Contacts of the helix formed by residues 36 - 53 (chain A) in PDB entry 4PYP
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 PRO 36 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A VAL* 3.1 20.6 - - + +
33A ILE* 3.9 7.9 - - - -
35A ALA* 1.3 95.2 - - + +
37A GLN* 1.3 61.8 + - - +
38A LYS 3.6 2.0 - - - -
39A VAL* 3.6 17.8 + - + +
40A ILE* 3.2 33.6 + - + +
175A GLY* 5.2 0.4 - - - -
181A GLY* 4.1 24.2 - - - +
186A TRP* 5.2 4.5 - - + -
189A LEU* 3.9 21.5 - - + -
190A LEU* 5.7 1.3 - - + -
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Residues in contact with GLN 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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33A ILE 3.9 13.0 - - - +
34A ASN 4.5 8.0 - - - +
35A ALA 3.5 3.2 + - - -
36A PRO* 1.3 73.8 - - - +
38A LYS* 1.3 62.5 + - + +
39A VAL 3.1 4.8 + - - -
40A ILE* 3.3 4.0 + - - +
41A GLU* 2.9 54.6 + - - +
65A TRP* 3.7 25.8 - - + +
292A TYR 4.5 3.1 - - - +
293A TYR* 3.9 11.1 - - - -
296A SER* 3.3 30.6 + - - -
423A GLN* 2.9 31.3 - - - +
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Residues in contact with LYS 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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36A PRO 3.6 0.4 - - - -
37A GLN* 1.3 82.9 - - + +
39A VAL* 1.3 66.6 + - + +
41A GLU* 3.7 16.3 + - + +
42A GLU* 3.0 45.0 + - - +
299A GLU* 4.0 26.9 + - - +
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Residues in contact with VAL 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 ALA 5.5 0.2 - - - +
36A PRO* 3.6 20.6 - - + +
37A GLN 3.1 0.4 - - - -
38A LYS* 1.3 84.0 - - + +
40A ILE* 1.3 63.5 + - + +
42A GLU* 3.4 13.8 + - - +
43A PHE* 3.3 16.3 + - - +
181A GLY 4.0 19.3 - - - +
182A ASN* 3.5 10.1 - - - +
183A LYS* 3.5 35.5 - - + +
186A TRP* 3.5 19.9 + - + -
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Residues in contact with ILE 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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33A ILE* 5.2 0.9 - - + -
36A PRO* 3.2 26.2 - - + +
37A GLN 3.3 1.3 + - - +
39A VAL* 1.3 73.3 - - - +
41A GLU* 1.3 55.1 + - - +
42A GLU 3.1 0.2 - - - -
43A PHE* 2.8 19.4 + - + +
44A TYR* 2.5 41.2 + - + -
65A TRP* 3.8 32.8 - - + -
122A LEU* 3.7 24.9 - - + -
186A TRP* 4.0 34.8 - - + -
190A LEU* 4.2 19.3 - - + -
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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 GLN* 2.9 49.9 + - - +
38A LYS* 3.9 14.2 + - + +
40A ILE* 1.3 76.6 - - - +
42A GLU* 1.3 53.0 + - - +
44A TYR* 2.9 9.3 + - - +
45A THR* 2.6 38.5 + - - +
61A LEU* 3.6 34.5 - - + +
62A THR* 5.6 0.3 - - - -
65A TRP* 3.5 28.3 - - + +
423A GLN* 4.7 3.5 + - - +
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Residues in contact with GLU 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 LYS* 3.0 40.6 + - + +
39A VAL* 3.4 12.4 - - - +
41A GLU* 1.3 75.4 - - - +
43A PHE* 1.3 56.6 - - - +
45A THR* 3.2 12.1 - - + +
46A GLN* 3.1 32.4 + - - +
183A LYS* 4.2 22.0 - - + +
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Residues in contact with PHE 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 VAL 3.3 5.0 + - - +
40A ILE* 2.8 13.3 + - + +
42A GLU* 1.3 76.9 - - - +
44A TYR* 1.3 81.8 + + - +
46A GLN* 4.8 3.4 - - + +
47A THR* 2.5 53.3 + - - -
113A SER* 3.1 28.9 - - - -
114A LYS* 4.3 9.2 - - - -
117A LYS* 4.5 5.4 - - - -
118A SER 4.2 21.1 - - - -
119A PHE* 4.6 3.8 - - + -
122A LEU* 5.0 1.8 - - + -
183A LYS* 4.7 13.4 - - - +
186A TRP* 3.3 45.3 - + + +
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Residues in contact with TYR 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 ILE* 2.5 23.4 + - + +
