Contacts of the helix formed by residues 31 - 51 (chain B) in PDB entry 3DJU
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 SER 31 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B CYS 4.2 1.0 + - - -
30B VAL* 1.3 79.1 - - - +
32B GLU* 1.3 58.1 + - - +
33B GLN* 3.5 12.6 + - - +
34B ARG* 3.0 32.8 + - - +
35B LEU* 3.0 22.4 + - - +
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Residues in contact with GLU 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B ARG* 2.5 50.6 + - - +
30B VAL 3.8 1.5 + - - +
31B SER* 1.3 69.5 - - - +
33B GLN* 1.3 66.6 + - - +
35B LEU* 3.5 11.8 - - - +
36B LYS* 2.8 26.9 + - - +
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Residues in contact with GLN 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B SER* 3.1 9.9 + - - +
32B GLU* 1.3 79.6 - - - +
34B ARG* 1.3 86.5 + - - +
36B LYS* 3.5 5.4 + - - +
37B VAL* 3.0 50.1 + - + +
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Residues in contact with ARG 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B CYS 3.9 19.8 + - - -
30B VAL* 3.6 22.5 - - + +
31B SER* 3.0 20.7 + - - +
33B GLN* 1.3 96.7 - - - +
35B LEU* 1.3 55.2 + - - +
37B VAL* 3.1 3.1 + - - +
38B PHE* 2.8 32.1 + - - +
85B ILE* 2.9 51.7 + - + +
86B GLY* 3.8 9.5 + - - -
87B LEU* 3.7 27.9 - - - +
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Residues in contact with LEU 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B SER* 4.0 12.7 + - - +
24B LEU* 3.6 36.3 - - + -
25B ARG* 3.5 47.3 - - + +
30B VAL* 3.7 30.5 - - + +
31B SER 3.0 13.5 + - - +
32B GLU* 3.5 22.0 - - - +
34B ARG* 1.3 75.1 - - - +
36B LYS* 1.3 56.4 + - - +
38B PHE* 3.6 6.6 + - + +
39B SER* 2.8 33.8 + - - +
85B ILE* 5.4 1.8 - - + -
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Residues in contact with LYS 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B GLU 2.8 18.0 + - - +
33B GLN* 3.6 6.1 - - - +
35B LEU* 1.3 75.8 - - - +
37B VAL* 1.3 66.6 + - + +
39B SER* 3.5 10.7 + - - +
40B GLY* 3.1 22.4 + - - +
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Residues in contact with VAL 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B GLN* 3.0 39.0 + - + +
34B ARG 3.1 6.9 + - - +
36B LYS* 1.3 75.7 - - + +
38B PHE* 1.3 57.1 + - - +
40B GLY* 4.0 0.2 - - - -
41B ALA* 2.9 39.4 + - + +
84B GLN* 4.9 11.0 - - + +
85B ILE* 3.6 18.6 - - + -
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Residues in contact with PHE 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B VAL* 4.7 1.3 - - + -
20B LEU* 4.3 7.4 - - + -
21B SER* 4.0 24.9 - - - -
24B LEU* 3.7 32.8 - - + -
34B ARG 2.8 20.2 + - - +
35B LEU* 3.7 7.4 - - + +
37B VAL* 1.3 73.3 - - - +
39B SER* 1.3 58.8 + - - +
42B LEU* 2.8 61.8 + - + +
78B ILE* 4.5 14.8 - - + -
81B VAL* 3.7 23.4 - - + +
82B ALA* 4.0 33.7 - - + -
85B ILE* 3.7 20.2 - - + +
87B LEU* 5.6 0.2 - - + -
92B LEU* 5.4 0.9 - - + -
96B LEU* 6.1 1.1 - - + -
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Residues in contact with SER 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B VAL* 3.5 16.7 - - - +
21B SER* 2.9 23.9 + - - -
35B LEU 2.8 22.8 + - - -
36B LYS* 3.9 14.4 - - - -
38B PHE* 1.3 75.9 - - - +
40B GLY* 1.3 57.7 + - - +
43B GLN* 2.9 42.3 + - - +
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Residues in contact with GLY 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B LYS* 3.1 15.3 + - - +
37B VAL 4.0 0.2 - - - -
39B SER* 1.3 76.7 - - - +
41B ALA* 1.3 58.4 + - - +
43B GLN* 3.2 10.9 + - - +
44B GLU* 2.9 42.9 + - - +
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Residues in contact with ALA 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B VAL* 2.9 26.0 + - + +
40B GLY* 1.3 75.8 - - - +
42B LEU* 1.3 56.1 + - - +
44B GLU* 3.5 13.1 + - - +
45B ALA* 2.8 29.1 + - - +
81B VAL* 3.7 20.5 - - + +
84B GLN* 4.4 19.5 + - + +
85B ILE* 6.4 0.2 - - + -
