Contacts of the helix formed by residues 135 - 143 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100C GLN 5.0 2.0 + - - -
102C PHE 5.6 1.5 + - - +
103C PRO* 5.0 11.0 - - + +
105C ILE* 4.5 11.9 - - + +
106C VAL* 3.7 15.7 - - + +
133C PHE 3.5 0.2 + - - -
134C GLY* 1.3 71.4 - - - -
136C ILE* 1.3 64.1 + - - +
137C LEU 3.3 2.9 - - - -
138C ASN* 3.0 38.3 + - - +
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Residues in contact with ILE 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C VAL* 5.0 7.3 - - + +
25C LEU* 4.4 8.6 - - + +
99C GLY 3.8 4.0 - - - +
100C GLN* 3.7 26.9 - - - +
105C ILE* 4.3 11.3 - - + +
121C VAL* 4.1 9.4 - - + -
123C ALA* 3.7 18.4 - - + -
124C LEU 3.5 21.8 - - - +
125C ASP* 4.4 2.7 - - - +
133C PHE 3.5 15.0 + - - +
134C GLY 3.3 2.8 - - - -
135C ALA* 1.3 76.4 - - - +
137C LEU* 1.3 74.6 + - + +
139C LEU* 3.1 50.7 + - + +
140C VAL* 4.3 1.9 + - - +
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Residues in contact with LEU 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A LEU* 3.2 56.8 - - + +
138A ASN* 5.3 0.2 - - - +
140A VAL* 4.2 21.5 - - + -
141A PRO* 3.9 12.8 - - + -
25C LEU* 4.5 8.7 - - + -
125C ASP* 4.2 13.7 - - + +
132C PRO* 3.7 33.4 - - + -
134C GLY 5.1 0.6 + - - -
135C ALA 3.1 1.4 + - - -
136C ILE* 1.3 86.3 - - + +
138C ASN* 1.3 60.4 + - - +
139C LEU 3.0 5.6 - - - -
140C VAL* 3.1 21.9 + - + +
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Residues in contact with ASN 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A ARG 5.4 0.3 - - - +
132A PRO* 3.3 28.0 - - + +
137A LEU* 5.5 0.2 - - - +
106C VAL* 3.7 17.8 - - + +
135C ALA* 3.0 33.2 + - - +
137C LEU* 1.3 77.4 - - - +
139C LEU* 1.3 59.5 + - - +
140C VAL 3.3 0.2 - - - -
141C PRO* 3.4 12.8 - - - +
142C LEU* 3.4 18.2 - - - +
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Residues in contact with LEU 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C ILE* 4.2 15.3 - - + -
23C VAL* 4.0 21.8 - - + -
105C ILE* 4.2 5.6 - - + -
106C VAL* 4.2 21.7 - - + +
109C CYS* 3.8 28.5 - - + -
121C VAL* 3.9 27.6 - - + -
135C ALA 4.2 0.6 + - - -
136C ILE* 3.1 33.4 + - + +
137C LEU 3.0 0.6 - - - -
138C ASN* 1.3 79.0 - - - +
140C VAL* 1.3 57.5 + - - +
141C PRO 3.5 0.2 - - - -
142C LEU* 2.9 28.1 + - + +
143C ALA* 3.0 15.4 + - - +
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Residues in contact with VAL 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A LEU* 4.1 12.8 - - + -
125A ASP* 4.0 15.0 - - + +
137A LEU* 3.8 23.8 - - + -
140A VAL* 5.4 2.5 - - + -
148A LYS* 3.1 20.7 + - + -
23C VAL* 5.2 5.4 - - + -
25C LEU* 4.5 14.1 - - + -
136C ILE 4.9 1.8 - - - +
137C LEU* 3.1 22.2 + - + +
139C LEU* 1.3 75.6 - - - +
141C PRO* 1.3 67.8 - - + +
142C LEU 3.2 0.9 + - - -
143C ALA* 3.2 8.7 + - - +
146C VAL* 4.2 33.5 - - + +
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Residues in contact with PRO 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A ASP* 3.3 30.4 - - - +
126A GLY* 3.9 13.1 - - - -
130A ARG* 3.5 33.1 - - - +
131A LYS 4.0 0.2 - - - -
132A PRO* 3.7 19.5 - - + -
137A LEU* 3.8 7.9 - - + -
148A LYS* 4.3 1.3 + - - -
162A TYR* 3.4 21.6 - - - -
137C LEU 3.4 9.9 - - - +
138C ASN 3.4 13.0 - - - +
140C VAL* 1.3 93.4 - - + +
142C LEU* 1.3 55.8 + - - +
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Residues in contact with LEU 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A GLN 5.6 0.2 - - - +
130A ARG* 3.5 51.5 + - + +
162A TYR* 2.7 23.5 + - - -
186A ARG* 3.0 14.4 + - - -
21C ILE* 3.8 7.4 - - + +
106C VAL* 3.8 25.4 - - + -
110C GLU* 3.6 24.5 - - + +
138C ASN 3.4 21.1 - - - +
139C LEU* 2.9 17.2 + - + +
141C PRO* 1.3 77.8 - - - +
143C ALA* 1.3 56.6 + - - +
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Residues in contact with ALA 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A LYS* 2.8 29.6 + - - -
161A ALA* 3.9 0.2 - - - +
162A TYR* 3.8 5.4 - - - -
21C ILE* 3.6 18.6 - - + +
23C VAL* 3.8 13.9 - - + -
139C LEU 3.0 12.5 + - - +
140C VAL 3.2 6.6 + - - +
142C LEU* 1.3 80.1 - - - +
144C GLU* 1.3 62.0 + - - +
145C SER 3.8 3.6 - - - +
146C VAL* 3.7 20.4 - - + -
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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