Contacts of the helix formed by residues 37 - 49 (chain A) in PDB entry 5JJA
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 ASP 37 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A VAL* 4.2 11.9 - - + -
34A PRO* 2.8 39.7 + - - +
36A ALA* 1.3 81.2 - - - +
38A GLN* 1.3 61.1 + - - +
39A GLU 3.5 1.8 - - - -
40A LYS* 3.5 17.6 + - + +
41A LEU* 3.2 21.9 + - + +
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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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30A ILE* 3.6 24.4 - - + +
31A ARG* 3.6 17.9 + - - +
33A VAL* 3.0 26.1 + - + +
34A PRO 3.6 10.3 - - - +
35A PRO* 3.6 27.2 + - + +
36A ALA 3.5 2.2 - - - -
37A ASP* 1.3 75.9 - - - +
39A GLU* 1.3 61.4 + - - +
41A LEU* 3.3 2.9 + - - +
42A PHE* 2.9 31.2 + - - +
79A TYR* 2.8 39.3 + - - +
86A VAL* 4.7 3.3 - - - +
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Residues in contact with GLU 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 PRO 4.9 1.6 + - - +
36A ALA 5.1 2.6 + - - +
37A ASP 3.5 0.4 - - - -
38A GLN* 1.3 77.7 - - - +
40A LYS* 1.3 58.2 + - - +
42A PHE* 3.2 8.2 + - - +
43A ILE* 2.9 44.5 + - + +
79A TYR* 4.9 1.3 + - - -
86A VAL 5.9 1.1 - - - +
88A THR* 2.6 39.5 + - + +
90A PRO* 3.9 22.5 - - - +
91A ILE* 4.2 8.5 - - + -
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Residues in contact with LYS 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 5.6 1.5 + - - +
37A ASP* 3.5 20.6 + - + +
38A GLN 3.3 0.2 - - - -
39A GLU* 1.3 79.6 + - - +
41A LEU* 1.3 57.5 + - - +
43A ILE* 3.4 9.8 + - - +
44A GLN* 2.9 41.1 + - + +
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Residues in contact with LEU 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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29A GLY 5.2 0.4 - - - +
30A ILE* 4.3 20.2 - - + -
33A VAL* 4.1 32.5 - - + -
37A ASP 3.2 10.6 + - - +
38A GLN* 3.7 7.2 - - - +
40A LYS* 1.3 78.2 - - - +
42A PHE* 1.3 60.9 + - - +
44A GLN* 3.2 29.3 + - + +
45A LYS* 2.9 52.2 + - + +
75A GLU* 5.6 0.4 - - - +
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Residues in contact with PHE 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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30A ILE* 4.0 18.6 - - + +
38A GLN 2.9 17.6 + - - +
39A GLU* 3.4 7.6 - - - +
41A LEU* 1.3 74.3 - - - +
43A ILE* 1.3 64.2 + - - +
45A LYS* 3.2 3.7 + - - +
46A LEU* 3.0 27.7 + - + +
76A MET* 3.7 31.2 - - + -
79A TYR* 3.7 21.5 - + + -
80A ILE* 3.6 29.4 - - + -
86A VAL 3.9 14.4 - - - -
87A ILE* 5.1 0.9 - - + -
91A ILE* 3.4 39.5 - - + -
140A PHE* 4.0 13.9 - + - -
144A PHE* 6.5 0.2 - + - -
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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 GLU* 2.9 37.3 + - + +
40A LYS* 3.6 7.6 - - - +
42A PHE* 1.3 75.8 - - - +
44A GLN* 1.3 65.2 + - - +
46A LEU* 3.2 9.6 + - - +
47A ARG* 3.0 54.9 + - - +
90A PRO* 4.3 22.0 - - + +
91A ILE* 3.8 14.8 - - + -
94A GLU* 4.0 20.0 - - + +
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Residues in contact with GLN 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 LYS* 2.9 28.3 + - - +
41A LEU* 3.2 30.5 + - + +
43A ILE* 1.3 77.5 - - - +
45A LYS* 1.3 58.9 + - + +
47A ARG* 3.3 8.7 + - - +
48A GLN* 3.1 47.8 + - + +
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Residues in contact with LYS 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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30A ILE* 3.8 26.7 - - + -
41A LEU* 2.9 33.0 + - + +
42A PHE 3.2 7.2 + - - +
44A GLN* 1.3 74.8 - - + +
46A LEU* 1.3 66.6 + - - +
48A GLN* 3.3 20.1 + - - +
49A CYS* 3.1 27.7 + - - -
72A ALA* 4.5 19.7 - - + +
75A GLU* 3.3 34.3 + - - +
76A MET* 3.7 19.7 - - + -
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Residues in contact with LEU 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 PHE* 3.0 29.5 + - + +
43A ILE* 3.2 12.1 + - - +
45A LYS* 1.3 75.7 - - - +
47A ARG* 1.3 62.4 + - + +
49A CYS* 3.4 8.4 + - - -
50A CYS* 3.5 5.4 + - - -
76A MET* 3.4 29.1 - - + -
91A ILE* 4.4 9.0 - - + -
94A GLU* 3.7 33.2 - - + +
95A VAL* 3.9 20.2 - - + -
98A MET* 3.4 37.2 - - + +
140A PHE* 4.0 16.8 - - + -
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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* 3.0 32.8 + - - +
44A GLN* 3.7 7.0 - - - +
46A LEU* 1.3 74.8 - - - +
48A GLN* 1.3 64.3 + - - +
50A CYS* 3.0 27.8 + - - +
51A VAL* 4.1 3.6 + - - +
94A GLU* 2.9 40.8 + - - +
97A HIS* 6.2 0.9 - - - +
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Residues in contact with GLN 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 GLN* 3.1 41.6 + - + +
45A LYS* 3.5 23.7 + - - +
47A ARG* 1.3 76.3 - - - +
49A CYS* 1.3 59.9 + - - +
50A CYS 3.1 0.2 - - - -
51A VAL* 3.2 32.1 + - - +
53A PHE* 5.8 0.2 - - - -
68A VAL* 5.0 10.6 - - - +
69A LYS* 4.8 4.4 - - - +
72A ALA* 4.8 9.6 - - + +
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Residues in contact with CYS 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 LYS 3.1 19.6 + - - +
46A LEU 3.7 7.9 - - - +
47A ARG 3.1 0.8 - - - -
48A GLN* 1.3 75.9 - - - +
50A CYS* 1.3 57.9 + - - +
51A VAL 3.2 1.1 - - - -
69A LYS* 2.9 39.4 + - - +
72A ALA* 3.9 18.2 - - - -
73A LEU* 3.8 26.9 - - + -
76A MET* 3.7 20.2 - - + -
98A MET* 4.1 11.0 - - + -
102A ASN* 3.0 14.7 + - - -
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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