Contacts of the helix formed by residues 14 - 27 (chain B) in PDB entry 1JEH
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 GLY 14 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12B GLY 3.7 2.6 - - - -
13B GLY* 1.3 76.1 - - - +
15B PRO* 1.3 75.9 - - - +
17B GLY 2.9 2.0 + - - +
18B TYR* 2.9 25.7 + - - -
42B GLY* 3.4 19.7 - - - +
152B ALA 4.9 0.2 + - - -
580B FAD 3.2 20.3 + - - -
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Residues in contact with PRO 15 (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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457A HIS* 6.0 0.4 - - + +
14B GLY* 1.3 81.7 - - - +
16B ALA* 1.3 62.5 + - - +
18B TYR* 3.6 15.7 - - + +
19B VAL* 3.1 28.9 + - - +
41B GLY 3.3 11.9 - - - +
44B CYS* 3.5 24.2 - - + -
45B LEU* 5.2 0.7 - - + -
333B ALA* 3.5 30.7 - - + +
336B ALA* 4.1 1.3 - - + -
337B GLU* 3.6 12.5 - - + +
580B FAD 3.2 29.6 - - - +
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Residues in contact with ALA 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B PRO* 1.3 75.0 - - - +
17B GLY* 1.3 60.3 + - - +
19B VAL* 3.7 3.1 - - - +
20B ALA* 3.1 29.7 + - - +
152B ALA* 4.0 5.4 - - + -
323B VAL* 3.8 22.8 - - + +
324B GLY* 3.8 15.9 - - - -
336B ALA* 3.5 26.3 - - + +
337B GLU 4.3 0.2 - - - +
340B GLY* 3.7 3.0 - - - -
580B FAD 2.9 17.2 + - - +
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Residues in contact with GLY 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ILE* 3.7 16.7 - - - +
12B GLY 3.6 23.1 - - - -
14B GLY 2.9 8.6 + - - -
16B ALA* 1.3 80.4 - - - +
18B TYR* 1.3 55.6 + - - -
20B ALA* 3.2 5.5 + - - +
21B ALA* 3.0 27.0 + - - +
33B CYS* 4.8 0.7 - - - -
152B ALA* 3.7 8.1 - - - +
580B FAD 3.8 0.2 + - - -
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Residues in contact with TYR 18 (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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457A HIS* 4.7 4.2 + - - -
477A HIS* 3.1 39.5 + + - -
13B GLY* 3.7 16.2 - - - +
14B GLY 2.9 31.0 + - - +
15B PRO* 3.6 22.2 - - + +
17B GLY* 1.3 70.9 - - - -
19B VAL* 1.3 67.4 + - + +
21B ALA* 3.3 2.5 + - - +
22B ILE* 3.0 39.6 + - + +
33B CYS* 5.0 0.4 - - - -
40B LEU* 4.7 1.3 - - + -
41B GLY* 4.1 6.5 - - - -
45B LEU* 4.1 15.7 - - + +
102B ILE* 3.7 42.1 - - + +
106B PHE* 3.8 25.7 - - + -
337B GLU* 4.0 8.7 + - - -
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Residues in contact with VAL 19 (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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476A ILE* 3.9 26.3 - - + +
477A HIS* 4.6 0.4 - - - +
15B PRO 3.1 24.8 + - - +
16B ALA 3.7 5.2 - - - +
18B TYR* 1.3 94.3 - - + +
20B ALA* 1.3 64.0 + - - +
22B ILE* 3.8 1.8 - - - +
23B LYS* 2.9 31.6 + - - +
337B GLU* 3.6 49.6 - - + +
340B GLY* 4.4 1.1 - - - -
341B ILE* 4.0 12.3 - - + +
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Residues in contact with ALA 20 (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 ILE* 4.1 15.3 - - + +
16B ALA 3.1 18.4 - - - +
17B GLY* 3.2 6.4 + - - +
19B VAL* 1.3 80.2 - - - +
21B ALA* 1.3 58.3 + - - +
23B LYS* 4.5 0.7 - - - -
24B ALA* 2.9 31.4 + - - +
150B ILE* 4.7 6.7 - - + -
340B GLY* 3.6 22.0 - - - +
344B VAL* 3.3 17.8 - - + +
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Residues in contact with ALA 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ILE* 4.1 9.6 - - + +
