Contacts of the strand formed by residues 148 - 154 (chain A) in PDB entry 1XXE
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 GLU 148 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A SER* 6.0 0.2 - - - +
146A THR* 3.3 10.1 + - - +
147A LEU* 1.3 77.3 - - - +
149A VAL* 1.3 71.6 + - - +
150A THR* 4.6 3.7 + - - +
165A THR* 3.8 15.4 - - + +
166A PHE* 3.3 11.7 - - - +
167A VAL* 3.2 31.6 - - + +
244A GLY 3.0 9.2 + - - +
245A LYS* 3.4 36.0 - - + +
246A PHE* 2.8 27.2 + - - -
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Residues in contact with VAL 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A LEU* 4.3 10.3 - - + -
148A GLU* 1.3 79.7 - - - +
150A THR* 1.3 67.1 + - - +
151A TYR* 5.6 0.2 - - + -
164A PHE 3.8 1.9 - - - +
166A PHE* 2.9 41.4 + - + +
228A VAL* 3.9 24.1 - - + +
231A LEU* 3.2 33.2 - - + -
232A ILE* 4.6 13.9 - - + -
235A LEU* 4.6 9.0 - - + -
246A PHE* 3.2 25.8 - - + +
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Residues in contact with THR 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A GLU* 4.6 3.3 - - - +
149A VAL* 1.3 77.4 - - - +
151A TYR* 1.3 63.0 + - - +
163A LYS* 5.3 5.4 - - + -
164A PHE 3.6 7.6 - - - +
165A THR* 3.1 32.6 + - - +
245A LYS* 4.4 9.1 + - - -
246A PHE 2.8 10.9 + - - -
247A TYR* 3.1 40.7 - - + +
248A SER* 2.6 35.2 + - - -
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Residues in contact with TYR 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A VAL* 4.2 1.5 + - + -
150A THR* 1.3 78.2 - - - +
152A GLU* 1.3 76.2 + - - +
153A GLY* 3.2 26.7 - - - -
154A GLU 4.7 0.2 + - - -
155A PHE* 4.4 10.1 - + - -
163A LYS* 3.2 5.2 - - - +
164A PHE 3.1 29.5 + - - -
180A PHE* 6.3 0.2 - + - -
224A VAL* 3.7 28.0 - - + -
227A LYS* 3.5 44.4 - - + +
228A VAL* 3.5 22.0 - - + +
231A LEU* 5.7 1.8 - - + -
248A SER* 3.2 19.3 - - - -
250A ARG* 3.5 21.9 - - - +
251A GLY 3.9 7.1 + - - -
320A TUX 5.9 1.2 - - - -
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Residues in contact with GLU 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A THR 4.3 0.2 - - - -
151A TYR* 1.3 73.2 - - - +
153A GLY* 1.3 66.1 + - - +
154A GLU* 6.0 0.7 - - + -
161A ARG* 5.6 12.2 + - + -
162A GLN 4.0 4.0 - - - +
163A LYS* 4.2 19.8 - - + +
247A TYR* 2.6 36.7 + - + +
248A SER 2.7 13.1 + - - +
249A PHE* 3.7 27.7 - - + -
250A ARG* 3.0 23.7 + - - +
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Residues in contact with GLY 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A TYR* 3.2 32.0 - - - -
152A GLU* 1.3 77.3 - - - +
154A GLU* 1.3 59.4 + - - +
155A PHE* 3.9 11.3 + - - -
161A ARG* 3.5 3.5 - - - +
162A GLN 3.0 38.1 + - - +
250A ARG* 4.7 1.1 - - - -
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Residues in contact with GLU 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A TYR* 4.7 0.2 + - - -
152A GLU* 4.0 2.1 + - + -
153A GLY* 1.3 73.3 - - - -
155A PHE* 1.3 65.5 + - - +
156A LYS* 4.0 22.8 + - - +
161A ARG* 4.0 28.3 - - + +
249A PHE* 4.8 2.9 - - + -
250A ARG* 2.4 61.6 + - - +
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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