.8 18.2 + - + +
141D PRO* 1.3 76.3 - - - +
143D ALA* 1.3 56.3 + - - +
82G ARG* 3.8 18.8 - - - +
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Residues in contact with ALA 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B LYS* 3.0 27.2 + - - -
161B ALA* 3.7 3.8 - - - +
162B TYR* 3.6 2.5 - - - -
21D ILE* 3.6 17.9 - - + +
23D VAL* 3.9 12.3 - - + -
139D LEU 3.0 13.0 + - - +
140D VAL 3.3 2.1 + - - +
142D LEU* 1.3 80.2 - - - +
144D GLU* 1.3 60.3 + - - +
145D SER 3.8 3.6 - - - +
146D VAL* 3.7 26.0 - - + -
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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