Contacts of the helix formed by residues 41 - 55 (chain D) in PDB entry 1JPL
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 GLU 41 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5D GLU* 6.3 1.0 - - + +
39D GLU* 3.2 1.7 - - - +
40D LEU* 1.3 97.9 - - + +
42D GLY* 1.3 63.9 + - - +
43D PRO 3.4 0.2 - - - -
44D GLN* 3.3 27.7 + - + +
45D ILE* 3.2 36.2 + - + +
204D GLY* 5.3 0.9 - - - -
205D SER* 2.8 37.2 + - - +
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Residues in contact with GLY 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D LEU* 4.1 12.0 - - - +
36D ILE* 3.8 13.0 - - - -
39D GLU* 3.0 27.6 + - - +
41D GLU* 1.3 77.6 - - - +
43D PRO* 1.3 64.1 - - - +
45D ILE* 3.8 0.7 - - - +
46D ALA* 2.8 34.5 + - - +
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Residues in contact with PRO 43 (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 ILE* 3.8 14.6 - - + +
42D GLY* 1.3 90.2 - - - +
44D GLN* 1.3 76.0 + - - +
45D ILE 3.2 0.2 + - - -
46D ALA* 3.8 0.7 - - + +
47D VAL* 3.1 28.9 + - - +
76D CYS 5.8 0.2 - - - +
79D ARG* 3.4 70.0 - - + +
80D PHE* 4.2 10.8 - - + +
83D GLU* 3.9 8.1 - - + -
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Residues in contact with GLN 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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40D LEU 4.1 3.0 + - - -
41D GLU* 3.3 36.8 - - + +
43D PRO* 1.3 98.9 - - - +
45D ILE* 1.3 62.3 + - + +
47D VAL* 3.4 15.4 - - - +
48D ARG* 3.8 13.5 + - - +
79D ARG* 4.7 0.8 - - - +
83D GLU* 3.6 36.2 - - - +
88D ARG* 5.5 4.7 - - - +
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Residues in contact with ILE 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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1D MSE 3.6 54.7 - - + +
5D GLU* 4.2 12.3 - - + -
6D GLY* 4.1 6.3 - - - +
9D LEU* 3.7 19.7 - - + -
41D GLU* 3.2 26.0 + - + +
42D GLY 3.8 2.2 - - - +
43D PRO 3.1 1.0 - - - -
44D GLN* 1.3 79.2 - - + +
46D ALA* 1.3 65.7 + - - +
48D ARG* 3.0 16.0 + - - +
49D LEU* 3.1 21.5 + - + +
205D SER* 3.9 20.2 - - - +
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Residues in contact with ALA 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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9D LEU* 4.7 2.7 - - + +
32D PHE* 3.9 10.3 - - + -
36D ILE* 3.4 34.5 - - + -
42D GLY 2.8 22.3 + - - +
43D PRO 3.8 2.9 - - - +
45D ILE* 1.3 75.9 - - - +
47D VAL* 1.3 56.2 - - - +
49D LEU* 3.2 9.3 + - - +
50D LEU* 2.7 35.3 + - - +
80D PHE* 4.1 6.1 - - + -
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Residues in contact with VAL 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 PRO 3.1 13.6 + - - +
44D GLN* 3.4 20.4 - - - +
46D ALA* 1.3 77.0 - - - +
48D ARG* 1.3 64.1 + - + +
50D LEU* 3.9 4.5 - - - -
51D ALA* 3.0 29.3 + - - +
80D PHE* 3.6 25.8 - - + -
83D GLU* 3.9 29.2 - - + +
84D VAL* 4.2 11.7 - - + -
89D PHE* 3.3 27.7 - - + -
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Residues in contact with ARG 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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57C PRO* 4.0 25.2 - - + +
105C ARG* 4.1 30.7 + - - +
1D MSE 3.6 46.9 - - + +
44D GLN 3.8 14.2 + - - +
45D ILE 3.0 10.0 + - - +
47D VAL* 1.3 81.1 - - + +
49D LEU* 1.3 65.7 + - - +
51D ALA* 3.7 4.4 + - - +
52D HIS* 3.2 23.2 + - - +
88D ARG 6.0 1.3 - - - +
203D MSE 4.2 15.6 + - - +
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Residues in contact with LEU 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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56C SER* 5.2 0.2 - - - +
57C PRO* 4.7 10.1 - - + -
58C GLN* 4.6 6.5 - - + -
