Contacts of the helix formed by residues 29 - 48 (chain B) in PDB entry 1JEQ
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 29 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B MET 3.6 10.2 + - - -
21B SER* 3.6 11.6 + - - -
22B ASN 3.4 21.5 - - - -
23B SER* 4.3 8.6 - - - +
24B ILE 5.8 0.2 - - - +
27B ILE 3.4 3.5 + - - -
28B GLU* 1.3 75.7 - - - +
30B PRO* 1.3 71.7 - - - +
31B PHE* 4.0 3.8 - - - +
32B GLU* 2.8 35.2 + - - +
33B GLN* 3.0 10.6 + - - +
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Residues in contact with PRO 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B THR 4.7 3.8 - - - +
20B MET* 3.4 41.1 - - + +
22B ASN* 3.7 10.5 - - + +
28B GLU 4.3 2.2 - - - +
29B SER* 1.3 82.3 - - - +
31B PHE* 1.3 56.7 + - - +
33B GLN* 3.2 8.3 + - + +
34B ALA* 2.8 32.4 + - - +
137B ASP* 4.7 4.5 - - + +
166B PRO* 3.9 30.3 - - + -
227B PHE* 3.8 8.9 - - + -
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Residues in contact with PHE 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B MET* 3.8 21.5 - - + -
15B ASP 4.6 8.1 - - - -
16B VAL* 4.2 15.9 - - + -
20B MET* 2.9 34.4 + - + +
21B SER* 4.5 2.0 - - - +
29B SER* 3.1 4.7 - - - +
30B PRO* 1.3 76.9 - - - +
32B GLU* 1.3 79.5 + - + +
34B ALA* 3.8 1.9 - - - +
35B LYS* 2.9 46.2 + - + +
94B ILE 5.7 0.2 - - - -
98B ILE* 4.0 11.9 - - + -
99B GLN* 3.9 12.6 - - - -
100B PRO* 3.5 49.6 - - + -
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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
----------------------------------------------------------
28B GLU* 3.8 28.1 - - + +
29B SER* 2.8 21.4 + - - +
31B PHE* 1.3 94.5 - - + +
33B GLN* 1.3 60.6 + - - +
35B LYS* 3.5 27.9 + - - +
36B LYS* 3.0 30.5 + - - +
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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
----------------------------------------------------------
27B ILE* 4.1 2.8 - - - +
28B GLU* 3.0 31.4 + - + +
29B SER 3.0 12.3 + - - +
30B PRO* 3.7 5.8 - - - +
32B GLU* 1.3 72.9 - - - +
34B ALA* 1.3 67.9 + - - +
36B LYS* 2.8 19.8 + - - +
37B VAL* 2.9 15.9 + - - +
166B PRO* 4.8 11.3 + - - +
183B PHE* 3.9 23.6 - - - -
185B LEU* 3.8 27.9 - - + +
192B PHE* 5.6 1.6 - - - -
227B PHE* 3.2 41.9 + - + +
228B SER* 3.9 3.8 + - - -
231B LEU* 5.7 1.2 - - + +
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Residues in contact with ALA 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B MET* 3.7 20.4 - - + -
20B MET* 4.2 6.7 - - + -
30B PRO 2.8 17.5 + - - +
31B PHE 3.8 0.2 - - - +
33B GLN* 1.3 76.3 - - - +
35B LYS* 1.3 65.5 + - - +
37B VAL* 3.2 3.2 + - - +
38B ILE* 2.8 29.4 + - + +
135B PHE* 4.2 13.7 - - + -
227B PHE* 4.0 28.4 - - + -
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Residues in contact with LYS 35 (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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14B MET* 3.8 10.0 - - + +
31B PHE* 2.9 35.7 + - + +
32B GLU* 3.5 31.6 + - - +
34B ALA* 1.3 78.2 - - - +
36B LYS* 1.3 61.7 + - + +
38B ILE* 3.9 4.4 - - - +
39B THR* 2.8 31.6 + - - +
94B ILE* 2.8 38.8 - - + +
95B GLU* 2.9 27.0 + - - +
98B ILE 4.9 2.3 + - - -
