Contacts of the helix formed by residues 35 - 50 (chain B) in PDB entry 2PI8
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B PRO* 4.2 4.4 - - - +
34B ILE* 1.3 81.1 + - - +
36B ALA* 1.3 58.9 + - - +
37B GLY 3.3 2.9 - - - +
38B ASP* 3.7 19.5 - - + +
39B PHE* 2.8 25.6 + - - +
68B LEU* 5.5 0.2 - - - -
255B ARG 3.6 17.4 + - - -
256B ALA* 4.1 7.1 - - - +
291B ARG* 3.5 28.9 - - - +
292B LEU* 2.7 52.8 + - - +
38D ASP* 4.5 1.6 - - - -
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Residues in contact with ALA 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B PRO* 4.0 3.4 + - - +
34B ILE 3.6 3.2 + - - -
35B ASN* 1.3 75.9 - - - +
37B GLY* 1.3 58.0 + - - +
39B PHE* 4.0 1.2 - - - +
40B ALA* 3.1 30.3 + - - +
65B GLN* 4.7 0.5 + - - -
68B LEU* 3.9 27.9 - - + +
34D ILE* 4.0 35.2 - - + +
35D ASN* 6.2 0.4 - - + -
38D ASP* 4.2 4.1 + - - +
291D ARG* 5.8 3.8 - - - +
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Residues in contact with GLY 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B ASN 3.3 0.2 - - - -
36B ALA* 1.3 77.7 - - - +
38B ASP* 1.3 65.7 + - - +
40B ALA* 4.0 5.0 - - - +
41B GLU* 3.2 25.6 + - - +
38D ASP* 3.8 16.1 + - - -
255D ARG* 6.0 4.5 - - - -
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Residues in contact with ASP 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ILE 5.2 0.7 - - - +
35B ASN* 3.3 27.6 + - + +
37B GLY* 1.3 77.1 - - - +
39B PHE* 1.3 59.8 + - - +
41B GLU* 3.5 9.9 + - - +
42B GLN* 3.0 26.9 + - - +
253B VAL* 3.8 13.5 - - + +
254B GLY 4.2 12.2 - - - +
256B ALA* 3.7 19.0 - - + +
291B ARG* 4.2 5.5 + - - -
38D ASP* 4.8 5.2 + - - +
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Residues in contact with PHE 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B ASN 2.8 18.0 + - - +
36B ALA 4.0 2.9 - - - +
38B ASP* 1.3 74.3 - - - +
40B ALA* 1.3 63.2 + - - +
42B GLN* 3.0 7.1 + - + +
43B ILE* 2.9 46.3 + - + +
64B VAL* 3.3 30.3 - - + -
65B GLN* 3.0 22.0 - - - -
68B LEU* 4.1 3.4 - - + -
256B ALA* 4.3 5.3 - - - +
270B THR* 3.6 30.5 - - + -
292B LEU* 3.6 47.6 - - + +
293B MSE 4.4 0.9 - - - -
294B VAL* 3.5 28.3 - - + -
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Residues in contact with ALA 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ALA 3.1 16.6 + - - +
37B GLY* 4.0 6.5 - - - +
39B PHE* 1.3 75.4 - - - +
41B GLU* 1.3 61.7 + - - +
43B ILE* 3.3 5.6 + - - +
44B ASN* 3.1 34.1 + - - +
65B GLN* 3.3 34.7 + - - +
69B ARG* 6.1 0.7 - - - +
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Residues in contact with GLU 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B GLY 3.2 18.2 + - - +
38B ASP* 3.5 10.6 - - - +
40B ALA* 1.3 76.6 - - - +
42B GLN* 1.3 64.7 + - - +
44B ASN* 3.2 11.3 + - + +
45B HIS* 3.0 51.7 + - + +
253B VAL* 3.7 21.7 - - - +
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Residues in contact with GLN 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B ASP 3.0 15.6 + - - +
39B PHE* 3.3 12.1 - - + +
41B GLU* 1.3 76.8 - - - +
43B ILE* 1.3 61.1 + - - +
45B HIS* 3.2 6.4 + - - +
46B ILE* 3.1 18.8 + - + +
250B VAL* 4.0 1.8 - - - +
251B PRO 3.2 20.9 + - - +
252B LEU* 4.1 0.2 - - - -
253B VAL* 3.3 23.9 + - + +
256B ALA* 3.7 15.4 - - + +
257B SER* 3.2 25.8 - - - -
