Contacts of the helix formed by residues 41 - 55 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5B GLU* 5.4 0.4 - - + -
39B GLU* 3.2 5.4 - - + +
40B LEU* 1.3 93.1 - - + +
42B GLY* 1.3 64.4 + - - +
43B PRO 3.3 3.7 - - - -
44B GLN* 3.4 32.3 + - - +
45B ILE* 3.2 40.4 + - + +
204B GLY* 5.9 0.7 - - - -
205B SER* 2.5 34.7 + - - +
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Residues in contact with GLY 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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9B LEU* 4.1 7.4 - - - -
36B ILE* 3.3 22.2 - - - +
39B GLU* 2.8 27.1 + - - +
41B GLU* 1.3 76.8 - - - +
43B PRO* 1.3 60.9 - - - +
45B ILE* 4.0 0.3 - - - +
46B ALA* 3.0 33.1 + - - +
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Residues in contact with PRO 43 (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 ILE* 4.0 7.6 - - + -
41B GLU 3.7 2.5 - - - -
42B GLY* 1.3 86.1 - - - +
44B GLN* 1.3 72.0 + - - +
47B VAL* 3.1 30.1 + - - +
79B ARG* 3.5 60.6 - - + +
80B PHE* 3.9 18.6 - - + +
83B GLU* 3.4 22.2 - - + -
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Residues in contact with GLN 44 (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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40B LEU* 4.1 4.7 + - - +
41B GLU* 3.4 48.7 + - - +
43B PRO* 1.3 82.8 - - - +
45B ILE* 1.3 63.6 + - + +
47B VAL* 3.3 16.7 - - - +
48B ARG* 3.6 14.4 + - - +
83B GLU* 3.8 30.4 - - - +
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Residues in contact with ILE 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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1B MSE 3.0 48.7 - - + +
5B GLU* 3.7 28.7 - - + -
6B GLY* 4.3 1.6 - - - +
9B LEU* 3.6 17.5 - - + -
41B GLU* 3.2 24.5 + - + +
42B GLY 4.0 1.8 - - - +
44B GLN* 1.3 77.0 - - + +
46B ALA* 1.3 61.0 + - - +
48B ARG* 3.1 8.9 + - - +
49B LEU* 2.9 31.6 + - + +
205B SER* 3.8 26.5 - - - +
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Residues in contact with ALA 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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32B PHE* 3.9 14.1 - - + -
36B ILE* 3.1 36.8 - - + -
42B GLY 3.0 10.1 + - - +
43B PRO 3.9 2.2 - - - +
45B ILE* 1.3 74.8 - - - +
47B VAL* 1.3 61.0 + - - +
49B LEU* 3.1 8.5 + - - +
50B LEU* 2.7 36.2 + - + +
80B PHE* 4.2 11.7 - - + -
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Residues in contact with VAL 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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43B PRO 3.1 13.9 + - - +
44B GLN* 3.3 17.0 - - - +
46B ALA* 1.3 74.9 - - - +
48B ARG* 1.3 65.3 + - + +
50B LEU* 4.6 4.0 - - - -
51B ALA* 2.9 32.2 + - - +
80B PHE* 3.7 22.0 - - + -
83B GLU* 3.8 27.8 - - + +
84B VAL* 4.0 18.2 - - + +
88B ARG* 6.5 1.3 - - - -
89B PHE* 3.4 30.5 - - + -
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Residues in contact with ARG 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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57A PRO* 4.1 30.0 + - + +
105A ARG* 3.0 60.6 + - - +
1B MSE 3.3 37.1 - - + +
44B GLN 3.6 13.8 + - - +
45B ILE* 3.1 9.7 + - - +
47B VAL* 1.3 80.3 - - + +
49B LEU* 1.3 68.1 + - + +
51B ALA* 3.6 5.4 + - - +
52B HIS* 3.2 22.5 + - - +
88B ARG* 5.6 7.6 - - + +
203B MSE 4.4 16.0 + - - +
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Residues in contact with LEU 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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57A PRO* 3.6 25.1 - - + -
58A GLN* 4.5 7.2 - - + -
1B MSE 3.7 21.8 - - + -
