Contacts of the strand formed by residues 112 - 118 (chain B) in PDB entry 2XUG
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 THR 112 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B PRO* 3.3 26.5 - - - +
110B SER 3.3 4.5 + - - -
111B PRO* 1.3 73.1 - - - +
113B PRO* 1.3 89.0 - - + +
114B VAL 3.4 0.2 + - - -
142B GLU 5.6 0.7 - - - +
143B GLY 3.0 28.6 + - - +
144B ALA* 4.0 4.9 - - - -
145B VAL* 4.1 10.8 - - - +
191B GLY 2.9 10.5 + - - -
192B GLY* 3.5 3.5 - - - -
193B ASP* 2.7 28.4 + - - +
485B ARG* 6.1 2.5 - - - +
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Residues in contact with PRO 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B PRO 4.3 4.0 - - - +
112B THR* 1.3 104.5 - - + +
114B VAL* 1.3 60.3 + - - +
115B LEU* 4.2 2.3 + - + +
144B ALA* 4.3 4.0 - - - +
145B VAL 3.5 12.0 + - - +
193B ASP* 5.2 1.3 - - + +
196B SER* 3.6 29.2 - - - +
481B THR 5.8 0.2 - - - +
484B ALA* 4.3 16.8 - - + +
485B ARG* 3.7 40.6 - - + +
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Residues in contact with VAL 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B THR 3.6 2.7 - - - +
113B PRO* 1.3 73.2 - - - +
115B LEU* 1.3 72.7 + - - +
116B ILE* 4.0 16.8 - - + -
145B VAL* 3.4 12.3 - - + +
147B VAL* 4.0 14.4 - - + -
183B VAL* 4.4 6.5 - - + -
187B ILE* 3.9 17.0 - - + -
192B GLY* 3.8 11.0 - - - -
193B ASP 3.6 34.1 - - - +
196B SER 2.9 11.4 + - - +
197B VAL* 3.5 7.4 - - + +
198B THR* 2.8 28.8 + - - +
484B ALA* 5.1 0.2 - - - +
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Residues in contact with LEU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B PRO* 4.8 4.3 - - + +
114B VAL* 1.3 75.6 - - - +
116B ILE* 1.3 62.0 + - - +
117B TRP 4.1 0.4 - - - -
138B LEU* 5.2 4.3 - - + -
144B ALA* 4.0 25.6 - - + -
145B VAL 2.9 9.1 + - - +
146B LEU* 3.4 13.1 - - + +
147B VAL* 2.8 27.9 + - - +
198B THR* 3.4 10.5 - - + +
200B PHE* 3.7 36.3 - - + -
226B VAL* 6.4 0.4 - - + -
480B TRP* 4.7 15.5 - - + +
481B THR* 4.3 15.5 - - + -
484B ALA* 3.7 31.4 - - + -
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Residues in contact with ILE 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B VAL* 4.0 11.4 - - + -
115B LEU* 1.3 79.2 - - - +
117B TRP* 1.3 62.3 + - - +
118B ILE* 3.9 2.7 + - + +
147B VAL* 3.2 19.7 - - + +
149B MET* 3.7 29.8 - - + -
179B ALA 6.2 0.2 - - - -
180B LEU* 4.0 22.2 - - + +
183B VAL* 3.9 28.5 - - + -
197B VAL* 3.5 28.0 - - + -
198B THR 2.9 9.1 + - - -
199B LEU* 3.5 12.5 - - + +
200B PHE* 2.8 30.5 + - - +
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Residues in contact with TRP 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B ILE* 1.3 73.8 - - - +
118B ILE* 1.3 72.3 + - - +
119B TYR* 3.5 22.1 + + + +
120B GLY 5.2 0.4 - - - -
128B ALA* 5.5 0.2 - - - -
133B TYR* 3.4 56.8 - + + -
146B LEU* 4.7 4.0 - - + -
147B VAL 2.8 14.3 + - - +
148B SER* 3.7 29.4 - - - -
149B MET* 3.8 9.7 + - - +
200B PHE* 3.3 60.2 - + + -
201B GLY* 3.6 12.6 - - - -
202B GLU* 3.6 29.8 - - + -
228B GLN* 3.9 9.2 - - - -
451B ILE* 4.3 10.5 - - + -
455B PHE* 3.5 19.1 - + + -
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Residues in contact with ILE 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B ILE* 4.5 4.5 - - + +
117B TRP* 1.3 81.2 - - - +
119B TYR* 1.3 65.2 + - - +
149B MET* 4.1 20.0 - - + -
151B TYR* 3.7 25.8 - - + -
176B GLN* 3.7 29.8 - - + +
180B LEU* 5.2 2.0 - - + -
199B LEU* 4.8 12.3 - - + -
200B PHE 2.9 12.4 + - - +
201B GLY* 3.3 13.0 - - - -
202B GLU 3.7 1.2 + - - -
205B GLY* 3.2 23.5 - - - +
208B SER* 4.1 1.1 - - - -
209B VAL* 3.9 22.9 - - + +
212B HIS* 4.3 15.7 - - + +
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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