Contacts of the strand formed by residues 146 - 151 (chain H) in PDB entry 1PV2
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 TYR 146 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49H HIS* 4.2 3.7 - - - -
50H LYS* 3.3 16.2 - - + -
51H ILE 4.6 2.0 - - - -
52H LEU* 3.6 40.2 - - + +
93H GLU* 2.9 29.9 + - + -
131H LYS* 3.8 7.3 + - - -
136H VAL* 3.5 34.5 - - + +
140H LEU* 3.9 23.6 - - + -
144H SER* 2.8 13.6 + - - -
145H GLU* 1.3 82.2 - - - +
147H ALA* 1.3 61.8 + - - +
148H ALA 4.5 6.5 - - - +
149H ILE* 6.0 0.2 - - + -
173H TRP* 3.6 16.6 - + + -
179H ARG* 3.1 30.5 + - - +
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Residues in contact with ALA 147 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49H HIS* 4.1 9.8 - - + +
50H LYS 2.9 11.4 + - - +
51H ILE* 5.1 0.4 - - + -
90H PHE* 3.8 29.6 - - + -
146H TYR* 1.3 72.6 - - - +
148H ALA* 1.3 60.6 + - - +
179H ARG* 3.8 4.5 - - - +
180H PHE* 3.0 29.7 + - - +
277H MET* 3.9 10.1 - - + -
281H TYR* 3.3 27.2 + - + +
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Residues in contact with ALA 148 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50H LYS 4.0 2.3 + - - +
51H ILE* 3.6 11.6 - - + +
52H LEU* 2.8 34.8 + - - +
146H TYR* 3.3 5.2 - - - +
147H ALA* 1.3 83.4 - - - +
149H ILE* 1.3 58.0 + - - +
150H PHE 4.0 0.4 - - - -
173H TRP* 6.0 0.4 - - - -
179H ARG* 4.8 2.7 - - - -
180H PHE* 3.1 26.0 - - + +
182H ILE* 3.9 21.8 - - + -
277H MET* 4.1 7.6 - - - -
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Residues in contact with ILE 149 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52H LEU* 3.2 29.8 - - + +
54H ILE* 4.0 14.6 - - + -
140H LEU* 5.8 0.2 - - + -
148H ALA* 1.3 73.5 - - - +
150H PHE* 1.3 59.6 + - - +
151H VAL* 3.9 20.6 - - + -
170H ALA* 3.2 39.5 - - + +
171H LEU* 3.9 18.6 - - + +
173H TRP* 4.2 14.4 - - + -
174H ALA* 3.7 18.4 - - + +
180H PHE 2.9 10.0 + - - +
181H VAL* 3.6 3.1 - - + +
182H ILE* 2.9 27.0 + - - +
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Residues in contact with PHE 150 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51H ILE* 3.7 19.3 - - + -
52H LEU 2.6 10.7 + - - +
53H VAL* 3.4 14.6 - - + -
54H ILE* 2.8 29.1 + - - +
77H GLU 3.5 22.0 - - - -
78H THR* 3.5 26.7 - - - -
81H PRO* 4.0 15.9 - - + -
82H LEU* 3.9 23.6 - - + -
85H LEU* 6.1 2.2 - - + -
148H ALA 4.0 0.6 - - - -
149H ILE* 1.3 72.8 - - - +
151H VAL* 1.3 70.7 + - - +
152H PRO* 3.4 22.3 - - + +
182H ILE* 3.7 34.1 - - + -
184H LEU* 4.1 10.5 - - + -
269H LEU* 4.8 0.7 - - + -
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Residues in contact with VAL 151 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54H ILE* 4.0 15.7 - - + +
149H ILE* 3.9 19.7 - - + -
150H PHE* 1.3 79.9 - - - +
152H PRO* 1.3 73.0 - - - +
153H GLY 3.9 0.2 + - - -
157H ALA* 5.3 0.2 - - + -
161H LEU* 3.9 20.6 - - + -
167H VAL* 6.4 0.2 - - + -
171H LEU* 5.0 3.1 - - + -
181H VAL* 5.5 0.4 - - + -
182H ILE 2.9 11.7 + - - +
183H SER* 2.5 37.7 + - - +
184H LEU 3.9 0.2 + - - -
187H GLY* 3.5 20.1 - - - +
190H ALA* 3.9 19.3 - - + -
191H PHE* 4.9 9.6 - - + -
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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