Contacts of the helix formed by residues 48 - 68 (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 48 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43B THR 2.5 18.7 + - - -
44B CYS* 3.2 4.6 + - - -
47B VAL* 1.3 76.0 - - - +
49B CYS* 1.3 59.5 + - - -
50B ILE 3.6 0.2 - - - -
51B PRO* 3.4 3.7 - - - +
52B SER* 2.6 35.5 + - - -
580B FAD 3.4 26.7 - - - +
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Residues in contact with CYS 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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457A HIS* 4.0 4.3 - - + +
458A PRO* 3.8 18.4 - - + -
44B CYS* 2.0 53.6 + - - -
48B GLY* 1.3 69.6 - - - -
50B ILE* 1.3 64.0 + - - +
52B SER* 3.2 3.6 + - - -
53B LYS* 3.1 31.3 + - - +
333B ALA* 4.0 0.4 - - - -
580B FAD 3.5 46.5 - - + -
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Residues in contact with ILE 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A SER* 4.0 15.9 - - - -
401A THR* 3.3 35.9 - - - +
457A HIS* 4.0 22.4 - - + -
458A PRO* 4.2 8.7 - - + -
44B CYS 3.1 2.6 + - - +
45B LEU* 3.6 35.2 - - + +
49B CYS* 1.3 78.7 - - + +
51B PRO* 1.3 68.5 - - + +
54B ALA* 3.1 19.2 + - - +
94B ALA* 4.1 5.2 - - + -
95B VAL* 4.1 26.5 - - + +
98B LEU* 4.1 16.4 - - + -
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Residues in contact with PRO 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B CYS 3.7 3.8 - - - +
45B LEU 3.4 14.8 - - - +
46B ASN 3.7 8.7 - - - +
47B VAL* 3.6 7.6 - - - -
48B GLY 3.4 23.6 - - - +
50B ILE* 1.3 94.9 - - + +
52B SER* 1.3 62.3 + - - +
54B ALA 3.4 1.0 + - - -
55B LEU* 3.1 28.1 + - - +
91B LYS* 3.5 32.4 - - + +
95B VAL* 3.9 9.9 - - + -
177B LEU* 3.6 13.2 - - + -
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Residues in contact with SER 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B GLY 2.6 23.3 + - - -
49B CYS 3.2 0.2 + - - -
51B PRO* 1.3 77.9 - - - +
53B LYS* 1.3 84.5 + - - +
55B LEU* 3.3 5.6 + - - +
56B LEU* 2.9 31.5 + - - +
177B LEU* 3.5 16.7 - - - +
197B GLU* 4.3 7.4 - - - -
198B MET* 4.5 11.7 - - - -
201B VAL* 4.5 3.0 - - - +
580B FAD 3.6 14.0 - - - -
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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
----------------------------------------------------------
398A ARG* 5.1 6.3 - - + +
401A THR* 3.7 17.0 - - + +
402A ASN* 5.0 3.2 - - - +
458A PRO* 3.6 22.4 - - + +
49B CYS 3.1 20.3 + - - +
52B SER* 1.3 95.3 + - - +
54B ALA* 1.3 61.3 + - - +
56B LEU* 3.5 12.7 - - + +
57B ASN* 3.0 30.5 + - - +
197B GLU* 2.9 28.8 + - - -
364B TYR* 3.7 29.2 - - + -
580B FAD 2.7 37.9 + - - +
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Residues in contact with ALA 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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401A THR* 3.5 23.3 - - + +
50B ILE 3.1 19.5 + - - +
51B PRO* 3.5 6.1 - - + +
53B LYS* 1.3 75.8 - - - +
55B LEU* 1.3 61.5 + - - +
57B ASN* 4.1 0.8 - - - +
58B ASN* 3.2 36.6 + - - +
90B ALA 5.0 0.9 - - - +
91B LYS* 4.0 26.0 - - + +
94B ALA* 4.6 6.1 - - + -
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Residues in contact with LEU 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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51B PRO 3.1 16.7 + - - +
52B SER 3.7 5.8 - - - +
