Contacts of the helix formed by residues 33 - 45 (chain A) in PDB entry 1JUV
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 VAL 33 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A TRP* 3.9 32.5 - - + +
31A GLY 3.8 2.0 + - - -
32A ARG* 1.3 74.6 - - - +
34A LYS* 1.3 67.4 + - + +
35A LYS 4.1 3.1 - - - +
36A ASP* 2.9 39.2 + - + +
37A LEU* 3.0 17.7 + - - +
148A ILE* 5.1 4.9 - - + -
150A LYS* 4.8 11.4 - - - +
181A ILE* 3.9 37.2 - - + -
185A THR* 4.9 6.7 - - + -
187A LEU* 4.9 3.1 - - + -
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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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32A ARG 4.0 3.6 + - - +
33A VAL* 1.3 71.4 - - - +
35A LYS* 1.3 57.4 + - - +
37A LEU* 3.2 12.6 + - + +
38A GLN* 2.8 54.9 + - - +
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Residues in contact with LYS 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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33A VAL* 3.3 2.2 - - - +
34A LYS* 1.3 78.4 - - - +
36A ASP* 1.3 58.2 + - - +
38A GLN* 3.6 23.8 - - + +
39A ASN* 2.8 50.5 + - - +
179A TYR* 3.8 42.0 + - + -
181A ILE* 3.8 20.4 - - + -
187A LEU* 3.4 17.9 - - + -
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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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7A ARG* 2.5 52.0 + - - +
28A LEU* 4.1 2.8 - - - +
30A TRP* 3.2 21.9 + - - +
33A VAL* 2.9 26.1 + - + +
35A LYS* 1.3 77.8 - - - +
37A LEU* 1.3 60.4 + - - +
39A ASN* 3.3 5.1 + - - +
40A PHE* 3.0 27.9 + - - +
146A SER* 4.6 3.8 + - - -
148A ILE* 4.3 6.4 - - + +
187A LEU* 3.7 17.1 - - + +
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Residues in contact with LEU 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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7A ARG* 4.6 15.0 - - - +
28A LEU* 5.2 4.5 - - + -
32A ARG* 3.7 57.4 - - + +
33A VAL 3.0 22.6 + - - +
34A LYS* 3.7 12.1 - - + +
36A ASP* 1.3 78.8 - - - +
38A GLN* 1.3 64.6 + - + +
40A PHE* 3.3 9.2 + - + +
41A LYS* 3.1 22.9 + - - +
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Residues in contact with GLN 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* 2.8 38.2 + - - +
35A LYS* 3.6 40.0 - - + +
37A LEU* 1.3 78.6 - - + +
39A ASN* 1.3 64.1 + - - +
41A LYS* 3.4 7.6 + - - +
42A ALA* 3.1 21.7 + - - +
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Residues in contact with ASN 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 LYS* 2.8 45.4 + - - +
36A ASP* 3.6 5.8 - - - +
37A LEU 3.3 0.2 - - - -
38A GLN* 1.3 77.6 - - - +
40A PHE* 1.3 63.8 + - - +
42A ALA* 3.1 8.0 + - - +
43A ARG* 2.9 29.7 + - - +
146A SER* 5.1 4.2 + - - +
179A TYR* 4.3 11.5 + - - -
187A LEU* 3.9 9.7 - - - +
189A GLU* 3.5 39.5 + - + +
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Residues in contact with PHE 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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5A VAL* 4.2 18.4 - - + -
7A ARG* 3.4 39.0 - - - +
36A ASP 3.0 14.7 + - - +
37A LEU* 3.4 14.1 - - + +
38A GLN 3.3 0.2 - - - -
39A ASN* 1.3 75.8 - - - +
41A LYS* 1.3 62.4 + - + +
43A ARG* 3.2 5.5 + - - +
44A THR* 2.8 47.3 + - + +
49A MET* 4.0 1.6 - - - -
59A LEU* 6.4 0.4 - - + -
63A LEU* 3.6 26.2 - - + -
66A ARG* 4.1 5.8 - - - -
127A ILE* 3.7 47.8 - - + -
194A NDP 5.8 0.2 - + - -
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Residues in contact with LYS 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 LEU 3.1 10.4 + - - +
38A GLN* 3.7 9.9 - - - +
39A ASN 3.3 0.2 - - - -
40A PHE* 1.3 78.9 - - - +
42A ALA* 1.3 59.3 + - - +
44A THR* 3.4 7.7 + - - -
45A GLU* 3.0 36.7 + - + +
64A PRO* 4.6 6.7 + - - +
66A ARG* 4.2 31.2 + - - +
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Residues in contact with ALA 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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3A LYS* 5.4 0.3 + - - -
38A GLN 3.1 12.5 + - - +
39A ASN* 3.6 11.0 - - - +
41A LYS* 1.3 78.1 - - - +
43A ARG* 1.3 67.5 + - + +
45A GLU* 3.6 23.9 + - - +
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Residues in contact with ARG 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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3A LYS* 2.8 38.2 + - + +
5A VAL* 4.0 22.7 - - + -
39A ASN 2.9 21.1 + - - +
40A PHE 3.8 3.4 - - - +
42A ALA* 1.3 80.9 - - + +
44A THR* 1.3 61.0 + - - +
45A GLU 3.4 0.7 + - - +
47A THR* 4.3 0.9 - - - +
125A SER* 3.9 1.7 + - - -
142A GLU* 4.2 9.7 + - - -
144A VAL* 3.8 18.9 - - + +
175A GLU* 3.3 26.1 + - - -
177A HIS* 3.7 5.3 - - - -
189A GLU* 2.9 40.6 + - - +
191A VAL* 3.6 23.4 - - - +
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Residues in contact with THR 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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5A VAL* 4.5 6.3 - - + -
40A PHE* 2.8 48.7 + - + +
41A LYS 3.4 5.4 + - - -
43A ARG* 1.3 75.7 - - - +
45A GLU* 1.3 65.1 + - - +
46A GLY 3.4 0.3 + - - -
47A THR* 2.8 26.8 + - - -
49A MET* 3.9 23.3 - - + -
66A ARG* 3.4 30.5 + - - +
125A SER* 4.1 13.0 - - - -
127A ILE* 4.3 4.9 - - + -
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Residues in contact with GLU 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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3A LYS* 5.2 1.0 + - - -
41A LYS* 3.0 24.4 + - + +
42A ALA* 3.6 19.3 - - - +
43A ARG 3.4 2.5 - - - +
44A THR* 1.3 79.1 - - - +
46A GLY* 1.3 66.1 + - - +
47A THR* 3.3 8.0 + - - +
66A ARG* 4.6 8.1 - - - +
123A LYS* 5.4 1.4 - - - -
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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