Contacts of the helix formed by residues 41 - 55 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A GLU* 4.3 12.9 - - - +
39A GLU* 3.2 2.5 - - - +
40A LEU* 1.3 102.3 + - + +
42A GLY* 1.3 63.4 + - - +
43A PRO* 3.4 3.1 - - - -
44A GLN* 3.5 22.6 + - + +
45A ILE* 3.1 37.9 + - + +
205A SER* 2.5 33.3 + - - +
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Residues in contact with GLY 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A LEU* 4.1 11.6 - - - +
36A ILE* 3.7 14.8 - - - -
39A GLU* 3.1 25.2 + - - +
41A GLU* 1.3 77.9 - - - +
43A PRO* 1.3 64.9 - - - +
45A ILE* 3.9 0.9 - - - +
46A ALA* 2.8 33.6 + - - +
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Residues in contact with PRO 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A ILE* 4.1 7.6 - - + -
41A GLU* 3.5 0.4 - - - -
42A GLY* 1.3 85.6 - - - +
44A GLN* 1.3 76.8 + - - +
46A ALA* 4.4 0.2 - - + -
47A VAL* 3.1 30.8 + - - +
79A ARG* 3.7 57.9 - - + +
80A PHE* 4.2 19.1 - - + -
83A GLU* 3.6 20.4 - - + -
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Residues in contact with GLN 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A LEU 4.2 4.7 + - - +
41A GLU* 3.7 25.7 - - + +
42A GLY 3.4 0.6 - - - -
43A PRO* 1.3 94.4 - - - +
45A ILE* 1.3 66.3 + - + +
47A VAL* 3.3 17.2 - - - +
48A ARG* 3.5 14.6 - - - +
83A GLU* 3.9 28.1 + - - +
88A ARG* 4.9 7.6 - - - +
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Residues in contact with ILE 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MSE 4.0 25.6 - - + +
5A GLU* 3.8 29.2 - - + -
6A GLY* 4.0 7.4 - - - +
9A LEU* 3.6 15.7 - - + -
39A GLU* 6.3 0.4 - - + -
41A GLU* 3.1 26.1 + - + +
44A GLN* 1.3 74.5 - - + +
46A ALA* 1.3 67.2 + - - +
48A ARG* 2.9 20.8 + - - +
49A LEU* 2.9 34.7 + - + +
205A SER* 3.9 24.2 - - - +
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Residues in contact with ALA 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A LEU* 4.4 2.0 - - + +
32A PHE* 3.8 15.3 - - + -
36A ILE* 3.4 31.2 - - + -
42A GLY 2.8 24.0 + - - +
43A PRO 4.0 2.5 - - - +
45A ILE* 1.3 74.9 - - - +
47A VAL* 1.3 52.4 + - - +
49A LEU* 3.1 6.5 + - - +
50A LEU* 2.6 40.7 + - - +
80A PHE* 4.2 7.9 - - + -
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Residues in contact with VAL 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A PRO 3.1 21.3 + - - +
44A GLN* 3.3 10.1 - - - +
46A ALA* 1.3 73.6 - - - +
48A ARG* 1.3 65.6 + - + +
50A LEU* 4.3 6.5 - - + -
51A ALA* 2.8 31.4 + - - +
80A PHE* 3.7 27.4 - - + -
83A GLU* 4.0 21.1 - - + +
84A VAL* 4.0 17.5 - - + +
88A ARG* 6.1 3.6 - - - +
89A PHE* 3.5 27.9 - - + -
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Residues in contact with ARG 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MSE 3.2 41.8 - - - +
44A GLN 3.5 15.3 + - - +
45A ILE* 2.9 9.2 + - - +
47A VAL* 1.3 81.3 - - + +
49A LEU* 1.3 64.9 + - + +
51A ALA* 3.5 6.3 + - - +
52A HIS* 3.1 22.9 + - - +
88A ARG* 5.9 12.1 - - + +
203A MSE 4.1 12.9 + - - +
57B PRO* 4.0 22.1 + - + +
105B ARG* 3.5 37.8 + - - +
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Residues in contact with LEU 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MSE 3.5 31.0 - - + -
6A GLY 4.3 2.2 - - - +
9A LEU* 3.8 10.8 - - + +