54B ALA* 1.3 74.4 - - - +
56B LEU* 1.3 51.4 + - - +
57B ASN 3.4 0.2 - - - -
58B ASN* 4.2 0.7 - - - +
59B SER* 2.7 36.4 + - - -
87B PHE* 3.6 36.3 - - + +
88B GLN* 4.2 6.7 - - - +
91B LYS* 3.7 26.7 - - + -
176B ALA 4.3 2.7 - - - +
177B LEU* 3.5 37.5 - - + +
198B MET* 3.8 15.7 - - + -
201B VAL* 3.7 19.7 - - + +
202B TYR* 4.5 5.4 - - - +
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Residues in contact with LEU 56 (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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52B SER* 2.9 17.4 + - - +
53B LYS* 3.5 20.2 - - - +
54B ALA 3.2 0.2 - - - -
55B LEU* 1.3 78.4 - - - +
57B ASN* 1.3 56.7 + - - +
59B SER* 3.2 13.2 + - - -
60B HIS* 3.3 9.7 - - - +
197B GLU* 3.3 42.4 - - + +
200B SER* 4.2 5.8 - - - -
201B VAL* 3.4 9.9 - - + -
204B ARG* 3.3 33.6 + - - +
364B TYR* 3.2 43.1 - - + +
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Residues in contact with ASN 57 (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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72A ARG* 2.8 27.1 + - - -
402A ASN* 3.3 41.4 + - - +
53B LYS 3.0 16.7 + - - +
54B ALA* 4.1 4.3 - - - +
56B LEU* 1.3 75.9 - - - +
58B ASN* 1.3 58.9 + - - +
60B HIS* 3.4 10.0 + - - +
61B LEU* 3.1 38.0 + - - +
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Residues in contact with ASN 58 (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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72A ARG* 3.0 62.7 + - + +
74A ILE* 3.4 12.3 - - - +
401A THR 5.2 1.2 - - - +
54B ALA* 3.2 22.0 + - - +
55B LEU* 5.2 0.2 - - - +
57B ASN* 1.3 77.0 - - - +
59B SER* 1.3 58.3 + - - +
61B LEU* 3.4 2.5 + - - +
62B PHE* 3.0 22.5 + - - +
87B PHE* 3.6 19.0 + - + -
90B ALA* 3.4 31.7 - - - +
91B LYS 4.9 0.2 - - - +
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Residues in contact with SER 59 (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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55B LEU 2.7 23.1 + - - -
56B LEU* 3.2 9.9 + - - -
58B ASN* 1.3 75.2 - - - +
60B HIS* 1.3 61.7 + - - +
62B PHE* 3.4 4.6 + - - +
63B HIS* 2.9 27.7 + - - +
82B ILE* 5.6 0.2 - - - -
87B PHE* 3.8 2.8 - - - -
201B VAL* 3.9 17.2 - - - -
204B ARG* 3.3 18.4 + - - +
205B LEU* 3.6 33.0 - - - -
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Residues in contact with HIS 60 (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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56B LEU 3.3 16.5 + - - +
57B ASN* 3.5 12.5 + - - +
58B ASN 3.3 0.2 - - - -
59B SER* 1.3 82.4 + - - +
61B LEU* 1.3 59.1 + - - +
63B HIS* 3.2 16.1 + + - +
64B GLN* 2.8 58.3 + - + +
68B GLU* 5.0 4.0 + - - -
204B ARG* 3.7 16.6 - - - +
366B HIS* 3.3 57.8 + + + -
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Residues in contact with LEU 61 (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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61A LEU* 4.4 11.2 - - + -
64A GLN* 3.7 34.1 - - + +
72A ARG* 3.5 34.1 - - - +
74A ILE* 3.9 12.1 - - + -
57B ASN* 3.1 28.9 + - - +
58B ASN 3.7 8.3 - - - +
59B SER 3.3 0.2 - - - -
60B HIS* 1.3 75.9 - - - +
62B PHE* 1.3 63.6 + - - +
64B GLN* 3.4 18.0 + - - +
65B MET* 3.1 47.8 + - + +
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Residues in contact with PHE 62 (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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74A ILE* 3.6 34.0 - - + +
