Contacts of the helix formed by residues 35 - 50 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A PRO* 4.6 1.8 - - - +
34A ILE* 1.3 73.9 + - + +
36A ALA* 1.3 63.4 + - - +
37A GLY 3.2 3.1 - - - +
38A ASP* 3.9 21.8 - - + +
39A PHE* 3.1 19.1 + - - +
255A ARG 3.1 27.3 + - - -
256A ALA* 3.9 7.9 - - - +
291A ARG* 3.3 34.6 - - - +
292A LEU* 3.2 36.1 + - - +
37C GLY* 5.3 1.8 - - - -
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Residues in contact with ALA 36 (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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33A PRO* 4.7 12.9 - - + +
34A ILE 3.3 5.7 + - - +
35A ASN* 1.3 76.6 - - - +
37A GLY* 1.3 61.3 + - - +
39A PHE* 3.6 5.6 + - - +
40A ALA* 3.4 18.7 + - - +
68A LEU* 4.1 36.3 - - + +
292A LEU* 5.4 1.8 - - + -
34C ILE* 3.7 25.1 - - + +
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Residues in contact with GLY 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 ILE 5.0 0.4 + - - -
35A ASN* 3.2 0.6 - - - +
36A ALA* 1.3 76.9 - - - +
38A ASP* 1.3 65.2 + - - +
39A PHE 3.1 1.6 - - - -
40A ALA* 3.1 18.6 + - - +
41A GLU* 3.1 22.6 + - - +
38C ASP* 5.0 15.7 + - - -
255C ARG* 6.2 1.8 - - - -
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Residues in contact with ASP 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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35A ASN* 3.5 25.2 + - + +
37A GLY* 1.3 75.7 - - - +
39A PHE* 1.3 57.4 + - - +
41A GLU* 3.3 20.7 + - - +
42A GLN* 3.1 25.3 + - - +
253A VAL* 3.8 25.3 - - + +
254A GLY* 4.2 8.8 - - - +
256A ALA* 4.0 7.1 - - + +
291A ARG* 5.9 0.4 - - - -
37C GLY* 5.9 2.6 - - - -
38C ASP* 4.4 12.3 - - - +
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Residues in contact with PHE 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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35A ASN 3.1 17.6 + - - +
36A ALA* 3.7 6.5 - - - +
37A GLY 3.1 0.2 - - - -
38A ASP* 1.3 75.3 - - - +
40A ALA* 1.3 60.0 + - - +
42A GLN* 3.0 7.9 + - + +
43A ILE* 2.9 57.2 + - + +
64A VAL* 3.6 24.7 - - + -
65A GLN* 4.6 4.3 - - - -
68A LEU* 4.2 10.3 - - + -
256A ALA* 4.4 6.5 - - - +
270A THR* 3.6 28.5 - - + -
292A LEU* 3.4 50.7 - - + +
293A MSE 4.2 1.1 - - - -
294A VAL* 3.4 27.6 - - + -
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Residues in contact with ALA 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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36A ALA 3.4 9.4 + - - +
37A GLY* 3.1 13.1 + - - +
39A PHE* 1.3 78.4 - - - +
41A GLU* 1.3 60.9 + - + +
43A ILE* 3.2 17.9 + - - +
44A ASN* 3.0 18.6 + - - +
65A GLN* 4.6 17.4 + - - +
68A LEU* 6.0 2.0 - - + -
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Residues in contact with GLU 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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37A GLY 3.1 20.3 + - - +
38A ASP* 3.4 24.9 + - - +
39A PHE 3.2 0.2 - - - -
40A ALA* 1.3 73.4 - - + +
42A GLN* 1.3 58.7 + - - +
44A ASN* 2.6 24.1 - - - +
45A HIS* 3.1 27.9 + - + +
253A VAL* 4.6 11.6 - - + +
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Residues in contact with GLN 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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38A ASP 3.1 11.9 + - - +
39A PHE* 3.0 13.4 + - - +
41A GLU* 1.3 77.3 - - - +
43A ILE* 1.3 64.3 + - - +
45A HIS* 3.3 5.9 + - - +
46A ILE* 3.1 26.1 + - + +
250A VAL* 3.9 1.6 - - - +
251A PRO 3.0 22.5 + - - +
252A LEU* 3.8 0.3 - - - -
253A VAL* 2.9 35.3 + - + +
256A ALA* 3.8 15.9 - - + +
