Contacts of the helix formed by residues 31 - 49 (chain D) in PDB entry 4JCQ
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 ASN 31 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29D GLU* 3.3 36.7 + - - +
30D ILE* 1.3 75.5 - - - +
32D GLN* 1.3 59.5 + - - +
33D GLU* 3.3 21.9 + - - +
34D LEU* 2.9 35.1 + - - +
35D ALA 2.9 23.9 + - - -
63D HIS* 4.0 12.1 - - + +
66D ALA* 3.4 14.9 - - - +
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Residues in contact with GLN 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D ASN* 1.3 75.2 - - - +
33D GLU* 1.3 65.7 + - - +
35D ALA* 3.4 7.7 + - - +
36D GLU* 2.9 30.1 + - - +
63D HIS* 5.5 1.0 + - - +
65D GLU* 4.4 15.2 - - - +
66D ALA* 3.8 6.9 - - + +
27E TYR* 3.7 9.4 - - + +
28E GLY* 3.4 26.2 - - - +
58E ASN* 3.1 41.7 + - - +
60E GLN* 3.2 29.8 + - - +
88E TRP* 3.4 9.5 - - - +
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Residues in contact with GLU 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D ASN* 3.3 26.0 + - - +
32D GLN* 1.3 85.1 + - - +
34D LEU* 1.3 60.8 + - - +
36D GLU* 3.4 9.4 + - - +
37D ASP* 3.1 22.3 + - - +
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Residues in contact with LEU 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D LEU 4.9 9.2 - - - +
26D ILE* 3.7 24.7 - - + -
27D TYR 5.0 11.4 - - - +
28D GLY 5.8 0.2 - - - +
29D GLU 4.0 14.6 - - - +
30D ILE* 4.1 10.8 - - + -
31D ASN* 2.9 20.3 + - - +
33D GLU* 1.3 72.8 - - - +
35D ALA* 1.3 59.7 + - - +
37D ASP* 3.2 14.1 + - + +
38D VAL* 2.8 47.8 + - + +
70D ILE* 3.7 23.6 - - + -
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Residues in contact with ALA 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D ASN 2.9 16.3 + - - +
32D GLN* 3.6 10.1 - - - +
34D LEU* 1.3 78.8 - - - +
36D GLU* 1.3 54.0 + - - +
38D VAL* 3.9 0.7 - - - +
39D SER* 2.7 37.6 + - - -
66D ALA* 3.9 26.5 - - + +
69D THR* 4.5 4.7 - - + -
70D ILE* 3.8 16.3 - - + +
27E TYR* 3.6 13.9 - - + -
58E ASN* 5.4 0.7 - - - +
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Residues in contact with GLU 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D GLN 2.9 16.5 + - - +
33D GLU* 3.6 8.4 - - - +
34D LEU 3.2 0.2 - - - -
35D ALA* 1.3 73.9 - - - +
37D ASP* 1.3 61.1 + - - +
39D SER 3.4 0.5 + - - -
40D LYS* 3.0 56.4 + - + +
25E LEU* 3.6 33.7 - - + +
27E TYR* 3.5 33.2 + - + +
37E ASP* 5.6 2.1 - - - +
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Residues in contact with ASP 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C GLU* 5.5 2.6 - - - +
33D GLU 3.1 11.7 + - - +
34D LEU* 3.2 18.9 + - + +
36D GLU* 1.3 80.6 - - - +
38D VAL* 1.3 56.8 + - - +
40D LYS* 3.5 9.1 + - - +
41D GLN* 3.1 48.5 + - - +
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Residues in contact with VAL 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D VAL* 4.4 13.0 - - + -
25D LEU 4.8 2.2 - - - +
26D ILE* 3.8 29.8 - - + -
34D LEU* 2.8 42.5 + - + +
35D ALA 4.0 2.9 - - - +
37D ASP* 1.3 69.2 - - - +
39D SER* 1.3 60.1 + - - +
41D GLN* 3.3 10.2 + - - +
42D LEU* 2.9 50.4 + - + +
55D ILE* 5.5 1.1 - - + -
70D ILE* 4.0 24.5 - - + -
73D MET* 6.2 0.2 - - + -
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Residues in contact with SER 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D ALA 2.7 24.7 + - - -
36D GLU 3.6 4.3 - - - -
38D VAL* 1.3 77.7 - - - +
40D LYS* 1.3 58.0 + - - +
42D LEU* 3.9 5.9 - - - +
43D LEU* 3.0 36.5 + - - +
69D THR* 4.0 3.1 - - - +
70D ILE* 5.5 1.7 - - - +
73D MET* 3.7 25.6 - - - +
25E LEU* 3.8 12.6 - - - -
27E TYR* 3.0 26.6 + - - -
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Residues in contact with LYS 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D GLU* 3.0 49.9 + - + +
37D ASP* 3.7 9.9 - - - +
39D SER* 1.3 76.8 - - - +
41D GLN* 1.3 57.8 + - + +
43D LEU* 3.9 5.9 - - + -
44D LEU* 3.0 30.9 + - - +
