Contacts of the strand formed by residues 147 - 151 (chain H) in PDB entry 2QXU
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 ARG 147 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178G GLN* 3.4 26.1 + - - +
180G THR* 3.4 20.7 - - - +
125H TYR 3.1 17.2 + - - +
126H THR* 3.4 16.9 + - - +
127H SER 2.9 25.2 + - - -
146H ALA* 1.3 69.8 - - - +
148H ASN* 1.3 60.1 - - - +
149H VAL* 3.6 25.5 + - + +
168H LEU* 3.7 16.8 - - - +
171H GLU* 2.9 37.4 + - - +
176H GLY 3.5 12.4 + - - -
178H GLN* 3.7 22.1 - - + +
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Residues in contact with ASN 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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127H SER* 3.5 18.5 - - - -
129H TYR* 3.4 20.7 + - + +
142H ARG* 3.5 25.0 - - - +
143H LEU 3.0 45.2 + - - +
144H ASP* 5.2 0.4 - - - +
145H GLY 5.2 0.8 - - - +
146H ALA* 3.1 14.8 + - - +
147H ARG* 1.3 72.2 - - - +
149H VAL* 1.3 62.4 + - - +
150H GLN 3.9 1.7 + - - -
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Residues in contact with VAL 149 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126H THR* 4.3 11.0 - - + -
127H SER 2.8 12.0 + - - +
128H ILE* 3.6 5.8 - - - +
129H TYR* 3.1 28.0 + - - +
147H ARG* 3.6 41.7 - - + +
148H ASN* 1.3 74.2 - - - +
150H GLN* 1.3 64.4 + - - +
151H ILE* 3.6 9.3 + - + -
168H LEU* 3.7 32.8 - - + -
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Residues in contact with GLN 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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129H TYR* 3.2 31.5 + - + +
130H SER 3.6 1.4 - - - -
131H SER* 3.0 27.6 - - - +
138H ASN* 3.4 16.9 + - - +
148H ASN 3.9 2.8 + - - -
149H VAL* 1.3 74.8 - - - +
151H ILE* 1.3 89.2 + - - +
152H HIS* 4.1 20.0 - - + +
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Residues in contact with ILE 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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128H ILE* 4.2 5.4 - - + -
129H TYR 2.8 19.5 + - - +
130H SER* 3.3 7.4 - - - +
131H SER 3.0 8.1 + - - -
149H VAL* 4.1 20.9 - - + +
150H GLN* 1.3 98.9 + - - +
152H HIS* 1.3 69.0 + - - +
154H VAL* 3.8 33.4 - - + -
159H LEU* 4.0 10.8 - - + -
164H GLN* 3.7 24.0 - - - +
165H VAL* 3.8 20.0 - - + -
168H LEU* 4.1 13.0 - - + -
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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
------------------------------------------------------------
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