41A GLU* 2.9 11.6 + - - +
43A PHE* 1.3 81.6 - + - +
45A THR* 1.3 58.0 + - - +
47A THR* 3.5 5.1 - - - -
48A TRP* 3.0 29.1 + - - +
56A ILE* 4.5 3.2 - - + +
61A LEU* 4.0 16.4 - - + -
64A LEU* 3.7 35.7 - - + -
65A TRP* 3.8 26.0 - + + -
68A SER* 2.4 32.3 + - - -
119A PHE* 3.3 38.3 + + + +
122A LEU* 3.0 32.0 - - + +
123A ILE* 4.2 0.7 - - + +
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Residues in contact with THR 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 2.6 22.8 + - - +
42A GLU* 3.2 18.2 - - + +
44A TYR* 1.3 74.1 - - - +
46A GLN* 1.3 63.1 + - + +
48A TRP* 3.6 2.6 + - - +
49A VAL* 3.1 27.4 + - - +
55A SER* 4.3 8.0 + - - -
56A ILE* 3.3 34.9 - - - +
61A LEU* 4.7 6.5 - - + -
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Residues in contact with GLN 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 GLU* 3.1 19.6 + - - +
43A PHE* 4.1 4.6 - - + +
45A THR* 1.3 76.4 - - + +
47A THR* 1.3 66.5 + - - +
49A VAL* 3.2 5.8 + - + +
50A HIS* 3.1 56.0 + - + +
183A LYS* 4.7 15.8 - - - +
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Residues in contact with THR 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 PHE* 2.5 46.8 + - + -
44A TYR* 3.5 4.9 - - - -
46A GLN* 1.3 79.3 - - - +
48A TRP* 1.3 61.8 + - - +
50A HIS* 3.5 6.6 + - - +
51A ARG* 3.1 36.8 + - - +
117A LYS* 3.3 36.8 - - + +
119A PHE* 3.9 18.4 - - + -
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Residues in contact with TRP 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 TYR 3.0 15.8 + - - +
45A THR 3.7 6.3 - - - +
47A THR* 1.3 77.6 - - - +
49A VAL* 1.3 56.5 + - - +
51A ARG* 3.3 1.4 + - - +
52A TYR* 2.9 66.1 + + + +
54A GLU* 3.3 38.6 + - - -
55A SER 3.9 11.1 + - - -
56A ILE* 3.7 28.3 - - + -
57A LEU 5.7 0.9 - - - -
60A THR* 3.7 28.5 - - + -
64A LEU* 4.2 17.0 - - + -
119A PHE* 4.6 14.6 - + - -
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Residues in contact with VAL 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 THR* 3.1 18.2 - - - +
46A GLN* 3.2 9.9 + - + +
48A TRP* 1.3 73.0 - - - +
50A HIS* 1.3 75.6 + - + +
53A GLY* 3.1 23.4 + - - -
54A GLU 3.0 20.0 - - - +
55A SER* 3.5 28.0 - - - +
56A ILE 4.5 0.2 - - - +
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Residues in contact with HIS 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 GLN* 3.1 43.5 + - + +
47A THR* 3.9 6.1 - - - +
49A VAL* 1.3 86.7 - - + +
51A ARG* 1.3 64.4 + - - +
53A GLY* 4.1 3.1 + - - -
117A LYS* 5.7 11.2 - - + -
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Residues in contact with ARG 51 (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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47A THR* 3.1 21.1 + - - +
48A TRP* 3.8 2.5 - - - +
50A HIS* 1.3 82.6 - - - +
52A TYR* 1.3 100.1 + - + +
53A GLY 3.5 0.3 + - - -
117A LYS* 2.6 53.0 + - + +
118A SER* 3.4 5.5 - - - +
119A PHE* 3.6 18.2 - - - -
120A GLU* 2.6 41.5 + - - -
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Residues in contact with TYR 52 (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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48A TRP* 2.9 66.9 + + + +
51A ARG* 1.3 116.3 + - + +
53A GLY* 1.3 64.0 + - - +
54A GLU* 3.1 10.4 + - + +
119A PHE* 5.1 4.7 - + - -
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Residues in contact with GLY 53 (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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49A VAL* 3.1 14.6 + - - -
50A HIS 4.1 2.8 + - - -
51A ARG 3.4 3.6 + - - -
52A TYR* 1.3 77.4 - - - +
54A GLU* 1.3 57.7 + - - +
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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