Contacts of the helix formed by residues 35 - 45 (chain A) in PDB entry 4D87
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 TYR 35 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A VAL* 4.2 21.1 - - + -
29A LEU* 2.8 7.8 + - + +
30A LYS* 3.4 43.5 - - + +
33A GLY 3.4 0.4 - - - -
34A ILE* 1.3 78.1 - - - +
36A ASP* 1.3 61.8 + - - +
37A ARG 3.1 2.0 - - - -
38A TYR* 2.9 30.5 + - - +
39A ILE* 3.7 10.6 + - + -
76A PHE* 4.0 29.6 - + - -
136A TRP* 3.7 26.0 - + - -
222A PRO 2.9 28.0 + - - -
223A ASN 3.6 9.3 + - - -
225A PRO* 3.8 10.6 - - + +
228A PHE* 3.7 16.0 - + - -
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Residues in contact with ASP 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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30A LYS* 3.4 32.3 + - - +
33A GLY* 4.4 13.8 - - - +
34A ILE 3.4 1.0 - - - +
35A TYR* 1.3 77.7 - - - +
37A ARG* 1.3 60.8 + - - +
38A TYR 2.9 6.4 + - - -
39A ILE* 3.0 19.0 + - - +
40A ALA* 3.1 12.3 + - - +
137A THR* 5.1 0.9 + - - -
139A ILE* 3.2 33.8 - - - +
48B PHE* 4.4 14.3 - - + -
52B PRO* 4.5 12.1 - - - +
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Residues in contact with ARG 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 GLY 4.4 4.8 + - - +
34A ILE* 2.7 40.6 - - - +
36A ASP* 1.3 74.2 - - - +
38A TYR* 1.3 60.2 + - + +
40A ALA* 4.0 8.5 - - - -
41A TRP* 3.3 52.7 + - + -
79A ASP* 5.4 3.1 + - - -
48B PHE* 4.4 10.7 - - + -
258B PHE* 4.6 11.9 - - - -
265B PRO* 3.7 21.5 - - - +
266B MET 4.4 0.2 - - - -
267B TYR* 3.7 30.7 - - + +
269B TRP 3.0 23.4 + - - -
270B ASN* 3.5 20.9 - - - +
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Residues in contact with TYR 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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34A ILE* 3.8 19.7 - - + -
35A TYR* 2.9 12.7 + - + +
36A ASP 2.9 0.6 - - - -
37A ARG* 1.3 81.9 - - + +
39A ILE* 1.3 63.7 + - + +
40A ALA 3.3 0.2 - - - -
41A TRP* 4.0 23.5 - + - -
42A HIS* 3.5 4.2 + - - +
72A TYR* 2.0 70.3 + + + +
75A ARG* 2.5 16.9 + - + +
76A PHE* 2.5 69.9 + + + -
79A ASP* 3.7 21.0 + - + -
222A PRO* 4.7 0.4 - - - -
228A PHE* 4.2 9.2 - - + -
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Residues in contact with ILE 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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30A LYS* 4.1 20.9 - - - +
35A TYR* 4.0 15.5 - - + +
36A ASP* 3.0 14.5 + - - +
38A TYR* 1.3 76.1 - - - +
40A ALA* 1.3 66.1 + - - +
42A HIS* 3.1 5.5 + - - +
43A GLY* 3.0 19.2 + - - -
139A ILE* 4.4 24.0 - - + -
219A PRO 4.4 14.5 - - - +
220A THR* 5.1 0.9 - - - -
222A PRO* 3.9 22.9 - - + +
223A ASN* 3.7 42.8 - - - +
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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 ASP 3.1 12.1 + - - +
37A ARG 4.1 0.4 - - - +
39A ILE* 1.3 76.0 - - - +
41A TRP* 1.3 68.4 + - - +
43A GLY* 2.8 13.9 + - - +
44A ALA* 2.9 9.2 + - - +
48B PHE* 3.8 17.7 - - + -
267B TYR* 2.9 36.9 + - + +
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Residues in contact with TRP 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 ARG* 3.3 45.4 + - + +
38A TYR* 4.0 30.3 - + - -
40A ALA* 1.3 80.2 - - - +
42A HIS* 1.3 56.6 + - - +
44A ALA* 3.0 15.5 + - + +
45A ALA* 3.1 16.1 + - - +
68A TRP* 4.1 3.4 - - + -
72A TYR* 4.1 12.6 - - + -
75A ARG* 3.7 31.0 - - + -
268A PRO* 3.9 24.1 - - + +
269A TRP* 3.6 25.1 - + + -
267B TYR* 3.0 35.0 + + - -
268B PRO* 3.5 22.7 + - + +
269B TRP 5.1 0.4 - - - -
270B ASN* 4.1 18.2 - - - -
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Residues in contact with HIS 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 TYR 3.5 6.5 + - - +
39A ILE 3.1 6.4 + - - +
41A TRP* 1.3 77.2 - - - +
43A GLY* 1.3 59.2 + - - +
44A ALA 3.3 0.2 - - - -
45A ALA* 4.4 2.1 - - - +
46A GLY* 4.0 10.6 + - - -
59A ALA* 4.9 0.9 - - + -
60A HIS* 2.9 20.3 + + - -
68A TRP* 3.1 30.5 - + - -
69A HIS* 2.1 20.4 + + - -
72A TYR* 3.9 3.4 - + + +
208A HIS* 6.0 0.4 - + - -
218A VAL* 3.6 18.3 + - - +
219A PRO* 4.8 1.6 - - - +
221A ALA* 4.7 0.9 - - + -
222A PRO* 3.5 30.4 - - + +
227A PHE* 3.4 22.4 - + - -
401A CU 1.6 32.7 - - - -
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Residues in contact with GLY 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 ILE 3.0 8.4 + - - -
40A ALA* 2.8 7.7 + - - -
42A HIS* 1.3 78.0 - - - +
44A ALA* 1.3 60.3 + - - +
45A ALA 3.6 0.4 - - - -
46A GLY* 3.9 3.2 + - - -
47A LYS* 3.8 24.4 + - - +
219A PRO* 4.2 25.1 - - - +
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Residues in contact with ALA 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 2.9 14.7 + - - +
41A TRP* 3.4 7.0 - - + +
43A GLY* 1.3 78.2 - - - +
45A ALA* 1.3 63.8 + - - +
46A GLY 3.3 1.3 - - - -
47A LYS* 3.4 14.5 + - - +
48A PHE* 3.5 5.7 + - - +
267A TYR* 3.4 22.2 + - + -
268A PRO* 5.6 2.7 - - + -
40B ALA* 5.7 0.3 - - - +
44B ALA* 4.1 18.8 - - + -
267B TYR* 3.6 14.4 - - - +
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Residues in contact with ALA 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 TRP 3.1 6.3 + - - +
42A HIS 5.0 1.6 - - - +
44A ALA* 1.3 73.6 - - - +
46A GLY* 1.3 60.3 + - - +
47A LYS 3.1 4.9 - - - -
48A PHE 3.0 10.9 + - - +
57A ASN* 4.3 0.2 - - - -
58A ALA* 3.3 38.9 + - + -
59A ALA* 4.4 7.0 - - + +
68A TRP* 3.6 34.8 - - + +
267A TYR* 3.9 16.9 - - + +
268A PRO* 4.5 0.9 - - + -
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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