Contacts of the strand formed by residues 113 - 119 (chain B) in PDB entry 2PX7
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 113 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108B ALA* 4.1 1.8 + - - +
111B SER* 3.3 12.0 + - - -
112B GLY* 1.3 81.2 - - - +
114B ALA* 1.3 61.7 + - - +
149B GLY 3.3 8.1 - - - -
150B PHE* 3.5 19.7 - - + -
154B LEU* 4.3 0.2 - - + -
176B VAL* 4.1 5.2 - - + -
181B TYR* 4.1 6.3 - - + -
182B PRO 3.6 18.9 - - - +
183B VAL* 3.6 12.5 - - + -
184B ALA 2.8 22.8 + - - -
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Residues in contact with ALA 114 (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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104B VAL* 3.7 11.0 - - + +
107B ALA* 3.6 32.8 - - + +
108B ALA* 3.7 11.2 - - - +
113B ALA* 1.3 74.6 - - - +
115B VAL* 1.3 65.7 + - - +
148B GLN* 3.7 0.5 - - - -
149B GLY 2.9 32.3 + - - +
150B PHE* 4.6 1.2 - - - -
183B VAL* 4.3 1.2 - - - +
184B ALA* 3.4 13.5 - - + +
186B VAL* 4.9 3.8 - - + -
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Residues in contact with VAL 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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132A TYR* 3.7 19.1 - - + -
104B VAL* 5.1 0.2 - - - -
114B ALA* 1.3 80.8 - - - +
116B PRO* 1.4 65.2 - - + +
117B VAL* 3.9 3.7 + - + -
144B VAL* 4.1 9.0 - - + -
148B GLN* 3.4 38.8 - - + +
150B PHE* 4.5 2.0 - - + -
173B ALA* 3.7 15.0 - - + -
183B VAL* 4.2 3.6 - - + -
184B ALA 3.0 8.6 + - - +
185B LEU* 3.4 26.2 - - + -
186B VAL* 2.7 34.7 + - - -
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Residues in contact with PRO 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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100B LEU* 3.6 26.0 - - + -
104B VAL* 3.9 9.4 - - + -
115B VAL* 1.4 88.0 - - + +
117B VAL* 1.3 64.0 + - - +
144B VAL* 3.7 2.1 - - - +
145B GLN* 3.0 32.2 + - + +
146B THR 3.0 33.4 - - - +
147B PRO 3.0 22.4 - - - +
186B VAL* 3.3 10.7 - - + +
188B GLY* 3.7 11.9 - - - +
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Residues in contact with VAL 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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125A MET* 3.9 17.3 - - + -
115B VAL* 4.3 2.5 - - + +
116B PRO* 1.3 78.7 - - - +
118B LEU* 1.3 62.5 + - - +
119B PRO* 4.6 1.7 - - - +
142B ARG* 3.9 28.7 - - + +
143B LEU 3.2 10.5 - - - +
144B VAL* 4.2 8.5 - - + -
145B GLN* 4.8 0.7 - - - +
185B LEU* 3.8 39.3 - - + -
186B VAL 2.9 17.4 + - - +
187B GLU* 3.8 3.9 - - - +
188B GLY* 2.8 20.8 + - - -
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Residues in contact with LEU 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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122A ASP* 5.8 0.4 - - - +
199A GLN* 3.5 22.7 - - - +
117B VAL* 1.3 75.3 - - - +
119B PRO* 1.4 78.4 - - + +
142B ARG* 3.3 10.0 - - - -
143B LEU* 2.8 50.3 + - + +
145B GLN* 3.7 28.0 - - - +
187B GLU* 5.4 2.5 - - + -
188B GLY 3.6 7.4 - - - +
189B GLU 3.5 22.2 - - - +
190B ALA* 3.9 15.0 - - + +
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Residues in contact with PRO 119 (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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197A HIS* 3.8 35.7 - - + +
117B VAL 4.6 1.1 - - - +
118B LEU* 1.4 100.2 - - + +
120B VAL* 1.3 67.4 + - - +
121B PRO* 3.3 10.0 - - - +
138B ARG* 6.0 1.1 - - - +
141B PHE 4.5 0.7 - - - +
142B ARG* 4.3 15.0 - - - +
143B LEU* 4.2 2.8 - - - +
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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