Contacts of the helix formed by residues 23 - 39 (chain K) in PDB entry 3J8B
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 23 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21K TYR 3.7 4.8 - - - +
22K ASN* 1.3 65.0 - - - +
24K GLU* 1.3 60.2 + - - +
25K ASN 2.9 5.8 - - - -
26K LEU* 3.0 25.8 + - + +
27K ALA 4.7 0.2 + - - -
53K LEU* 5.1 13.6 - - + -
57K ASN* 4.3 23.6 - - + -
60K PHE* 5.3 8.5 - - + -
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Residues in contact with GLU 24 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22K ASN* 3.0 9.7 + - + +
23K PRO* 1.3 78.7 - - - +
25K ASN* 1.3 57.4 + - - +
26K LEU 3.3 1.3 + - - -
27K ALA* 4.3 10.0 + - - +
28K THR 5.3 0.2 + - - -
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Residues in contact with ASN 25 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14K LEU* 6.0 6.1 - - + -
19K ASP* 4.4 12.8 - - + +
20K ARG* 5.8 2.2 - - - -
22K ASN* 3.0 13.3 + - + +
23K PRO 2.9 0.6 - - - -
24K GLU* 1.3 79.1 - - - +
26K LEU* 1.3 61.9 + - - +
27K ALA 3.4 1.8 - - - -
28K THR* 3.3 12.8 + - - +
29K LEU* 3.1 20.5 + - - +
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Residues in contact with LEU 26 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22K ASN 4.4 0.4 + - - -
23K PRO* 3.0 21.9 + - + +
25K ASN* 1.3 75.1 - - - +
27K ALA* 1.3 58.9 + - - +
29K LEU* 3.0 7.5 + - - +
30K GLU* 2.7 38.6 + - + +
53K LEU* 5.8 7.0 - - + -
60K PHE* 5.5 10.1 - - + -
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Residues in contact with ALA 27 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24K GLU 4.3 9.0 + - - +
25K ASN 3.4 0.8 - - - -
26K LEU* 1.3 78.3 - - - +
28K THR* 1.3 61.9 + - - +
30K GLU* 4.0 5.3 - - - +
31K ARG* 3.3 21.5 + - - +
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Residues in contact with THR 28 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7K MET* 6.1 0.3 - - - +
24K GLU 5.3 0.2 + - - -
25K ASN* 3.3 14.4 + - - +
26K LEU 3.1 0.4 - - - -
27K ALA* 1.3 78.0 - - - +
29K LEU* 1.3 64.0 + - - +
31K ARG* 3.4 6.6 + - - +
32K TYR* 3.1 20.4 + - - +
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Residues in contact with LEU 29 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11K VAL* 6.6 0.2 - - - -
25K ASN 3.1 12.9 + - - +
26K LEU* 3.0 10.6 + - - +
28K THR* 1.3 76.5 - - - +
30K GLU* 1.3 58.4 + - - +
32K TYR* 3.2 10.4 - - - +
33K VAL* 3.0 24.6 + - - +
46K ALA* 5.4 7.9 - - + +
50K VAL* 5.0 17.5 - - + -
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Residues in contact with GLU 30 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26K LEU* 2.7 22.7 + - + +
27K ALA* 4.0 4.9 - - - +
29K LEU* 1.3 69.2 - - - +
31K ARG* 1.3 66.3 + - - +
33K VAL* 3.2 9.2 + - - +
34K GLU* 3.0 21.7 + - - +
65K VAL* 4.9 16.8 - - + +
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Residues in contact with ARG 31 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27K ALA 3.3 15.6 + - - +
28K THR* 3.8 7.2 - - - +
30K GLU* 1.3 79.6 - - - +
32K TYR* 1.3 56.9 + - - +
34K GLU* 3.3 9.0 + - - +
35K THR* 3.0 27.2 + - - -
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Residues in contact with TYR 32 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7K MET* 5.1 16.8 - - + -
11K VAL* 5.5 10.8 - - + -
28K THR 3.1 13.5 + - - +
29K LEU* 3.2 15.3 - - - +
30K GLU 3.1 0.2 - - - -
31K ARG* 1.3 75.8 - - - +
33K VAL* 1.3 63.3 + - - +
35K THR* 3.3 8.8 + - - +
36K GLN* 3.1 20.8 + - - +
46K ALA* 5.9 6.3 - - + -
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Residues in contact with VAL 33 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29K LEU 3.0 11.9 + - - +
30K GLU* 3.2 11.8 + - - +
32K TYR* 1.3 75.0 - - - +
34K GLU* 1.3 66.0 + - - +
36K GLN* 3.0 18.1 + - - +
37K ALA* 3.1 13.3 + - - +
47K ASN* 6.4 2.7 - - + -
65K VAL* 5.2 16.4 - - + +
68K GLN* 5.6 9.4 - - + +
69K ILE* 6.1 4.0 - - + +
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Residues in contact with GLU 34 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30K GLU 3.0 13.1 + - - +
31K ARG* 3.5 12.8 - - - +
33K VAL* 1.3 77.0 - - - +
35K THR* 1.3 57.2 + - - +
37K ALA* 3.3 7.7 + - - +
38K LYS* 3.1 28.4 + - - +
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Residues in contact with THR 35 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3K MET* 4.5 12.8 - - - -
4K PHE* 4.2 29.4 - - - -
7K MET* 6.4 0.7 - - - -
31K ARG 3.0 14.0 + - - -
32K TYR* 3.7 10.1 - - - -
33K VAL 3.2 0.4 - - - -
34K GLU* 1.3 74.0 - - - +
36K GLN* 1.3 65.3 + - - +
38K LYS* 4.2 4.9 - - - +
39K GLU* 3.0 30.2 + - - +
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Residues in contact with GLN 36 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4K PHE* 5.4 0.6 - - - +
32K TYR 3.1 11.1 + - - +
33K VAL* 3.0 14.5 + - - +
35K THR* 1.3 77.0 - - - +
37K ALA* 1.3 56.9 + - - +
40K ASN* 2.8 10.9 + - - -
41K ALA* 2.8 53.9 + - + +
42K TYR* 4.5 6.5 - - - +
43K ASP* 5.3 1.8 - - + +
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Residues in contact with ALA 37 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33K VAL 3.1 8.5 + - - +
34K GLU* 3.5 11.4 - - - +
35K THR 3.2 0.2 - - - -
36K GLN* 1.3 82.3 - - - +
38K LYS* 1.3 62.2 + - - +
40K ASN* 3.4 2.8 + - - +
68K GLN* 5.3 12.6 - - + -
130K GLY 3.3 14.6 - - - +
131K ILE* 4.2 12.6 - - + +
132K THR* 2.9 26.7 + - - +
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Residues in contact with LYS 38 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34K GLU 3.1 13.3 + - - +
35K THR* 4.2 4.5 - - - +
37K ALA* 1.3 78.6 - - - +
39K GLU* 1.3 58.5 + - - +
130K GLY 3.6 9.4 + - - +
132K THR* 3.3 17.7 - - - -
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Residues in contact with GLU 39 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2K ALA* 5.8 7.2 - - + -
4K PHE* 4.8 9.6 - - + +
35K THR* 3.0 18.2 + - - +
38K LYS* 1.3 76.2 - - + +
40K ASN* 1.3 70.4 + - - +
41K ALA* 4.4 11.0 - - + +
132K THR* 4.8 0.4 - - - -
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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