Contacts of the strand formed by residues 153 - 161 (chain A) in PDB entry 2Q4E
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 153 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150A PHE* 4.2 24.3 - - + -
151A GLY 3.7 3.8 + - - -
152A GLN* 1.3 96.1 + - - +
154A LYS* 1.3 66.6 + - - +
155A THR* 3.5 27.8 - - - +
156A VAL* 4.4 10.3 - - + -
199A ALA* 3.8 19.3 - - + +
200A ASN* 2.9 44.9 - - - +
231A TRP* 5.5 0.4 - - + -
235A ARG* 3.3 16.6 - - + +
253A ALA* 4.5 4.3 - - + -
254A ILE 3.8 6.3 - - - +
255A GLY* 3.9 5.8 - - - -
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Residues in contact with LYS 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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152A GLN* 3.2 31.8 - - + +
153A LEU* 1.3 78.9 + - - +
155A THR* 1.3 60.2 + - - +
233A ASP 5.4 1.4 + - - -
234A GLY* 3.2 25.3 + - - +
235A ARG* 2.9 30.0 - - - +
236A THR* 3.0 3.0 + - - -
254A ILE* 2.7 19.4 + - + +
255A GLY 3.9 6.1 - - - -
256A THR* 3.7 13.1 + - - +
240B TYR* 4.7 8.9 + - - +
242B SER* 5.9 0.4 - - - -
244B LEU* 3.9 15.0 + - - +
245B ALA* 3.7 27.8 - - + -
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Residues in contact with THR 155 (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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153A LEU* 3.5 5.8 - - - +
154A LYS* 1.3 79.5 - - - +
156A VAL* 1.3 70.5 + - - +
157A GLN* 3.4 22.9 + - - +
236A THR* 2.9 35.7 + - - -
237A ALA 3.6 1.2 + - - -
238A THR* 5.6 0.2 - - - +
254A ILE* 2.7 58.3 + - + +
240B TYR* 3.8 21.9 - - + -
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Residues in contact with VAL 156 (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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153A LEU* 4.4 5.8 - - + -
155A THR* 1.3 83.1 + - - +
157A GLN* 1.3 70.7 + - - +
158A SER* 5.4 0.4 - - - -
195A ALA 4.9 0.9 - - - +
196A THR* 4.0 17.7 + - - +
199A ALA* 4.0 20.9 - - + -
200A ASN* 3.6 25.1 - - - +
231A TRP* 4.3 0.7 - - + -
236A THR 3.1 3.0 + - - +
237A ALA* 2.9 42.9 - - + +
238A THR 2.9 8.0 + - - +
251A ILE* 4.7 7.0 - - + -
252A THR 2.9 16.8 - - - +
253A ALA* 4.2 5.6 - - + -
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Residues in contact with GLN 157 (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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155A THR* 3.4 36.7 + - - +
156A VAL* 1.3 75.1 + - - +
158A SER* 1.3 63.6 + - - +
238A THR* 3.1 32.5 + - - +
251A ILE* 3.5 2.9 - - - +
252A THR* 2.4 77.4 + - + +
254A ILE* 4.0 4.5 - - - +
157B GLN* 4.5 23.3 - - - +
159B CYS* 5.4 3.6 - - - -
238B THR* 6.0 1.3 - - - +
240B TYR* 4.6 17.9 - - - +
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Residues in contact with SER 158 (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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156A VAL* 5.4 0.2 - - - -
157A GLN* 1.3 79.3 - - - +
159A CYS* 1.3 55.6 + - - +
192A ALA* 2.8 44.4 + - - +
195A ALA* 4.3 10.8 - - - +
196A THR* 4.5 4.0 - - - -
238A THR* 2.8 12.5 + - - -
239A ILE* 2.9 11.3 - - - +
240A TYR* 2.7 32.3 + - - +
250A GLU 3.3 11.6 + - - -
251A ILE* 4.6 0.6 - - - +
265A PHE* 4.4 5.0 - - - -
157B GLN* 6.3 0.7 - - - -
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Residues in contact with CYS 159 (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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158A SER* 1.3 76.3 + - - +
160A PHE* 1.3 68.2 + - - +
192A ALA* 5.1 1.1 - - - -
240A TYR* 3.2 23.3 - - + +
248A THR* 3.3 28.9 - - - -
249A MSE 3.7 2.3 - - - -
250A GLU* 3.0 51.0 + - + +
265A PHE* 4.2 5.9 - - - -
157B GLN* 5.3 9.0 - - - +
252B THR* 5.2 5.8 - - + -
254B ILE* 4.7 6.5 - - + -
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Residues in contact with PHE 160 (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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159A CYS* 1.3 81.1 - - - +
161A SER* 1.3 69.7 + - - +
162A PHE* 4.7 18.6 - + - -
187A ASP* 4.5 3.1 - - - -
188A ALA* 3.5 37.9 - - + +
191A TYR* 3.5 26.7 - + + -
192A ALA* 5.5 3.1 - - + -
240A TYR* 2.8 9.2 + - - +
241A CYS* 2.8 32.4 - - - +
242A SER 3.1 0.7 + - - -
247A LEU* 4.1 17.3 - - + -
248A THR* 3.0 19.3 - - - -
249A MSE 3.6 22.0 - - + -
265A PHE* 5.4 0.2 - - + -
266A ILE* 3.4 26.9 - - + -
254B ILE* 6.1 0.6 - - - +
284B PHE* 5.5 5.2 - + - -
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Residues in contact with SER 161 (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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160A PHE* 1.3 84.5 - - - +
162A PHE* 1.3 53.9 + - - +
188A ALA* 5.4 0.9 - - - -
240A TYR* 5.5 5.3 - - - -
241A CYS 4.3 0.4 - - - -
242A SER* 2.8 37.7 - - - -
245A ALA* 2.6 35.9 - - - +
246A ASN 2.6 19.4 + - - +
247A LEU* 3.3 3.8 + - - -
248A THR* 3.5 4.0 + - - +
254B ILE* 4.5 9.9 - - - +
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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