1D MSE 3.9 24.2 - - + -
6D GLY 4.2 1.1 - - - +
9D LEU* 3.6 18.2 - - + +
10D GLU* 3.2 53.6 - - + +
13D LEU* 3.6 16.2 - - + -
32D PHE* 4.8 1.8 - - + -
45D ILE* 3.1 21.0 + - + +
46D ALA* 3.7 9.2 - - - +
48D ARG* 1.3 75.6 - - - +
50D LEU* 1.3 64.8 + - - +
52D HIS* 3.3 5.0 + - - +
53D LYS* 3.0 27.0 + - - +
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Residues in contact with LEU 50 (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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13D LEU* 4.1 13.7 - - + -
32D PHE* 4.0 20.2 - - + -
46D ALA 2.7 23.7 + - - +
47D VAL* 4.1 4.7 - - - +
49D LEU* 1.3 73.8 - - - +
51D ALA* 1.3 62.1 + - - +
53D LYS* 3.1 3.4 + - - +
54D ILE* 2.9 36.1 + - + +
65D ALA* 3.5 28.5 - - + +
68D VAL* 3.8 18.8 - - + -
69D LEU* 4.0 15.5 - - + +
72D CYS* 4.1 5.8 - - - -
80D PHE* 3.7 30.7 - - + -
89D PHE* 4.9 3.6 - - + -
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Residues in contact with ALA 51 (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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47D VAL 3.0 21.0 + - - +
48D ARG* 3.9 6.1 - - - +
50D LEU* 1.3 76.1 - - - +
52D HIS* 1.3 60.6 + - - +
54D ILE* 3.7 9.0 + - - +
55D GLN* 3.1 31.0 + - - +
89D PHE* 3.7 18.5 - - + -
92D GLU* 3.8 28.3 - - + +
93D LEU* 5.5 3.3 - - + +
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Residues in contact with HIS 52 (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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52C HIS* 2.7 86.2 + + - -
53C LYS* 5.6 0.4 - - - -
55C GLN* 3.2 31.8 + - + -
56C SER* 3.7 14.3 - - - -
57C PRO* 4.1 15.2 - - + +
61C GLU* 5.6 0.9 - - - -
102C LEU* 6.2 0.2 - - + -
48D ARG 3.2 18.4 + - - +
49D LEU* 3.7 4.3 - - - +
50D LEU 3.1 0.6 - - - -
51D ALA* 1.3 74.8 - - - +
53D LYS* 1.3 66.6 + - + +
55D GLN* 3.0 20.5 + - - +
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Residues in contact with LYS 53 (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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14C ASN* 4.1 5.1 + - - +
52C HIS* 4.9 1.1 - - - -
53C LYS* 4.4 6.7 - - - +
61C GLU* 4.5 0.4 + - - -
10D GLU* 3.2 20.8 + - - -
13D LEU* 3.5 32.1 - - + -
14D ASN* 2.7 29.9 - - - +
17D THR* 3.5 21.8 + - - +
49D LEU 3.0 8.9 + - - +
50D LEU 3.1 4.9 + - - +
52D HIS* 1.3 77.0 - - + +
54D ILE* 1.3 57.9 + - - +
56D SER* 2.8 30.9 + - - +
61D GLU* 3.7 28.9 + - + +
62D ALA* 3.6 7.4 - - - -
65D ALA* 3.4 22.4 - - + -
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Residues in contact with ILE 54 (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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50D LEU* 2.9 28.8 + - + +
51D ALA* 3.8 7.2 - - - +
52D HIS 3.2 0.2 - - - -
53D LYS* 1.3 76.4 - - - +
55D GLN* 1.3 58.3 + - - +
56D SER 3.1 2.4 + - - +
62D ALA* 3.5 19.0 - - - +
65D ALA* 3.9 17.0 - - + +
66D LEU* 3.5 42.6 - - + -
69D LEU* 3.9 25.4 - - + -
89D PHE* 5.0 1.3 - - + -
93D LEU* 4.1 22.9 - - + -
96D VAL* 4.2 16.8 - - + +
106D VAL* 5.7 1.9 - - - +
110D VAL* 4.3 7.2 - - + +
114D VAL* 4.5 5.4 - - + -
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Residues in contact with GLN 55 (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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52C HIS* 3.5 14.8 + - + -
51D ALA 3.1 16.5 + - - +
52D HIS* 3.0 28.0 + - - +
54D ILE* 1.3 74.2 - - - +
56D SER* 1.3 66.1 + - - +
57D PRO* 3.6 4.0 - - - +
92D GLU* 2.9 44.5 + - - +
95D LYS* 4.2 4.2 - - - +
96D VAL* 3.5 24.0 - - + -
102D LEU* 3.5 25.9 - - + +
106D VAL* 5.8 4.2 - - - +
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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