17B GLY 3.0 13.4 + - - +
18B TYR* 3.4 9.2 - - - +
20B ALA* 1.3 76.5 - - - +
22B ILE* 1.3 63.7 + - - +
25B ALA* 3.1 25.5 + - - +
31B THR* 3.6 19.0 - - + +
33B CYS* 4.2 3.6 - - + -
106B PHE* 4.0 12.1 - - + -
111B VAL* 3.6 25.8 - - + +
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Residues in contact with ILE 22 (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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476A ILE* 3.7 28.7 - - + +
18B TYR* 3.0 36.5 + - + +
19B VAL* 3.8 4.9 - - - +
21B ALA* 1.3 75.9 - - - +
23B LYS* 1.3 58.3 + - - +
25B ALA* 3.5 2.9 + - - +
26B GLN* 3.0 47.4 + - - +
102B ILE* 4.8 0.7 - - + -
105B LEU* 3.9 33.4 - - + -
106B PHE* 4.0 18.4 - - + -
109B ASN* 3.4 25.9 - - - +
111B VAL* 4.4 5.6 - - + -
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Residues in contact with LYS 23 (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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452A ARG* 5.9 1.7 - - - +
469A MET* 4.0 21.2 - - - +
472A TYR* 5.9 0.6 + - - -
473A ASP* 3.3 24.1 + - - -
474A LYS 4.0 5.5 + - - -
476A ILE* 3.9 13.0 - - + +
19B VAL 2.9 19.3 + - - +
20B ALA* 4.0 1.8 - - - +
22B ILE* 1.3 75.8 - - - +
24B ALA* 1.3 59.7 + - - +
26B GLN* 3.2 20.5 + - + +
27B LEU* 2.9 45.9 + - + +
341B ILE* 4.0 22.4 - - + -
344B VAL* 3.8 18.4 - - + -
345B GLU* 3.7 25.9 + - + -
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Residues in contact with ALA 24 (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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8B VAL* 4.6 9.4 - - + -
20B ALA 2.9 20.5 + - - +
22B ILE 3.4 0.2 - - - -
23B LYS* 1.3 75.2 - - - +
25B ALA* 1.3 57.6 + - - +
27B LEU 3.0 10.2 + - - -
28B GLY 3.3 0.2 + - - -
29B PHE* 3.0 40.7 + - + +
31B THR* 3.3 24.7 - - + +
344B VAL* 3.4 19.7 - - + +
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Residues in contact with ALA 25 (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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21B ALA 3.1 16.8 + - - +
22B ILE 3.6 4.7 - - - +
24B ALA* 1.3 80.1 - - - +
26B GLN* 1.3 56.9 + - - +
28B GLY* 3.2 17.7 + - - -
29B PHE 3.7 8.6 - - - +
31B THR* 3.3 11.1 + - - +
109B ASN* 3.2 30.6 - - + +
110B LYS 5.0 1.6 - - - +
111B VAL* 3.9 12.1 - - + +
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Residues in contact with GLN 26 (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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474A LYS* 4.0 48.6 + - + +
475A ALA 3.2 25.0 + - - +
476A ILE* 4.4 3.0 + - - +
478A CYS 4.7 4.6 + - - -
22B ILE* 3.0 34.5 + - - +
23B LYS* 3.2 31.1 + - + +
25B ALA* 1.3 73.0 - - - +
27B LEU* 1.3 61.1 + - + +
28B GLY 3.2 5.3 + - - -
108B LYS* 5.5 1.8 - - - +
109B ASN* 3.4 24.1 + - - +
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Residues in contact with LEU 27 (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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473A ASP* 6.2 0.2 - - - +
23B LYS* 2.9 27.7 + - + +
24B ALA 3.0 5.8 + - - +
26B GLN* 1.3 78.9 - - + +
28B GLY* 1.3 55.8 + - - +
29B PHE* 3.3 15.7 + - + -
344B VAL* 3.7 33.7 - - + +
345B GLU* 4.0 21.1 - - + +
348B LYS* 3.2 49.7 + - + -
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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