Contacts of the strand formed by residues 36 - 42 (chain A) in PDB entry 2W5X
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 ASN 36 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A PRO* 3.7 3.8 - - - +
35A LYS* 1.3 89.9 - - - +
37A VAL* 1.3 69.4 - - - +
247A SER 4.1 1.4 - - - +
248A ALA* 3.1 13.2 - - - -
249A PHE* 2.9 59.0 + - + +
287A PHE* 5.0 0.4 - - - -
291A ASP* 3.7 15.4 + - - -
293A ASN* 3.1 5.5 + - - +
294A THR* 3.2 24.7 + - + +
295A LEU 2.9 24.6 + - - -
373A TRP* 5.0 0.2 - - - -
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Residues in contact with VAL 37 (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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34A PRO* 4.7 0.4 - - + -
36A ASN* 1.3 80.8 - - - +
38A ILE* 1.3 75.7 + - - +
39A LEU* 4.4 0.9 - - + +
249A PHE* 3.0 9.1 + - - +
250A PHE* 3.3 29.3 - - + -
251A ILE 3.0 23.9 + - - +
295A LEU* 3.3 19.3 - - + +
297A ILE* 4.1 21.5 - - + -
367A ILE* 4.4 10.8 - - + -
371A THR* 3.5 31.6 - - + -
373A TRP* 3.9 6.7 - - + -
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Residues in contact with ILE 38 (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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37A VAL* 1.3 79.0 - - - +
39A LEU* 1.3 61.3 + - - +
40A LEU* 3.8 28.2 + - + -
235A THR* 5.0 4.0 - - + -
239A ILE* 3.9 27.6 - - + -
249A PHE* 3.8 16.6 - - + -
251A ILE* 3.5 20.2 - - + +
284A ALA* 4.1 24.9 - - + +
287A PHE* 4.5 2.7 - - + -
294A THR* 3.9 20.0 - - + -
295A LEU 2.9 11.9 + - - +
296A VAL* 3.4 7.7 - - + +
297A ILE* 2.9 27.2 + - - +
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Residues in contact with LEU 39 (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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37A VAL* 4.1 4.1 - - + -
38A ILE* 1.3 71.6 - - - +
40A LEU* 1.3 66.2 + - - +
41A ILE* 4.2 15.3 - - + -
91A PHE* 4.5 11.9 - - + +
141A PHE* 3.8 33.4 - - + -
250A PHE* 4.3 15.3 - - + -
251A ILE 2.8 13.2 + - - +
252A MET* 3.1 9.6 - - + +
253A SER 3.0 23.7 + - - -
297A ILE* 3.4 39.9 - - + +
299A THR* 4.7 8.7 - - + -
363A ILE* 4.8 7.2 - - + -
367A ILE* 4.7 11.2 - - + -
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Residues in contact with LEU 40 (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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38A ILE* 3.8 20.6 - - + -
39A LEU* 1.3 73.4 - - - +
41A ILE* 1.3 62.8 + - - +
235A THR* 4.9 5.2 - - + +
253A SER* 3.3 31.4 - - - +
277A PHE* 3.8 17.4 - - + -
280A ALA* 4.0 10.8 - - + +
281A ILE* 3.8 33.0 - - + +
284A ALA* 3.9 18.2 - - + -
296A VAL* 4.4 4.3 - - + -
297A ILE 2.8 14.7 + - - +
298A VAL* 3.4 16.1 - - + -
299A THR 3.1 26.3 + - - +
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Residues in contact with ILE 41 (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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39A LEU* 4.2 12.3 - - + -
40A LEU* 1.3 75.4 - - - +
42A SER* 1.3 68.3 + - - +
43A ASP* 4.2 4.7 - - - +
88A ALA* 5.3 0.2 - - + -
91A PHE* 3.9 28.0 - - + -
137A THR* 3.9 24.0 - - + -
141A PHE* 3.9 10.5 - - + -
252A MET* 3.7 28.9 - - + -
253A SER 2.9 10.6 + - - +
254A GLU* 3.2 14.1 - - + +
255A GLY 2.8 25.3 + - - -
277A PHE* 3.5 3.1 - - - -
299A THR* 3.3 8.7 - - + +
300A SER* 4.5 0.7 - - - -
301A ASP* 4.3 18.2 - - + +
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Residues in contact with SER 42 (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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41A ILE* 1.3 71.7 - - - +
43A ASP* 1.3 65.0 + - - +
44A GLY 3.2 2.9 + - - -
45A ALA* 3.4 10.8 + - - +
50A ILE* 5.6 0.7 - - - +
63A TYR* 4.4 4.3 + - - -
255A GLY 3.9 5.2 - - - -
258A ILE* 3.7 13.7 - - - -
277A PHE* 3.4 34.3 - - - -
298A VAL* 5.2 0.9 - - - +
299A THR 3.0 10.2 + - - -
300A SER* 2.6 43.1 + - - -
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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