Contacts of the helix formed by residues 35 - 50 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A ILE 4.7 2.0 - - - -
33C PRO 4.3 2.3 - - - -
34C ILE* 1.3 79.5 + - - +
36C ALA* 1.3 58.8 + - - +
37C GLY 3.2 3.1 - - - -
38C ASP* 3.0 15.1 + - + +
39C PHE* 2.9 26.4 + - - +
255C ARG 3.3 19.8 + - - -
256C ALA* 4.0 6.1 - - - +
291C ARG* 3.1 35.8 - - - +
292C LEU* 2.7 52.8 + - - +
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Residues in contact with ALA 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ILE* 3.6 29.5 + - + -
33C PRO* 3.7 18.6 + - + +
34C ILE 3.6 2.0 - - - -
35C ASN* 1.3 77.1 + - - +
37C GLY* 1.3 61.1 + - - +
39C PHE* 3.5 5.8 + - - +
40C ALA* 3.1 24.3 + - - +
68C LEU* 3.6 33.5 - - + +
69C ARG* 5.0 0.3 + - - -
292C LEU* 5.3 0.4 - - - -
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Residues in contact with GLY 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ILE* 3.1 31.6 + - - +
35A ASN* 5.3 2.0 - - - -
38A ASP* 5.9 2.5 - - - -
36C ALA* 1.3 76.6 - - - +
38C ASP* 1.3 65.4 + - - +
40C ALA* 3.4 6.7 + - - +
41C GLU* 3.1 22.2 + - - +
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Residues in contact with ASP 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ILE 4.6 2.3 + - - +
37A GLY* 5.0 14.2 + - - -
38A ASP* 4.4 12.0 - - - +
35C ASN* 3.0 22.3 + - + +
37C GLY* 1.3 77.0 - - - +
39C PHE* 1.3 62.3 + - - +
41C GLU* 3.4 15.0 + - - +
42C GLN* 3.3 15.8 + - - +
253C VAL* 3.7 11.4 - - + +
254C GLY 3.8 14.6 - - - +
256C ALA* 3.5 26.1 - - + +
291C ARG* 4.4 4.5 + - - -
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Residues in contact with PHE 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C ASN 2.9 15.5 + - - +
36C ALA* 3.8 6.1 - - - +
38C ASP* 1.3 75.4 - - - +
40C ALA* 1.3 65.4 + - - +
41C GLU 3.1 0.2 - - - -
42C GLN* 3.1 14.5 + - + +
43C ILE* 3.3 35.3 + - + +
61C TYR* 4.5 1.1 - + - -
64C VAL* 3.5 27.4 - - + -
65C GLN* 4.3 9.4 - - - -
68C LEU* 4.4 4.3 - - + -
256C ALA* 4.2 6.9 - - - +
270C THR* 3.6 31.0 - - + -
292C LEU* 3.7 50.3 - - + +
293C MSE 4.5 1.8 - - - -
294C VAL* 3.5 31.0 - - + -
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Residues in contact with ALA 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C ALA 3.1 17.7 + - - +
37C GLY* 3.7 7.2 - - - +
38C ASP 3.4 0.2 - - - -
39C PHE* 1.3 76.2 - - - +
41C GLU* 1.3 60.9 + - - +
43C ILE* 3.6 6.1 + - - +
44C ASN* 3.4 19.6 + - - +
47C ARG* 4.9 2.3 + - - -
65C GLN* 4.0 17.6 + - - +
69C ARG* 4.0 26.7 - - - +
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Residues in contact with GLU 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C GLY 3.1 13.4 + - - +
38C ASP* 3.5 14.3 - - - +
39C PHE 3.1 0.4 - - - -
40C ALA* 1.3 76.2 - - - +
42C GLN* 1.3 63.0 + - - +
44C ASN* 3.3 9.1 + - + +
45C HIS* 3.1 42.3 + - + +
253C VAL* 3.3 28.2 - - + +
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Residues in contact with GLN 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C ASP 3.3 6.2 + - - +
39C PHE* 3.1 12.8 + - - +
41C GLU* 1.3 77.0 - - - +
43C ILE* 1.3 59.6 + - - +
45C HIS* 3.0 7.6 + - - +
46C ILE* 2.9 35.4 + - + +
250C VAL* 4.3 0.4 - - - +
251C PRO 3.2 17.8 + - - -
252C LEU* 3.6 3.3 - - - -
253C VAL* 2.9 43.6 + - + +
256C ALA* 3.6 18.8 - - + +