257A SER* 3.4 14.3 - - - -
294A VAL* 4.3 14.1 - - + -
296A LEU* 3.3 28.6 - - + +
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Residues in contact with ILE 43 (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 PHE* 2.9 57.7 + - + +
40A ALA* 3.2 10.0 + - - +
42A GLN* 1.3 77.8 - - - +
44A ASN* 1.3 61.4 + - - +
46A ILE* 3.2 11.0 + - + +
47A ARG* 3.2 15.8 + - - +
54A TYR* 3.8 27.0 - - + +
61A TYR* 3.7 39.3 - - + -
65A GLN* 4.0 20.4 - - - +
294A VAL* 4.3 7.0 - - + -
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Residues in contact with ASN 44 (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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40A ALA 3.0 9.7 + - - +
41A GLU* 2.6 36.2 + - - +
43A ILE* 1.3 76.9 - - - +
45A HIS* 1.3 69.6 + - - +
47A ARG* 3.1 19.3 + - + +
48A ASN* 2.9 52.2 + - - +
110D HIS* 5.9 0.4 + - - -
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Residues in contact with HIS 45 (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 GLU* 3.1 22.0 + - - +
42A GLN* 3.3 19.2 + - - +
43A ILE 3.2 0.6 - - - -
44A ASN* 1.3 90.9 + - - +
46A ILE* 1.3 56.2 + - - +
48A ASN* 4.2 7.4 + - - +
49A SER* 3.0 35.9 + - - -
243A PRO* 6.0 1.3 - - + -
250A VAL* 3.6 2.2 - - + +
251A PRO* 3.5 42.0 - - + +
253A VAL* 3.6 19.1 - - + +
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Residues in contact with ILE 46 (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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42A GLN 3.1 17.5 - - - +
43A ILE* 3.2 12.3 + - - +
45A HIS* 1.3 76.0 - - - +
47A ARG* 1.3 59.0 + - - +
50A SER* 2.8 47.4 + - - +
53A LEU* 4.2 15.5 - - + -
54A TYR* 4.1 17.0 - - + +
61A TYR* 3.4 36.3 - - + +
250A VAL* 3.8 20.6 - - + -
294A VAL* 3.9 22.0 - - + -
296A LEU* 4.1 11.0 - - + -
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Residues in contact with ARG 47 (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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43A ILE* 3.2 7.2 + - - +
44A ASN* 3.1 18.6 + - - +
46A ILE* 1.3 79.6 - - - +
48A ASN* 1.3 73.1 + - - +
51A PRO* 3.9 19.4 - - - +
54A TYR* 2.8 60.2 + - + -
62A ASN* 5.5 2.2 + - - -
110D HIS* 5.7 0.7 - - - -
111D THR* 3.5 31.9 - - - +
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Residues in contact with ASN 48 (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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44A ASN* 2.9 36.0 + - - +
45A HIS* 4.2 8.5 + - - +
47A ARG* 1.3 89.5 - - - +
49A SER* 1.3 61.3 + - - +
51A PRO* 4.6 2.8 - - - +
110D HIS* 3.4 58.3 + - + +
146D ILE 5.7 0.3 - - - +
147D LEU* 5.6 8.8 - - - +
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Residues in contact with SER 49 (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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45A HIS 3.0 18.7 + - - -
48A ASN* 1.3 81.1 - - - +
50A SER* 1.3 62.7 + - - +
51A PRO* 3.2 9.5 - - - +
245A LYS* 4.7 6.1 + - - -
249A ALA 3.5 21.9 + - - +
250A VAL* 3.9 5.8 - - - -
251A PRO* 3.0 24.4 - - - +
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Residues in contact with SER 50 (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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46A ILE 2.8 23.2 + - - +
49A SER* 1.3 74.8 + - - +
51A PRO* 1.3 60.5 - - - +
52A ARG* 3.2 3.1 - - - +
53A LEU* 3.3 23.2 + - - +
54A TYR 3.0 20.1 + - - -
248A SER 3.2 23.9 + - - -
249A ALA* 4.6 1.9 + - - +
250A VAL* 3.4 11.7 - - - +
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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