Contacts of the helix formed by residues 35 - 50 (chain X) in PDB entry 2AE0
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 35 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33X PRO* 3.4 3.1 - - - +
34X ILE* 1.3 79.8 - - - +
36X ALA* 1.3 58.1 + - - +
37X GLY 3.2 3.1 - - - -
38X ASP* 3.1 15.3 + - + +
39X PHE* 2.9 26.4 + - - +
255X ARG 3.3 18.6 + - - -
256X ALA* 4.0 10.9 - - - +
291X ARG* 3.4 30.6 - - - +
292X LEU* 2.9 49.2 + - - +
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Residues in contact with ALA 36 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33X PRO* 4.6 5.5 + - - +
34X ILE 3.7 2.8 + - - -
35X ASN* 1.3 74.2 - - - +
37X GLY* 1.3 56.4 + - - +
39X PHE* 3.4 4.1 + - - +
40X ALA* 3.0 30.0 + - - +
65X GLN* 4.6 3.5 + - - -
68X LEU* 4.1 37.9 - - + -
292X LEU* 5.6 0.9 - - - -
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Residues in contact with GLY 37 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35X ASN 3.2 1.0 - - - -
36X ALA* 1.3 77.9 - - - +
38X ASP* 1.3 57.6 + - - +
40X ALA* 3.3 7.1 + - - +
41X GLU* 3.0 28.3 + - - +
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Residues in contact with ASP 38 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35X ASN* 3.1 25.4 + - + +
37X GLY* 1.3 72.2 - - - +
39X PHE* 1.3 61.6 + - - +
41X GLU* 3.3 14.8 + - - +
42X GLN* 2.9 28.9 + - - +
253X VAL* 3.8 23.1 - - + +
254X GLY 4.1 9.8 - - - +
255X ARG* 5.8 1.9 + - - -
256X ALA* 4.1 8.5 - - + -
291X ARG* 4.3 6.9 + - - -
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Residues in contact with PHE 39 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35X ASN 2.9 15.7 + - - +
36X ALA* 3.6 6.3 - - - +
37X GLY 3.2 0.2 - - - -
38X ASP* 1.3 77.4 - - - +
40X ALA* 1.3 56.4 + - - +
42X GLN* 3.1 8.3 + - + +
43X ILE* 2.9 54.7 + - + +
61X TYR* 4.4 7.6 - + - -
64X VAL* 3.5 30.5 - - + -
65X GLN* 3.4 25.4 - - + -
68X LEU* 4.0 7.6 - - + -
256X ALA* 4.4 5.3 - - - +
270X THR* 4.1 19.5 - - + -
292X LEU* 3.6 36.6 - - + +
293X MET* 4.8 1.3 - - - -
294X VAL* 3.8 27.1 - - + -
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Residues in contact with ALA 40 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36X ALA 3.0 17.6 + - - +
37X GLY* 3.3 7.6 + - - +
39X PHE* 1.3 76.2 - - - +
41X GLU* 1.3 57.5 + - - +
43X ILE* 3.3 5.5 + - - +
44X ASN* 2.9 29.1 + - - +
65X GLN* 3.7 27.8 - - - +
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Residues in contact with GLU 41 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37X GLY 3.0 13.8 + - - +
38X ASP* 3.5 16.6 - - - +
40X ALA* 1.3 75.1 - - - +
42X GLN* 1.3 63.2 + - - +
44X ASN* 3.4 8.5 + - + +
45X HIS* 3.1 40.3 + - + +
253X VAL* 4.0 25.2 - - + +
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Residues in contact with GLN 42 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38X ASP 2.9 14.6 + - - +
39X PHE* 3.1 10.3 + - + +
41X GLU* 1.3 77.0 - - - +
43X ILE* 1.3 62.0 + - + +
45X HIS* 3.2 3.9 + - - +
46X ILE* 3.2 17.5 + - + +
250X VAL* 3.7 4.6 - - - +
251X PRO 2.9 23.6 + - - -
252X LEU* 3.7 0.5 - - - -
253X VAL* 2.8 36.9 + - + +
