Contacts of the helix formed by residues 28 - 41 (chain A) in PDB entry 3V50
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 GLN 28 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A PRO* 1.3 76.4 - - - +
29A PRO* 1.3 74.1 - - + +
30A LEU* 3.4 3.1 - - + +
31A GLU* 3.1 20.5 + - + +
32A GLN* 2.9 26.0 + - - +
289A HIS* 3.3 40.3 + - - +
292A ARG* 4.4 11.1 - - - +
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Residues in contact with PRO 29 (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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27A PRO 3.8 0.4 - - - -
28A GLN* 1.3 93.7 - - + +
30A LEU* 1.3 56.4 + - - +
32A GLN* 3.2 4.0 + - - +
33A ILE* 2.9 37.7 + - + +
46A MET* 5.2 0.2 - - + -
58A THR* 4.5 14.6 - - + +
282A ILE* 5.1 2.2 - - + +
285A ALA* 3.8 31.2 - - + +
286A LEU* 3.9 28.3 - - + -
289A HIS* 4.1 5.8 - - + -
292A ARG* 4.0 22.4 - - - +
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Residues in contact with LEU 30 (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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28A GLN* 3.4 3.2 - - + +
29A PRO* 1.3 78.6 - - + +
31A GLU* 1.3 57.9 + - - +
33A ILE* 3.3 6.7 + - + +
34A LYS* 3.0 43.8 + - - +
58A THR* 3.7 27.1 - - + -
59A ALA 4.1 16.4 - - - +
60A TRP* 4.2 26.2 - - + -
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Residues in contact with GLU 31 (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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27A PRO* 3.3 26.2 - - + +
28A GLN* 3.1 24.7 + - + +
30A LEU* 1.3 78.6 - - - +
32A GLN* 1.3 57.3 + - - +
34A LYS* 3.4 11.9 + - + +
35A LEU* 3.0 40.9 + - + +
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Residues in contact with GLN 32 (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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26A SER* 5.3 2.2 - - - -
27A PRO* 3.6 28.5 - - + +
28A GLN 2.9 13.5 + - - +
29A PRO 3.5 7.2 - - - +
31A GLU* 1.3 75.6 - - - +
33A ILE* 1.3 65.3 + - - +
35A LEU* 3.2 14.7 + - - +
36A SER* 2.9 32.9 + - - -
39A GLN* 5.4 0.9 - - - +
278A GLN* 3.7 8.5 - - - +
281A GLY* 3.4 36.7 + - - +
282A ILE* 3.8 9.9 - - + +
285A ALA* 3.9 11.9 - - + -
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Residues in contact with ILE 33 (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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29A PRO 2.9 26.0 + - - +
30A LEU* 3.3 11.9 + - - +
32A GLN* 1.3 74.1 - - - +
34A LYS* 1.3 64.5 + - - +
36A SER* 3.2 5.4 + - - -
37A GLU* 3.1 20.8 + - - +
44A VAL* 3.9 12.2 - - + +
46A MET* 3.8 39.7 - - + -
58A THR* 4.3 4.7 - - + -
60A TRP* 3.3 48.5 - - + +
282A ILE* 4.0 29.6 - - + -
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Residues in contact with LYS 34 (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 LEU* 3.0 32.4 + - - +
31A GLU* 3.7 9.2 - - + +
32A GLN 3.2 0.2 - - - -
33A ILE* 1.3 77.0 - - - +
35A LEU* 1.3 61.9 + - + +
37A GLU* 3.1 10.0 + - - +
38A SER* 3.0 22.1 + - - -
60A TRP* 3.8 39.0 - - + -
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Residues in contact with LEU 35 (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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27A PRO* 4.0 24.0 - - + -
31A GLU* 3.0 27.7 + - + +
32A GLN* 3.2 19.0 + - - +
34A LYS* 1.3 75.6 - - + +
36A SER* 1.3 57.6 + - - +
38A SER* 3.2 9.6 + - - -
39A GLN* 2.8 53.9 + - + +
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Residues in contact with SER 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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32A GLN* 2.9 19.6 + - - -
33A ILE* 3.2 11.2 + - - -
35A LEU* 1.3 77.4 - - - +
37A GLU* 1.3 57.7 + - - +
39A GLN 3.3 0.5 + - - -
40A LEU* 2.8 37.9 + - - +
44A VAL* 4.4 13.0 - - - -
265A LEU* 6.0 0.2 - - - -
278A GLN* 2.8 45.9 + - - +
282A ILE* 4.0 7.8 - - - +
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Residues in contact with GLU 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 3.1 9.8 + - - +
34A LYS* 3.1 9.0 + - - +
36A SER* 1.3 74.2 - - - +
38A SER* 1.3 58.4 + - - +
40A LEU* 4.6 0.7 - - - +
41A SER* 2.8 31.5 + - - -
42A GLY 3.3 21.5 + - - +
43A ARG* 4.1 1.1 - - - -
44A VAL* 2.9 32.6 + - + +
60A TRP* 2.9 22.5 + - + +
61A ARG* 2.7 45.0 + - - -
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Residues in contact with SER 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 LYS 3.0 12.7 + - - -
35A LEU* 3.5 14.4 - - - -
37A GLU* 1.3 78.0 - - - +
39A GLN* 1.3 65.6 + - - +
41A SER* 3.8 9.5 + - - -
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Residues in contact with GLN 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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32A GLN* 5.4 0.5 - - - +
35A LEU* 2.8 39.1 + - + +
36A SER 4.0 0.4 - - - +
38A SER* 1.3 82.6 - - - +
40A LEU* 1.3 61.0 + - - +
41A SER* 3.7 2.3 + - - -
278A GLN* 2.6 42.0 + - - +
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Residues in contact with LEU 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A SER* 2.8 24.5 + - - +
37A GLU* 4.9 0.4 - - - -
39A GLN* 1.3 78.9 - - - +
41A SER* 1.3 68.0 + - - +
42A GLY* 4.0 7.9 - - - +
44A VAL* 4.9 4.0 - - + -
265A LEU* 3.8 32.5 - - + -
268A THR* 2.6 30.5 + - + +
269A PRO* 3.5 6.6 - - - +
270A ALA* 3.6 28.0 - - + +
274A GLU* 4.1 15.3 - - + +
275A ARG* 4.3 4.5 - - + +
278A GLN* 3.7 35.0 - - + +
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Residues in contact with SER 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 GLU 2.8 12.9 + - - -
38A SER* 3.8 8.2 + - - +
39A GLN 3.4 3.4 + - - -
40A LEU* 1.3 78.7 - - - +
42A GLY* 1.3 56.0 + - - +
267A ASP 3.2 11.8 - - - +
268A THR* 4.4 0.9 - - - -
269A PRO* 4.5 10.6 - - - +
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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