Contacts of the helix formed by residues 136 - 143 (chain A) in PDB entry 2XDS
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 VAL 136 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A LEU* 4.0 19.1 - - + -
111A ALA* 3.5 41.3 - - + +
114A GLY* 4.5 0.7 - - - +
115A THR* 3.6 10.8 - - - +
118A PHE* 4.5 11.0 - - + -
131A ILE* 3.3 32.7 + - + +
134A PHE* 4.0 17.5 - - + +
135A GLY* 1.3 82.6 - - - +
137A GLY* 1.3 63.7 + - - +
138A PHE* 3.2 5.3 + - - +
139A TYR* 3.3 19.6 + - + -
1225A MT0 6.2 1.1 - - - -
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Residues in contact with GLY 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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47A GLU* 3.7 29.2 - - - +
48A LEU* 5.0 0.9 - - - +
51A ASN* 4.6 5.2 + - - +
131A ILE* 3.9 17.2 + - - -
132A GLY* 4.4 2.7 - - - -
135A GLY 3.5 3.2 + - - -
136A VAL* 1.3 74.3 - - - +
138A PHE* 1.3 63.8 + - - +
139A TYR 3.2 0.2 - - - -
140A SER* 2.7 28.3 + - - -
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Residues in contact with PHE 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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48A LEU* 4.0 18.5 - - + +
51A ASN* 3.6 17.2 - - - +
136A VAL 3.2 1.4 + - - -
137A GLY* 1.3 76.6 - - - +
139A TYR* 1.3 79.2 + + + +
141A ALA* 3.0 29.6 + - + +
142A TYR* 4.8 6.3 - + - -
148A VAL* 4.2 13.2 - - + -
150A VAL* 4.1 9.4 - - + -
162A TRP* 3.9 28.7 - + - -
186A VAL* 4.4 7.6 - - + -
1225A MT0 3.3 86.4 - + + +
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Residues in contact with TYR 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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22A PHE* 4.5 9.4 - + - -
26A ILE* 3.7 29.3 - - + +
29A LEU* 3.8 16.6 - - + -
30A MET* 3.8 30.0 - - + +
33A ILE* 3.6 26.0 - - + +
108A GLY* 4.2 16.5 - - - -
111A ALA* 4.2 17.5 - - + +
136A VAL* 3.5 20.2 - - + +
137A GLY 3.2 1.4 - - - -
138A PHE* 1.3 89.5 - + + +
140A SER* 1.3 61.3 + - - +
141A ALA 2.9 7.3 + - - -
142A TYR* 3.0 23.5 + + - +
1225A MT0 3.8 35.8 - + + +
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Residues in contact with SER 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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33A ILE* 4.0 8.5 - - - +
43A ILE* 3.9 23.1 - - - -
44A PHE* 3.4 24.4 + - - +
47A GLU* 3.6 7.6 - - - +
48A LEU* 5.6 0.2 - - - +
128A ILE* 5.7 0.9 - - - -
131A ILE* 4.1 15.7 - - - +
137A GLY 2.7 21.7 + - - -
139A TYR* 1.3 76.4 - - - +
141A ALA* 1.3 63.4 + - - +
142A TYR 2.9 0.4 - - - -
143A LEU* 2.9 31.9 + - - +
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Residues in contact with ALA 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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44A PHE* 4.2 10.8 - - - -
48A LEU* 4.5 11.6 - - + +
138A PHE* 3.0 19.6 + - + +
139A TYR 2.9 1.0 + - - -
140A SER* 1.3 79.3 + - - +
142A TYR* 1.3 60.9 + - + +
144A VAL* 3.3 9.7 + - - +
145A ALA* 3.1 26.5 + - - +
148A VAL* 3.9 15.5 - - + -
188A LEU* 3.7 26.0 - - + +
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Residues in contact with TYR 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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30A MET* 3.6 28.0 - - + +
33A ILE* 3.7 9.9 - - + +
34A ILE* 3.9 33.2 - - + +
138A PHE* 4.8 14.8 - + - -
139A TYR* 3.0 22.0 + + - +
140A SER 2.9 2.0 - - - -
141A ALA* 1.3 77.4 - - + +
143A LEU* 1.3 59.0 + - - +
144A VAL 3.1 1.6 - - - -
145A ALA 3.7 18.6 - - - +
146A GLU 4.6 2.7 - - - -
148A VAL* 3.5 31.2 - - + +
162A TRP* 3.6 5.2 - + - -
164A SER* 2.7 41.5 + - - -
165A SER* 4.4 2.9 - - - -
166A ALA* 4.1 12.1 - - + -
191A LYS* 3.0 24.3 + - - -
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Residues in contact with LEU 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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33A ILE* 3.6 33.1 - - + +
36A THR 5.9 0.9 - - - +
38A TYR* 4.5 14.6 - - + -
41A LYS* 2.8 66.7 + - + +
43A ILE* 3.8 31.9 - - + -
44A PHE 4.7 0.4 - - - +
128A ILE* 4.3 22.0 - - + -
140A SER* 2.9 22.3 + - - +
142A TYR* 1.3 78.7 - - - +
144A VAL* 1.3 61.0 + - + +
191A LYS* 3.2 9.2 + - - +
194A GLN* 4.5 0.3 - - - +
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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