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Residues in contact with LEU 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B VAL* 3.9 22.2 - - + -
20B LEU* 3.8 25.4 - - + -
38B PHE* 2.8 49.1 + - + +
39B SER 4.0 2.2 - - - +
41B ALA* 1.3 69.8 - - - +
43B GLN* 1.3 66.6 + - - +
45B ALA* 3.7 0.6 - - - +
46B LEU* 2.9 36.7 + - + +
77B ILE* 4.0 20.4 - - + +
78B ILE* 4.4 12.3 - - + +
81B VAL* 3.7 25.7 - - + +
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Residues in contact with GLN 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU* 3.3 27.4 - - + +
13B ILE* 4.0 16.8 - - + +
14B ALA* 4.0 19.7 - - - +
17B VAL* 3.7 22.5 - - + +
39B SER* 2.9 29.4 + - - +
40B GLY* 3.5 7.7 - - - +
42B LEU* 1.3 77.2 - - - +
44B GLU* 1.3 52.3 + - + +
46B LEU* 3.8 0.3 - - - -
47B THR* 2.6 41.9 + - + +
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Residues in contact with GLU 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B GLY* 2.9 30.0 + - - +
41B ALA* 3.9 8.1 + - - +
43B GLN* 1.3 73.1 - - + +
45B ALA* 1.3 66.9 + - - +
46B LEU 3.1 0.2 + - - -
47B THR* 3.2 7.3 + - - +
48B GLU* 3.0 39.2 + - + +
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Residues in contact with ALA 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B ALA 2.8 22.0 + - - +
42B LEU 3.7 4.0 - - - +
44B GLU* 1.3 73.8 - - - +
46B LEU* 1.3 57.5 + - - +
48B GLU* 3.5 9.5 - - - +
49B HIS* 3.0 27.3 + - - +
77B ILE* 3.5 28.8 - - + +
80B ARG* 4.3 17.0 + - - +
81B VAL* 3.8 13.5 - - + -
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Residues in contact with LEU 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ILE* 4.0 18.6 - - + -
16B ALA* 5.0 7.9 - - + -
17B VAL* 4.1 13.9 - - + -
20B LEU* 5.8 0.4 - - + -
42B LEU* 2.9 40.9 + - + +
43B GLN 4.0 2.0 - - - +
45B ALA* 1.3 74.3 - - - +
47B THR* 1.3 60.8 + - - +
49B HIS* 4.1 2.5 - - + -
50B TYR* 2.9 60.1 + - + +
68B ILE* 4.1 27.4 - - + -
75B ASP* 5.5 0.7 - - - +
77B ILE* 4.2 28.0 - - + -
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Residues in contact with THR 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B MET* 3.3 20.3 - - - +
10B LEU* 5.7 7.6 - - + -
13B ILE* 3.8 20.8 - - + +
43B GLN* 2.6 34.4 + - + +
44B GLU* 3.2 7.8 + - - +
46B LEU* 1.3 74.0 - - - +
48B GLU* 1.3 64.9 + - - +
51B LYS* 3.1 21.7 + - - +
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Residues in contact with GLU 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B GLU* 3.0 28.0 + - - +
45B ALA* 3.5 11.9 - - - +
47B THR* 1.3 78.1 + - - +
49B HIS* 1.3 61.3 + - - +
50B TYR 3.4 0.5 + - - -
51B LYS* 3.6 18.5 + - - +
52B HIS* 5.2 0.9 + - - -
80B ARG* 5.3 5.9 + - - -
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Residues in contact with HIS 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B ALA 3.0 18.2 + - - +
46B LEU* 3.3 8.3 + - + +
48B GLU* 1.3 77.2 - - - +
50B TYR* 1.3 81.6 + + - +
51B LYS 3.7 0.3 + - - -
53B HIS* 3.7 4.2 - - - -
65B TYR* 2.7 74.2 + + - -
66B ARG 5.6 0.7 - - - -
77B ILE* 3.4 31.2 - - + +
80B ARG* 6.2 0.2 - - - +
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Residues in contact with TYR 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B MET* 3.7 14.8 - - - -
13B ILE* 3.7 21.5 - - + -
46B LEU* 2.9 33.4 + - + +
49B HIS* 1.3 97.8 - + - +
51B LYS* 1.3 66.7 + - - +
52B HIS 3.3 2.7 - - - -
53B HIS* 2.9 25.0 + - - -
54B TRP* 3.5 15.9 + + + +
65B TYR* 4.4 0.9 - + - -
66B ARG* 2.7 60.6 + - + -
68B ILE* 3.6 11.1 - - - +
104B VAL* 3.6 40.0 - - + +
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Residues in contact with LYS 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B MET* 3.5 19.6 - - + +
47B THR* 3.1 9.3 + - - +
48B GLU* 3.6 17.9 - - - +
49B HIS 3.4 1.8 - - - -
50B TYR* 1.3 77.4 - - - +
52B HIS* 1.3 88.1 + - + +
53B HIS 3.4 1.6 + - - -
54B TRP* 4.3 10.2 + - - +
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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