Contacts of the strand formed by residues 150 - 154 (chain E) in PDB entry 1QRP
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 LEU 150 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137E PHE* 3.4 11.2 - - - -
148E GLN* 3.0 22.8 + - + +
149E ASP* 1.3 79.8 - - - +
151E PHE* 1.3 57.4 + - - +
168E GLY* 2.7 33.5 + - - -
169E GLY* 3.5 38.6 - - - +
170E ILE* 4.1 17.7 - - + -
181E TRP* 4.9 2.9 - - + -
312E VAL* 4.0 18.4 - - + -
313E PHE 3.3 16.6 - - - +
314E ASP* 3.8 22.9 - - - +
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Residues in contact with PHE 151 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E THR* 3.9 7.2 - - + -
123E LEU* 3.5 56.5 - - + -
137E PHE* 3.9 32.1 - + + -
150E LEU* 1.3 78.4 - - - +
152E SER* 1.3 63.6 + - - +
153E VAL* 4.3 10.3 - - + -
165E VAL* 4.4 4.5 - - + -
166E ILE 3.0 15.3 - - - +
167E PHE* 4.1 19.7 - + + -
190E TRP* 4.1 9.6 - + - -
312E VAL* 3.7 1.2 - - - +
313E PHE* 2.8 69.8 + + + -
315E ARG* 5.2 0.4 - - + -
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Residues in contact with SER 152 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151E PHE* 1.3 74.8 - - - +
153E VAL* 1.3 66.5 + - - +
154E TYR 4.2 0.2 - - - -
164E VAL 4.0 0.2 - - - +
165E VAL* 3.4 4.5 - - - +
166E ILE* 2.8 44.1 + - - +
169E GLY 3.0 19.6 + - - -
170E ILE* 3.9 1.9 - - - -
310E PHE* 3.4 26.0 - - - -
311E THR 3.3 11.4 - - - -
312E VAL* 3.9 15.0 - - - -
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Residues in contact with VAL 153 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E LEU* 5.1 0.2 - - + -
33E THR* 5.2 0.9 - - + -
123E LEU* 5.4 2.0 - - + -
151E PHE* 4.3 13.9 - - + -
152E SER* 1.3 81.0 - - - +
154E TYR* 1.3 62.5 + - - +
155E LEU* 3.7 33.5 + - + -
164E VAL 3.6 5.2 - - - +
165E VAL* 4.2 18.6 - - + -
216E THR* 4.0 19.1 - - + -
306E ILE* 4.5 5.6 - - + +
310E PHE* 3.4 9.0 - - - -
311E THR* 2.7 35.9 + - - +
313E PHE* 4.0 22.2 - - + -
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Residues in contact with TYR 154 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152E SER 4.2 0.2 - - - -
153E VAL* 1.3 73.2 - - - +
155E LEU* 1.3 80.7 + - - +
156E SER* 3.8 19.6 - - - -
157E ALA 4.8 0.9 + - - -
161E SER 5.5 0.2 - - - -
162E GLY* 3.3 35.2 - - - -
163E SER* 3.2 4.0 - - - -
164E VAL* 2.9 48.2 + - + +
174E TYR* 3.6 35.2 - + + -
306E ILE 6.0 0.2 - - - -
307E ARG 5.2 0.2 - - - -
310E PHE* 3.9 17.0 - + + +
325E VAL* 3.9 32.5 - - + +
326E ALA* 5.6 3.5 + - - -
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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