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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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28B GLU* 2.8 35.7 + - - +
32B GLU 3.0 15.1 + - - +
33B GLN* 2.8 10.8 + - - +
35B LYS* 1.3 74.3 - - - +
37B VAL* 1.3 65.5 + - - +
39B THR* 3.3 6.0 + - - -
40B MET* 3.0 21.8 + - - +
185B LEU* 3.7 19.4 - - + +
231B LEU* 4.3 14.7 - - + +
509B GLN* 5.3 10.3 - - - +
510B GLN* 5.6 3.0 - - - +
511B HIS* 3.5 35.1 - - + +
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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
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33B GLN 2.9 18.4 + - - +
34B ALA* 3.8 6.1 - - - +
36B LYS* 1.3 71.6 - - - +
38B ILE* 1.3 63.8 + - - +
40B MET* 3.0 20.8 + - + +
41B PHE* 3.1 11.8 + - + +
135B PHE* 3.4 29.8 - - + -
164B PHE* 4.6 1.1 - - + -
227B PHE* 3.5 37.0 - - + +
230B SER* 4.0 13.0 - - - -
231B LEU* 4.1 12.3 - - + -
236B VAL* 4.0 21.8 - - + +
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Residues in contact with ILE 38 (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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12B LEU* 4.1 20.4 - - + -
14B MET* 3.3 49.6 - - + -
34B ALA 2.8 23.2 + - - +
35B LYS* 3.9 4.0 - - - +
37B VAL* 1.3 73.9 - - - +
39B THR* 1.3 59.3 + - - +
41B PHE* 3.2 9.4 + - - +
42B VAL* 3.1 27.7 + - + +
56B LEU* 5.1 6.3 - - + -
94B ILE* 4.1 31.0 - - + -
135B PHE* 4.0 30.1 - - + -
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Residues in contact with THR 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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35B LYS* 2.8 21.5 + - - +
36B LYS* 3.7 5.6 - - - -
38B ILE* 1.3 75.0 - - - +
40B MET* 1.3 60.9 + - - +
42B VAL* 4.5 5.2 - - - +
43B GLN* 2.9 59.0 + - + +
91B LEU* 4.5 6.7 - - + +
94B ILE* 3.4 20.4 - - + +
95B GLU* 5.5 8.9 - - + +
495B LEU* 4.3 11.7 - - + -
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Residues in contact with MET 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 3.0 13.7 + - - +
37B VAL* 3.0 14.5 + - - +
39B THR* 1.3 77.9 - - - +
41B PHE* 1.3 64.8 + - - +
43B GLN* 3.9 10.9 - - - +
44B ARG* 3.4 21.0 + - - +
230B SER 3.7 15.0 - - - +
231B LEU* 3.7 19.1 - - + +
233B LYS 3.4 25.4 - - - +
234B LEU* 4.8 2.2 - - + -
236B VAL* 5.1 8.3 - - + -
237B PHE* 3.8 18.1 - - + -
483B PRO* 4.7 5.6 - - + -
488B GLN* 3.2 42.8 - - + +
491B PHE* 5.6 0.5 - - - -
511B HIS* 6.4 0.2 - - + -
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Residues in contact with PHE 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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10B VAL* 4.0 23.1 - - + -
12B LEU* 4.0 30.5 - - + -
37B VAL* 3.1 10.0 + - + +
38B ILE* 3.4 11.2 - - - +
39B THR 3.1 0.2 - - - -
40B MET* 1.3 75.4 - - - +
42B VAL* 1.3 69.7 + - + +
44B ARG* 3.3 5.9 + - - +
45B GLN* 3.1 33.0 + - + +
54B ILE* 3.9 26.0 - - + -
133B GLU* 4.0 6.7 - - - +
135B PHE* 6.1 1.1 - - + -
236B VAL* 3.5 36.3 - - + +
237B PHE* 3.6 30.0 - + - -
240B ILE* 4.0 19.7 - - + -
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Residues in contact with VAL 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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12B LEU* 4.0 19.7 - - + -