294B VAL* 4.1 19.5 - - + -
296B LEU* 3.2 24.6 - - + +
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Residues in contact with ILE 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B PHE* 2.9 47.9 + - + +
40B ALA* 3.5 9.4 - - - +
41B GLU 3.2 0.2 - - - -
42B GLN* 1.3 75.4 - - - +
44B ASN* 1.3 62.0 + - - +
46B ILE* 3.3 7.3 + - + +
47B ARG* 2.9 27.4 + - - +
54B TYR* 4.0 10.4 - - + -
61B TYR* 3.6 61.5 - - + +
62B ASN* 5.6 1.1 - - - +
65B GLN* 4.7 9.0 - - + +
294B VAL* 4.2 8.7 - - + -
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Residues in contact with ASN 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B ALA* 3.1 22.3 + - - +
41B GLU* 3.2 12.0 + - + +
43B ILE* 1.3 81.5 - - - +
45B HIS* 1.3 62.2 + - + +
47B ARG* 3.2 34.4 + - - +
48B ASN* 2.9 34.0 + - - +
316D GLU* 4.9 10.7 + - - -
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Residues in contact with HIS 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B GLU* 3.0 41.2 + - + +
42B GLN* 3.4 15.3 - - - +
43B ILE 3.1 0.2 - - - -
44B ASN* 1.3 76.1 - - + +
46B ILE* 1.3 61.0 + - - +
48B ASN* 3.4 3.5 + - - +
49B SER* 2.8 36.1 + - - -
243B PRO* 5.9 2.0 - - + -
250B VAL* 3.9 2.7 - - + -
251B PRO* 3.4 37.3 - - + +
253B VAL* 3.5 24.2 - - + +
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Residues in contact with ILE 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B GLN* 3.1 19.0 + - + +
43B ILE* 3.7 7.0 - - - +
45B HIS* 1.3 74.4 - - - +
47B ARG* 1.3 59.5 + - - +
50B SER* 2.8 51.4 + - - +
53B LEU* 4.3 13.2 - - + -
54B TYR* 4.0 20.6 - - + +
61B TYR* 3.7 30.3 - - + +
250B VAL* 3.7 20.6 - - + -
294B VAL* 3.8 25.4 - - + -
296B LEU* 3.9 12.8 - - + -
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Residues in contact with ARG 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B ILE 2.9 15.8 + - - +
44B ASN* 3.2 38.9 + - - +
46B ILE* 1.3 79.9 - - - +
48B ASN* 1.3 91.5 + - - +
51B PRO* 4.2 17.2 - - - +
54B TYR* 3.6 45.9 + - + +
110C HIS* 3.9 7.3 + - - +
111C THR* 3.7 31.6 + - - +
316D GLU* 4.8 10.9 + - - -
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Residues in contact with ASN 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B ASN* 2.9 23.1 + - - +
45B HIS* 4.2 3.7 + - - +
47B ARG* 1.3 107.0 - - - +
49B SER* 1.3 61.0 + - - +
50B SER 3.7 0.2 - - - -
51B PRO* 4.8 7.2 - - - +
110C HIS* 3.1 60.8 + - + +
147C LEU* 5.5 6.1 - - - +
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Residues in contact with SER 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B HIS* 2.8 19.3 + - - -
48B ASN* 1.3 79.5 - - - +
50B SER* 1.3 60.7 + - - +
51B PRO* 3.6 7.7 - - - +
245B LYS* 4.8 7.2 + - - -
248B SER 5.4 0.3 - - - +
249B ALA* 3.8 17.7 - - - +
250B VAL* 4.1 4.7 - - - -
251B PRO* 3.2 30.0 - - - +
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Residues in contact with SER 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B ILE* 2.8 22.3 + - - +
49B SER* 1.3 80.8 - - - +
51B PRO* 1.3 61.1 - - - +
52B ARG 3.4 1.1 - - - -
53B LEU* 2.9 33.7 + - - +
54B TYR* 3.0 21.7 + - - +
248B SER 4.8 4.9 + - - -
250B VAL* 3.8 21.3 - - - -
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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