256X ALA* 3.7 19.1 - - + +
257X SER* 3.3 14.2 - - - -
294X VAL* 4.4 11.0 - - + -
296X LEU* 3.3 28.2 - - + +
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Residues in contact with ILE 43 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39X PHE* 2.9 48.6 + - + +
40X ALA* 3.7 8.7 - - - +
42X GLN* 1.3 73.0 - - - +
44X ASN* 1.3 60.8 + - - +
46X ILE* 3.1 10.1 + - + +
47X ARG* 2.9 32.5 + - - +
54X TYR* 3.7 25.5 - - + -
61X TYR* 3.6 46.2 - - + -
65X GLN* 5.4 7.0 - - + +
294X VAL* 3.9 11.2 - - + -
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Residues in contact with ASN 44 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40X ALA 2.9 16.3 + - - +
41X GLU* 3.6 10.1 - - + +
42X GLN 3.3 0.2 - - - -
43X ILE* 1.3 77.1 - - - +
45X HIS* 1.3 62.5 + - - +
47X ARG* 3.2 27.3 - - - +
48X ASN* 3.1 41.8 + - - +
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Residues in contact with HIS 45 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41X GLU* 3.1 38.5 + - + +
42X GLN* 3.2 16.1 + - - +
44X ASN* 1.3 76.9 + - + +
46X ILE* 1.3 59.5 + - - +
48X ASN* 5.0 3.4 + - - +
49X SER* 2.8 38.2 + - - -
243X PRO* 6.5 0.2 - - + -
250X VAL* 3.8 9.4 - - + -
251X PRO* 3.6 33.9 - - + +
252X LEU 5.6 0.2 - - - -
253X VAL* 3.8 21.7 - - + +
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Residues in contact with ILE 46 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42X GLN 3.2 14.1 + - - +
43X ILE* 3.1 16.5 + - + +
45X HIS* 1.3 73.0 - - - +
47X ARG* 1.3 61.9 + - - +
50X SER* 2.8 40.3 + - - +
53X LEU* 4.2 16.6 - - + -
54X TYR* 3.8 28.9 - - + +
61X TYR* 3.6 28.9 - - + +
250X VAL* 3.8 20.6 - - + -
294X VAL* 3.9 20.9 - - + -
296X LEU* 3.9 13.2 - - + -
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Residues in contact with ARG 47 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43X ILE* 2.9 16.4 + - - +
44X ASN* 3.2 29.6 - - - +
46X ILE* 1.3 78.4 - - - +
48X ASN* 1.3 66.0 + - - +
51X PRO* 3.8 19.2 - - - +
54X TYR* 2.9 63.2 + - + +
62X ASN* 4.7 6.3 - - - +
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Residues in contact with ASN 48 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44X ASN* 3.1 36.5 + - - +
45X HIS* 4.3 4.5 + - - +
47X ARG* 1.3 86.9 - - - +
49X SER* 1.3 64.2 + - - +
51X PRO* 4.1 7.0 - - - +
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Residues in contact with SER 49 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45X HIS* 2.8 23.0 + - - -
48X ASN* 1.3 76.0 - - - +
50X SER* 1.3 59.1 + - - +
51X PRO* 3.6 4.9 - - - +
245X LYS* 5.4 1.5 - - - -
249X ALA* 3.6 28.3 - - - +
250X VAL* 4.1 3.4 - - - -
251X PRO* 3.3 23.9 - - - +
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Residues in contact with SER 50 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46X ILE* 2.8 19.2 + - - +
49X SER* 1.3 76.4 - - - +
51X PRO* 1.3 62.1 - - - +
52X ARG* 3.2 10.1 + - - +
53X LEU* 3.1 24.5 + - - +
54X TYR 2.9 22.7 + - - -
248X SER* 4.4 9.3 + - - -
250X VAL* 3.7 23.3 - - - -
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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