38B ILE* 3.1 22.0 + - + +
39B THR* 4.3 1.3 - - - +
41B PHE* 1.3 76.5 - - + +
43B GLN* 1.3 68.1 + - - +
45B GLN* 3.2 6.0 + - - +
46B VAL* 3.0 22.9 + - + +
54B ILE* 4.9 3.6 - - + -
86B PRO* 4.1 13.0 - - + -
90B LEU* 3.6 35.2 - - + -
91B LEU* 3.2 31.0 - - + -
94B ILE* 5.3 3.6 - - + -
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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
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39B THR* 2.9 45.8 + - + +
40B MET* 3.9 10.1 - - - +
42B VAL* 1.3 72.0 - - - +
44B ARG* 1.3 65.7 + - - +
46B VAL* 3.0 12.6 + - - -
47B PHE* 3.0 29.6 + - + -
91B LEU* 3.8 5.3 - - + +
488B GLN* 4.2 10.9 - - - +
491B PHE* 3.5 29.7 + - + +
492B GLN* 3.4 32.1 + - - +
495B LEU* 3.7 22.8 - - + +
509B GLN* 6.0 1.6 - - - +
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Residues in contact with ARG 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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441A ASP* 3.2 25.2 + - - -
40B MET 3.4 5.0 + - - +
41B PHE 3.3 4.6 + - - +
43B GLN* 1.3 78.9 - - - +
45B GLN* 1.3 64.2 + - - +
48B ALA* 2.8 43.6 + - - +
50B ASN* 4.7 3.6 - - - +
234B LEU* 4.6 9.7 - - - +
237B PHE* 3.2 48.1 - - + -
270B GLU* 5.1 10.9 + - - +
483B PRO* 5.7 1.6 - - - +
487B PHE* 4.0 25.7 - - - +
488B GLN* 6.1 2.0 - - - +
491B PHE* 3.8 32.4 - - + -
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Residues in contact with GLN 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 PHE* 3.1 23.1 + - + +
42B VAL 3.2 6.5 + - - +
44B ARG* 1.3 76.7 - - - +
46B VAL* 1.3 60.5 + - - +
49B GLU* 3.4 1.2 + - - -
50B ASN* 3.2 49.7 + - - +
52B ASP* 3.1 42.7 + - - +
54B ILE* 3.7 28.6 - - + +
86B PRO* 3.9 8.3 - - + +
237B PHE* 3.9 14.6 - - - -
240B ILE* 3.6 21.0 - - - +
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Residues in contact with VAL 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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322A TYR* 4.0 7.6 - - + +
42B VAL* 3.0 25.2 + - + +
43B GLN 3.0 5.5 + - - +
45B GLN* 1.3 74.9 - - - +
47B PHE* 1.3 64.6 + - + +
48B ALA 3.1 4.0 - - - -
49B GLU* 3.0 23.6 + - - +
86B PRO* 3.5 40.4 - - + +
87B ASP* 4.2 3.6 - - - +
88B PHE* 4.2 30.7 - - + -
91B LEU* 4.2 17.3 - - + -
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Residues in contact with PHE 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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322A TYR* 3.4 41.3 + + + -
327A ILE* 4.4 3.1 - - + -
43B GLN* 3.0 37.2 + - + +
46B VAL* 1.3 72.9 - - + +
48B ALA* 1.3 60.1 + - - +
49B GLU* 3.9 0.3 - - - +
88B PHE* 3.5 32.3 - + - -
91B LEU* 4.7 4.5 - - + -
273B LYS* 3.6 13.3 - - - +
274B LYS* 5.5 0.7 - - - +
491B PHE* 3.4 62.0 - + + -
494B LEU* 3.7 19.5 - - + -
495B LEU* 3.7 27.6 - - + -
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Residues in contact with ALA 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ARG* 2.8 37.4 + - - +
47B PHE* 1.3 76.5 - - - +
49B GLU* 1.3 63.8 + - - +
50B ASN* 3.3 25.9 + - - +
273B LYS* 2.7 28.4 + - - +
491B PHE* 4.8 4.0 - - + -
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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