18E LEU* 4.0 32.2 - - + +
25E LEU* 3.6 18.2 - - + +
41E GLN* 6.0 2.7 - - - +
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Residues in contact with GLN 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C LYS* 6.1 1.4 - - - +
23D THR 4.3 4.7 - - - +
24D VAL* 3.6 40.8 - - + +
25D LEU 4.6 6.3 + - - +
37D ASP* 3.1 49.2 + - - +
38D VAL* 3.6 7.7 - - - +
40D LYS* 1.3 76.6 - - + +
42D LEU* 1.3 57.6 + - - +
44D LEU* 3.4 6.7 + - - +
45D LEU* 3.0 38.6 + - + +
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Residues in contact with LEU 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D VAL* 4.2 15.0 - - + -
38D VAL* 2.9 37.2 + - + +
39D SER* 3.9 3.4 - - - +
41D GLN* 1.3 76.8 - - - +
43D LEU* 1.3 57.3 + - - +
45D LEU* 3.5 3.9 + - - +
46D GLU* 3.0 30.0 + - - +
53D ILE* 4.3 12.3 - - + -
55D ILE* 4.2 19.7 - - + -
70D ILE* 4.9 0.9 - - + +
73D MET* 4.2 24.2 - - + +
74D ILE* 4.1 25.4 - - + +
77D ILE* 3.9 31.1 - - + +
81D VAL* 5.0 1.6 - - + -
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Residues in contact with LEU 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D SER* 3.0 24.4 + - - +
40D LYS* 4.0 6.1 - - + +
42D LEU* 1.3 73.2 - - - +
44D LEU* 1.3 64.8 + - - +
46D GLU* 3.5 10.9 + - - +
47D SER* 3.1 23.6 + - - -
73D MET* 3.9 27.4 - - + -
76D PHE* 5.0 1.1 - - + -
77D ILE* 4.6 2.9 - - + -
18E LEU* 5.5 4.3 - - + -
21E THR* 4.4 14.2 - - + +
23E THR* 3.9 30.3 - - + +
25E LEU* 4.3 11.0 - - + -
56E PHE* 4.3 11.0 - - + -
186E ARG* 3.4 28.9 - - - +
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Residues in contact with LEU 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D ILE* 3.8 26.7 - - + -
40D LYS 3.0 19.7 + - - +
41D GLN* 3.7 7.9 - - - +
43D LEU* 1.3 76.7 - - - +
45D LEU* 1.3 64.2 + - + +
47D SER* 2.7 27.5 + - - +
48D ILE* 3.3 33.1 + - + +
14E LEU* 3.7 34.1 - - + +
17E LYS* 4.3 9.2 - - + -
18E LEU* 4.2 23.1 - - + +
21E THR* 5.4 1.1 - - - -
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Residues in contact with LEU 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D ILE* 3.5 42.4 - - + +
22D ARG* 2.8 54.0 + - - +
23D THR 4.6 2.2 - - - +
24D VAL* 3.8 26.9 - - + -
41D GLN* 3.0 23.4 + - + +
42D LEU* 3.9 0.9 - - - +
44D LEU* 1.3 74.3 - - + +
46D GLU* 1.3 65.0 + - - +
48D ILE* 3.4 5.0 + - + -
49D SER 3.2 7.8 + - - +
53D ILE* 3.8 33.7 - - + -
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Residues in contact with GLU 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D LEU 3.0 18.6 + - - +
43D LEU* 3.7 8.7 - - - +
44D LEU 3.3 0.2 - - - -
45D LEU* 1.3 77.8 - - - +
47D SER* 1.3 61.1 + - - +
49D SER* 3.2 20.3 + - - +
50D ASN* 4.8 4.1 + - - +
77D ILE* 3.4 19.7 - - + +
78D LYS* 3.0 29.0 + - + +
79D PRO* 3.7 22.6 - - + +
186E ARG* 3.1 49.3 + - - +
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Residues in contact with SER 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D LEU 3.1 12.9 + - - -
44D LEU* 2.7 30.5 + - - +
46D GLU* 1.3 76.8 - - - +
48D ILE* 1.3 60.5 + - - +
17E LYS* 4.0 23.3 + - - +
21E THR* 3.8 22.6 - - - +
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Residues in contact with ILE 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D ILE* 3.7 30.3 - - + -
20D ASP* 6.2 0.7 - - - +
22D ARG* 4.1 9.0 - - - +
44D LEU* 3.3 33.1 + - + +
45D LEU* 3.7 11.7 - - + +
46D GLU 3.2 0.8 - - - -
47D SER* 1.3 81.1 - - - +
49D SER* 1.3 66.3 + - - +
14E LEU* 5.9 1.1 - - + -
17E LYS* 4.1 31.8 + - + +
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Residues in contact with SER 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D ARG* 3.3 30.3 + - - -
45D LEU 3.2 10.4 + - - +
46D GLU 3.2 15.9 + - - +
48D ILE* 1.3 84.1 - - - +
50D ASN* 1.3 61.4 + - - +
51D ASP* 3.3 22.6 + - - +
79D PRO* 3.7 4.7 - - - +
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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