58B ASN 3.0 12.9 + - - +
59B SER* 3.5 9.9 - - - +
60B HIS 3.3 0.2 - - - -
61B LEU* 1.3 73.5 - - - +
63B HIS* 1.3 58.7 + - - +
65B MET* 3.1 4.6 + - - +
66B HIS* 2.8 53.3 + + + +
80B ILE* 3.7 22.7 - - + -
81B LYS* 3.9 1.8 - - - -
82B ILE* 3.6 40.2 - - + -
204B ARG 3.5 26.5 - - - -
205B LEU* 3.8 24.0 - - + -
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Residues in contact with HIS 63 (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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59B SER 2.9 14.7 + - - +
60B HIS* 3.3 19.7 - + - +
62B PHE* 1.3 82.2 - - - +
64B GLN* 1.3 55.2 + - - +
66B HIS* 4.6 4.0 - - - +
67B THR* 2.8 58.0 + - + +
68B GLU* 4.6 9.7 + - - -
204B ARG* 3.7 37.5 + - + +
237B GLN* 4.8 17.9 + - + +
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Residues in contact with GLN 64 (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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61A LEU* 4.1 29.2 - - + +
60B HIS* 2.8 46.3 + - - +
61B LEU* 3.7 19.9 - - - +
62B PHE 3.3 0.2 - - - -
63B HIS* 1.3 75.1 - - - +
65B MET* 1.3 60.1 + - - +
68B GLU* 3.0 43.9 + - + +
69B ALA* 2.9 26.7 + - - -
72B ARG* 3.8 14.1 - - - +
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Residues in contact with MET 65 (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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61A LEU* 4.7 3.6 - - + -
64A GLN* 4.6 2.5 - - + +
65A MET* 3.5 42.8 - - + +
69A ALA* 4.1 24.9 - - + -
72A ARG* 5.8 0.9 - - - -
74A ILE* 3.9 28.3 - - + -
76A VAL* 6.0 3.6 - - - -
61B LEU* 3.1 39.1 + - + +
62B PHE* 3.1 4.7 + - - +
64B GLN* 1.3 76.9 - - - +
66B HIS* 1.3 62.0 + - - +
69B ALA* 3.4 20.7 - - - +
76B VAL* 5.1 1.0 - - - +
80B ILE* 3.2 35.5 - - + +
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Residues in contact with HIS 66 (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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62B PHE* 2.8 36.6 + + + +
63B HIS* 4.1 5.8 - - - +
64B GLN 3.3 0.4 - - - -
65B MET* 1.3 79.9 - - - +
67B THR* 1.3 66.4 + - + +
69B ALA* 5.2 0.4 - - - -
80B ILE* 3.3 39.4 + - + +
81B LYS* 5.2 7.4 + - - +
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Residues in contact with THR 67 (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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63B HIS* 2.8 44.8 + - + +
66B HIS* 1.3 89.7 - - + +
68B GLU* 1.3 78.6 + - - +
69B ALA 3.6 0.7 - - - -
70B GLN* 4.8 4.6 + - - +
71B LYS* 4.6 14.7 + - - +
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Residues in contact with GLU 68 (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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61A LEU* 5.2 0.7 - - + -
60B HIS* 5.0 3.1 + - - -
63B HIS* 4.5 10.4 + - - +
64B GLN* 3.0 37.4 + - + +
67B THR* 1.3 90.6 + - - +
69B ALA* 1.3 64.5 + - - +
70B GLN 3.5 0.4 - - - -
71B LYS* 3.2 15.4 + - + +
72B ARG* 2.9 63.4 + - + +
403B GLN* 4.7 6.7 - - + +
404B ASP* 5.6 2.6 - - - +
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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
------------------------------------------------------------
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