Contacts of the helix formed by residues 135 - 143 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A GLN 4.9 2.8 + - - -
102A PHE 5.4 2.1 + - - +
103A PRO* 4.8 13.0 - - + +
105A ILE* 4.4 11.4 - - + +
106A VAL* 3.7 16.0 - - + +
134A GLY* 1.3 73.0 - - - -
136A ILE* 1.3 65.5 + - - +
137A LEU 3.3 2.5 - - - -
138A ASN* 3.0 38.4 + - - +
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Residues in contact with ILE 136 (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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23A VAL* 4.2 9.0 - - + -
25A LEU* 3.8 16.4 - - + -
99A GLY* 4.3 6.5 - - - +
100A GLN* 4.1 13.9 - - + +
105A ILE* 4.5 7.7 - - + +
121A VAL* 4.8 1.1 - - + -
123A ALA* 3.5 29.6 - - + -
124A LEU 3.5 19.7 - - - +
125A ASP* 4.4 6.5 - - - +
133A PHE 3.4 19.1 - - - +
134A GLY 3.3 2.0 - - - -
135A ALA* 1.3 77.7 - - - +
137A LEU* 1.3 74.0 + - + +
139A LEU* 3.1 38.1 + - + +
140A VAL* 4.3 1.6 + - - +
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Residues in contact with LEU 137 (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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25A LEU* 4.4 8.3 - - + -
125A ASP* 4.4 9.0 - - + +
132A PRO* 3.8 30.9 - - + +
134A GLY 5.1 0.6 + - - -
135A ALA 3.1 1.2 + - - -
136A ILE* 1.3 81.5 - - + +
138A ASN* 1.3 57.7 + - - +
139A LEU 3.0 5.2 - - - -
140A VAL* 3.0 35.6 + - + +
137C LEU* 3.2 52.8 - - + +
140C VAL* 3.8 27.8 - - + -
141C PRO* 3.8 16.4 - - + -
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Residues in contact with ASN 138 (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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106A VAL* 3.8 18.5 - - + +
135A ALA* 3.0 33.5 + - - +
137A LEU* 1.3 77.1 - - - +
139A LEU* 1.3 58.9 + - - +
140A VAL 3.3 0.2 - - - -
141A PRO* 3.4 13.6 - - - +
142A LEU* 3.6 17.5 - - - +
130C ARG 5.4 0.5 - - - +
132C PRO* 3.4 26.8 - - + +
137C LEU* 5.3 0.3 - - - +
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Residues in contact with LEU 139 (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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21A ILE* 4.5 9.4 - - + -
23A VAL* 4.1 22.2 - - + -
105A ILE* 3.7 26.5 - - + -
106A VAL* 4.1 21.8 - - + -
109A CYS* 3.8 25.8 - - + -
121A VAL* 4.2 15.3 - - + -
135A ALA 4.2 0.4 + - - -
136A ILE* 3.1 30.6 + - + +
137A LEU 3.0 0.8 - - - -
138A ASN* 1.3 78.2 - - - +
140A VAL* 1.3 58.4 + - + +
142A LEU* 2.9 31.0 + - + +
143A ALA* 3.0 15.5 + - - +
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Residues in contact with VAL 140 (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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23A VAL* 5.4 2.9 - - + -
25A LEU* 4.5 7.2 - - + -
136A ILE 4.9 1.3 - - - +
137A LEU* 3.0 33.6 + - + +
139A LEU* 1.3 75.0 - - + +
141A PRO* 1.3 68.6 - - + +
142A LEU 3.2 1.0 + - - -
143A ALA* 3.2 8.5 + - - +
146A VAL* 4.2 33.4 - - + -
25C LEU* 3.8 28.7 - - + -
125C ASP* 4.0 12.3 - - + +
137C LEU* 4.2 8.3 - - + -
140C VAL* 5.4 2.7 - - + -
148C LYS* 3.1 21.5 + - + +
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Residues in contact with PRO 141 (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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137A LEU 3.4 7.6 - - - +
138A ASN 3.4 16.4 - - - +
140A VAL* 1.3 95.4 - - + +
142A LEU* 1.3 56.4 + - - +
143A ALA 3.5 0.4 - - - -
125C ASP* 3.3 29.1 - - - +
126C GLY* 4.0 18.0 - - - -
130C ARG* 3.6 27.1 - - - +
131C LYS 4.1 0.2 - - - -
132C PRO* 3.9 17.7 - - + -
137C LEU* 3.9 8.1 - - + -
148C LYS* 4.3 0.9 + - - -
162C TYR* 3.3 23.3 - - - -
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Residues in contact with LEU 142 (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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21A ILE* 3.8 7.9 - - + +
106A VAL* 3.6 31.2 - - + -
110A GLU* 3.8 25.4 - - + +
138A ASN 3.6 13.5 - - - +
139A LEU* 2.9 17.3 + - + +
141A PRO* 1.3 77.3 - - - +
143A ALA* 1.3 56.4 + - - +
130C ARG* 3.4 49.8 - - + +
162C TYR* 2.6 27.1 + - - -
186C ARG* 2.9 17.3 + - - -
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Residues in contact with ALA 143 (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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21A ILE* 3.6 17.7 - - + +
23A VAL* 4.0 13.0 - - + -
139A LEU 3.0 13.1 + - - +
140A VAL 3.2 2.5 + - - +
142A LEU* 1.3 79.2 - - - +
144A GLU* 1.3 60.8 + - - +
145A SER 3.3 3.8 - - - +
146A VAL* 3.7 26.9 - - + -
148C LYS* 2.7 32.4 + - - -
161C ALA* 3.8 3.1 - - - +
162C TYR* 3.9 2.0 - - - -
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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