10A GLU* 3.2 47.7 - - + +
13A LEU* 3.8 11.9 - - + -
32A PHE* 5.0 1.8 - - + -
45A ILE* 2.9 31.1 + - + +
46A ALA* 3.4 10.1 - - - +
48A ARG* 1.3 76.6 - - - +
50A LEU* 1.3 65.2 + - - +
52A HIS* 3.1 7.0 + - - +
53A LYS* 3.1 24.6 + - - +
56B SER* 5.3 0.2 - - - +
57B PRO* 4.5 13.9 - - + -
58B GLN* 4.6 3.1 - - + -
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Residues in contact with LEU 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LEU* 4.0 16.2 - - + -
32A PHE* 4.1 18.8 - - + -
46A ALA 2.6 23.9 + - - +
47A VAL* 3.9 4.9 - - - +
49A LEU* 1.3 70.5 - - - +
51A ALA* 1.3 68.0 + - - +
53A LYS* 3.1 2.7 + - - +
54A ILE* 2.8 35.5 + - + +
65A ALA* 3.6 27.8 - - + +
68A VAL* 3.9 18.8 - - + -
69A LEU* 4.0 19.3 - - + +
72A CYS* 4.3 2.0 - - - -
80A PHE* 4.0 26.7 - - + -
89A PHE* 4.9 4.0 - - + -
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Residues in contact with ALA 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A VAL 2.8 22.6 + - - +
48A ARG* 3.7 7.0 - - - +
50A LEU* 1.3 72.7 - - - +
52A HIS* 1.3 62.6 + - - +
54A ILE* 3.5 6.8 + - - +
55A GLN* 3.0 31.1 + - - +
89A PHE* 3.7 21.0 - - + -
92A GLU* 3.8 28.9 - - + +
93A LEU* 5.6 1.6 - - - -
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Residues in contact with HIS 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A ARG 3.1 13.2 + - - +
49A LEU 3.5 7.9 - - - +
50A LEU 3.1 0.8 - - - -
51A ALA* 1.3 75.6 - - - +
53A LYS* 1.3 66.9 + - + +
55A GLN* 3.1 17.4 + - - -
52B HIS* 2.7 84.7 + + - -
53B LYS* 5.5 2.0 - - + -
55B GLN* 3.4 27.2 + - + -
56B SER* 3.5 19.9 - - - -
57B PRO* 3.8 16.7 - - + +
61B GLU* 5.2 2.2 - - - -
105B ARG* 5.0 4.5 + - - -
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Residues in contact with LYS 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A GLU* 3.0 27.0 + - - +
13A LEU* 3.3 29.4 - - + -
14A ASN* 2.7 29.3 + - - +
17A THR* 3.5 23.6 + - - +
49A LEU 3.1 8.6 + - - +
50A LEU 3.7 3.8 - - - +
52A HIS* 1.3 78.4 - - + +
54A ILE* 1.3 60.0 + - - +
56A SER* 2.9 29.8 + - - -
61A GLU* 3.9 23.9 + - + +
62A ALA* 3.6 7.6 + - - -
65A ALA* 3.6 20.0 - - + -
14B ASN* 3.9 5.1 + - - -
52B HIS* 4.8 0.9 - - - -
53B LYS* 4.1 6.9 - - - +
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Residues in contact with ILE 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A LEU* 2.8 26.7 + - + +
51A ALA* 3.8 6.5 - - - +
53A LYS* 1.3 76.0 - - - +
55A GLN* 1.3 58.9 + - - +
56A SER 3.1 4.7 + - - +
62A ALA* 3.4 17.4 - - - +
65A ALA* 3.6 20.4 - - + +
66A LEU* 3.5 39.7 - - + -
69A LEU* 3.6 28.7 - - + -
89A PHE* 4.9 1.1 - - + -
93A LEU* 4.1 21.1 - - + -
96A VAL* 4.3 15.0 - - + +
106A VAL* 5.8 0.9 - - - +
110A VAL* 4.4 8.2 - - + +
114A VAL* 4.4 6.5 - - + -
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Residues in contact with GLN 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A ALA* 3.0 17.7 + - - +
52A HIS* 3.1 19.8 + - - +
54A ILE* 1.3 73.8 - - + +
56A SER* 1.3 65.2 + - - +
57A PRO* 3.6 1.9 - - - +
92A GLU* 2.6 54.5 + - - +
95A LYS* 3.8 16.4 - - - +
96A VAL* 3.7 19.5 - - + -
102A LEU* 3.6 24.8 - - + +
106A VAL* 5.9 3.3 - - - +
52B HIS* 3.3 15.4 + - + -
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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