Contacts of the strand formed by residues 149 - 155 (chain A) in PDB entry 2XMS
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 149 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A ILE* 3.7 10.8 - - + +
141A TYR* 3.6 28.7 - - + -
142A ALA* 3.8 24.2 - - + -
145A HIS 3.8 2.9 - - - +
146A PRO* 3.3 15.3 + - + +
147A ASP 3.4 1.7 + - - -
148A THR* 1.3 85.2 - - - +
150A GLU* 1.3 62.2 + - - +
151A GLY 3.5 24.9 - - - +
152A LEU* 3.8 22.0 - - + -
241A CYS* 3.6 20.3 - - - +
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Residues in contact with GLU 150 (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 TYR 5.4 0.5 - - - +
48A ARG* 4.3 1.2 - - - -
49A PRO* 3.3 22.7 - - + +
125A THR* 2.5 40.4 + - + +
126A ILE 2.8 12.3 + - - +
127A ILE* 4.2 0.7 - - + -
149A VAL* 1.3 75.3 - - - +
151A GLY* 1.3 58.2 + - - +
241A CYS* 3.8 2.4 - - - +
242A PRO* 3.3 21.3 - - - +
300A MET* 3.7 19.8 - - + +
302A TYR* 2.6 36.0 + - - -
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Residues in contact with GLY 151 (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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126A ILE 3.9 1.4 + - - -
127A ILE* 3.3 11.2 - - - +
128A GLY 3.0 21.1 + - - -
149A VAL* 3.4 9.7 + - - +
150A GLU* 1.3 79.7 - - - +
152A LEU* 1.3 63.0 + - - -
241A CYS* 4.1 3.4 - - - -
242A PRO 3.2 14.1 - - - -
296A PHE* 4.2 9.4 - - - -
300A MET* 4.5 5.6 - - - -
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Residues in contact with LEU 152 (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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126A ILE* 5.5 1.3 - - + -
128A GLY* 3.3 24.0 - - - +
138A LEU* 3.9 28.3 - - + +
139A ALA* 4.3 6.1 - - - -
142A ALA* 3.6 24.2 - - + -
149A VAL* 3.8 15.7 - - + -
151A GLY* 1.3 81.5 - - - +
153A VAL* 1.3 57.4 + - - +
154A LEU* 3.9 16.6 - - + -
239A LEU* 3.9 25.1 - - + -
241A CYS* 4.1 9.2 - - - -
242A PRO 3.0 8.6 + - - +
243A VAL* 3.3 5.3 - - + +
244A MET 2.7 32.2 + - - +
296A PHE* 3.6 5.1 - - - -
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Residues in contact with VAL 153 (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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127A ILE* 4.9 0.9 - - + -
128A GLY 2.7 12.3 + - - +
129A VAL* 3.3 20.3 - - + -
130A GLY 2.9 28.2 + - - +
152A LEU* 1.3 76.9 - - - +
154A LEU* 1.3 61.8 + - - +
155A ILE* 4.1 20.2 - - + -
244A MET* 3.4 31.2 - - + +
246A VAL* 4.1 3.4 - - + -
289A LEU* 4.9 4.0 - - + -
293A PHE* 4.0 31.0 - - + -
296A PHE* 4.0 15.5 - - + -
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Residues in contact with LEU 154 (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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130A GLY 3.9 1.6 - - - +
135A ALA* 3.6 30.1 - - + +
138A LEU* 4.6 3.4 - - + -
139A ALA* 4.2 7.6 - - + +
152A LEU* 4.0 27.6 - - + -
153A VAL* 1.3 79.0 - - - +
155A ILE* 1.3 62.9 + - - +
156A ASN 3.9 0.3 + - - -
157A ILE* 4.0 27.7 - - + +
231A PHE* 5.5 1.1 - - + -
239A LEU* 4.1 20.4 - - + -
243A VAL* 4.0 19.3 - - + -
244A MET 2.8 8.1 + - - -
245A LEU* 3.4 20.8 - - + +
246A VAL 2.9 23.8 + - - +
257A VAL* 5.2 0.2 - - - +
260A CYS* 5.9 0.2 - - - -
264A LEU* 5.5 0.9 - - + -
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Residues in contact with ILE 155 (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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65A PHE* 5.0 1.1 - - + -
68A LEU* 5.5 0.2 - - + -
129A VAL* 4.3 11.9 - - + -
130A GLY 2.9 15.2 + - - +
131A VAL* 3.4 27.0 - - + -
132A GLY 2.8 31.4 + - - -
135A ALA* 3.6 2.1 - - - +
153A VAL* 4.1 14.6 - - + -
154A LEU* 1.3 73.8 - - - +
156A ASN* 1.3 74.8 + - - +
157A ILE 3.2 2.2 + - - -
246A VAL* 3.4 26.0 - - + +
281A PRO* 4.0 23.3 - - + -
282A GLN* 4.3 8.7 - - + +
289A LEU* 4.1 24.5 - - + -
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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