9B LEU* 3.9 8.3 - - + +
10B GLU* 3.2 46.9 - - + +
13B LEU* 3.8 14.1 - - + +
32B PHE* 5.1 1.6 - - + -
45B ILE* 2.9 33.9 + - + +
46B ALA* 3.5 10.1 - - - +
48B ARG* 1.3 77.2 - - - +
50B LEU* 1.3 62.1 + - - +
52B HIS* 3.1 7.5 + - - +
53B LYS* 3.0 21.3 + - - +
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Residues in contact with LEU 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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13B LEU* 3.7 20.2 - - + -
32B PHE* 4.2 15.9 - - + -
46B ALA 2.7 24.1 + - - +
47B VAL* 4.1 3.8 - - - +
49B LEU* 1.3 69.4 - - - +
51B ALA* 1.3 62.9 + - - +
53B LYS* 3.0 3.3 + - - +
54B ILE* 2.8 43.7 + - + +
65B ALA* 3.9 20.0 - - + +
68B VAL* 3.7 25.6 - - + -
69B LEU* 3.8 31.9 - - + -
72B CYS* 4.4 2.0 - - - -
80B PHE* 4.0 17.5 - - + -
89B PHE* 5.0 1.1 - - + -
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Residues in contact with ALA 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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47B VAL 2.9 20.7 + - - +
48B ARG* 3.9 6.3 - - - +
50B LEU* 1.3 76.8 - - - +
52B HIS* 1.3 61.7 + - - +
54B ILE* 3.4 8.2 + - - +
55B GLN* 3.0 32.6 + - - +
89B PHE* 3.9 17.0 - - + -
92B GLU* 3.7 33.4 - - + -
93B LEU* 5.5 2.0 - - + -
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Residues in contact with HIS 52 (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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52A HIS* 2.7 87.6 + + - -
53A LYS* 5.5 0.7 - - - -
55A GLN* 3.3 28.0 + - + -
56A SER* 3.5 19.6 - - - -
57A PRO* 3.9 14.2 - - + +
61A GLU* 5.2 2.9 - - - -
10B GLU* 5.9 1.3 - - - -
48B ARG 3.2 11.0 + - - +
49B LEU* 3.1 9.8 + - + +
50B LEU 3.1 0.8 - - - -
51B ALA* 1.3 81.1 - - - +
53B LYS* 1.3 62.1 + - + +
55B GLN* 3.3 15.9 + - - +
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Residues in contact with LYS 53 (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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14A ASN* 4.6 0.4 + - - +
52A HIS* 4.8 2.0 - - + -
53A LYS* 4.1 7.3 - - - +
10B GLU* 3.2 20.0 + - - -
13B LEU* 4.0 21.8 - - + -
14B ASN* 3.1 27.7 + - - +
17B THR* 3.6 24.1 + - + +
49B LEU 3.0 10.2 + - - +
50B LEU 3.0 7.4 + - - +
52B HIS* 1.3 77.4 - - + +
54B ILE* 1.3 65.8 + - - +
56B SER* 3.0 22.1 + - - -
61B GLU* 3.6 39.0 + - + +
62B ALA* 3.6 7.8 - - - -
65B ALA* 3.7 19.5 - - + -
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Residues in contact with ILE 54 (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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50B LEU* 2.8 34.9 + - + +
51B ALA* 3.8 6.5 - - - +
53B LYS* 1.3 71.9 - - - +
55B GLN* 1.3 58.3 + - + +
56B SER 3.2 1.0 - - - +
62B ALA* 3.5 18.6 - - - +
65B ALA* 3.8 19.1 - - + -
66B LEU* 3.6 37.2 - - + -
69B LEU* 4.0 17.0 - - + -
89B PHE* 4.9 2.2 - - + -
93B LEU* 4.0 23.1 - - + -
96B VAL* 4.3 19.4 - - + +
106B VAL* 5.7 1.7 - - - +
110B VAL* 4.2 11.8 - - + +
114B VAL* 4.5 6.3 - - + -
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Residues in contact with GLN 55 (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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52A HIS* 3.4 13.3 - - + -
51B ALA* 3.0 19.3 + - - +
52B HIS* 3.8 18.5 + - - +
53B LYS 3.1 1.0 - - - -
54B ILE* 1.3 76.5 - - + +
56B SER* 1.3 66.3 + - - +
92B GLU* 2.8 51.5 + - - +
95B LYS* 4.3 5.3 + - - +
96B VAL* 3.8 20.2 - - + -
102B LEU* 3.9 25.8 - - + +
105B ARG* 3.0 22.3 + - - +
106B VAL* 5.8 3.8 - - - -
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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