257C SER* 3.1 19.7 - - - -
294C VAL* 4.7 12.6 - - + -
296C LEU* 3.4 23.3 - - + +
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Residues in contact with ILE 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C PHE* 3.3 45.9 + - + +
40C ALA* 3.8 7.0 - - - +
41C GLU 3.3 0.2 - - - -
42C GLN* 1.3 76.4 - - + +
44C ASN* 1.3 56.9 + - - +
46C ILE* 3.7 8.7 - - + +
47C ARG* 2.9 37.0 + - - +
54C TYR* 3.5 30.1 - - + +
61C TYR* 3.9 28.7 - - + -
65C GLN* 3.8 32.8 - - + +
294C VAL* 5.5 0.4 - - + -
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Residues in contact with ASN 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316A GLU* 5.7 1.2 - - - +
40C ALA 3.4 9.2 + - - +
41C GLU* 3.3 12.0 + - + +
42C GLN 3.2 0.6 - - - -
43C ILE* 1.3 77.6 - - - +
45C HIS* 1.3 68.4 + - - +
47C ARG* 2.9 38.5 + - - +
48C ASN* 3.0 57.0 + - - +
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Residues in contact with HIS 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C GLU* 3.1 27.3 + - + +
42C GLN* 3.0 9.7 + - - +
44C ASN* 1.3 86.6 + - - +
46C ILE* 1.3 58.4 + - - +
48C ASN* 4.5 4.3 - - - +
49C SER* 2.8 37.6 + - - +
250C VAL* 3.9 4.4 - - + +
251C PRO* 3.3 50.0 + - + +
252C LEU 5.5 0.9 - - - -
253C VAL* 3.7 24.1 - - + +
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Residues in contact with ILE 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C GLN 2.9 24.7 + - - +
43C ILE* 3.7 7.4 - - - +
45C HIS* 1.3 76.3 - - - +
47C ARG* 1.3 57.4 + - - +
50C SER* 2.8 42.4 + - - +
53C LEU* 4.9 10.5 - - + -
54C TYR* 3.4 30.6 - - + +
61C TYR* 3.4 29.4 - - + +
250C VAL* 3.9 21.8 - - + -
294C VAL* 4.0 23.1 - - + -
296C LEU* 4.1 13.2 - - + -
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Residues in contact with ARG 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B THR* 5.8 9.4 - - + +
40C ALA 4.9 2.2 + - - -
43C ILE* 2.9 24.3 + - - +
44C ASN* 2.9 45.2 + - - +
45C HIS 3.2 0.2 - - - -
46C ILE* 1.3 80.2 - - - +
48C ASN* 1.3 64.3 + - - +
51C PRO* 4.0 17.0 - - - +
54C TYR* 3.2 50.4 + - + -
65C GLN* 6.0 1.6 - - - +
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Residues in contact with ASN 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B HIS* 3.7 50.2 + - + +
111B THR* 5.5 3.3 - - - +
146B ILE 5.7 1.4 - - - +
147B LEU* 6.1 1.2 - - - +
44C ASN* 3.0 40.8 + - - +
45C HIS* 4.2 4.4 - - - +
47C ARG* 1.3 90.3 + - - +
49C SER* 1.3 65.0 + - - +
50C SER 3.4 0.6 + - - -
51C PRO* 3.8 9.1 - - - +
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Residues in contact with SER 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C HIS* 2.8 21.3 + - - -
48C ASN* 1.3 76.2 - - - +
50C SER* 1.3 58.4 + - - +
51C PRO* 3.7 2.4 - - - +
52C ARG* 3.6 14.9 + - - -
245C LYS* 4.6 8.9 + - - -
249C ALA 3.9 14.6 - - - +
250C VAL* 4.4 2.7 - - - -
251C PRO* 3.3 31.1 - - - +
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Residues in contact with SER 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C ILE* 2.8 21.3 + - - +
49C SER* 1.3 80.8 - - - +
51C PRO* 1.3 59.0 - - - +
52C ARG* 3.0 35.2 + - - +
53C LEU* 3.5 16.0 - - - +
54C TYR 3.1 13.5 + - - -
248C SER 4.8 3.8 + - - -
250C VAL* 3.9 23.8 - - - -
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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