Contacts of the helix formed by residues 55 - 71 (chain B) in PDB entry 2JI8
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 HIS 55 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A HIS* 5.2 5.6 + + - -
57A GLN* 2.8 26.7 + - - -
58A HIS* 5.0 2.4 + - - -
429A GLY* 6.2 0.2 - - - -
456A GLY 5.1 1.3 - - - +
457A PHE* 3.4 44.4 - + + -
31B VAL* 3.9 4.5 - - - +
53B PHE* 3.5 17.5 - - - +
54B ARG* 1.3 76.7 - - - +
56B GLU* 1.3 64.4 + - - +
57B GLN* 3.1 39.6 + - + +
58B HIS* 3.5 28.6 + + + +
59B ALA 3.6 0.3 + - - -
86B ASN* 3.2 33.6 + - + -
461B GLU* 3.2 4.2 + - - +
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Residues in contact with GLU 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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457A PHE* 3.4 11.4 - - - -
1566A TPP 2.6 34.2 + - - +
30B GLY 5.3 0.2 - - - -
31B VAL* 3.6 26.7 - - + +
55B HIS* 1.3 71.3 + - - +
57B GLN* 1.3 61.3 + - - +
58B HIS 3.2 0.4 - - - -
59B ALA* 3.3 6.2 + - + +
60B GLY* 2.8 27.4 + - - -
76B CYS* 4.3 1.6 - - - -
78B THR* 3.8 28.7 - - + -
79B VAL* 4.3 2.4 - - - +
83B GLY* 3.7 23.1 - - - +
86B ASN* 2.8 33.6 + - + -
87B GLY* 4.0 7.5 - - - +
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Residues in contact with GLN 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A HIS* 2.8 25.4 + - - -
86A ASN* 2.7 29.5 + - - +
55B HIS* 3.1 23.3 + - + +
56B GLU* 1.3 79.0 - - - +
58B HIS* 1.3 73.3 + - + +
61B TYR* 2.9 47.6 + - + -
86B ASN* 3.6 9.7 + - - +
89B THR* 3.1 17.8 + - - +
90B SER* 2.6 29.0 + - - +
429B GLY* 5.5 1.6 - - - -
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Residues in contact with HIS 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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55A HIS* 5.0 2.2 - - - -
53B PHE* 3.6 6.5 - - + -
55B HIS* 3.5 22.3 + + + +
56B GLU 3.2 0.4 - - - -
57B GLN* 1.3 95.0 + - - +
59B ALA* 1.3 62.6 + - - +
60B GLY 3.1 0.9 - - - -
61B TYR* 4.0 7.5 - - - +
62B ALA* 3.0 28.9 + - - +
429B GLY* 3.5 18.7 + - - -
433B GLY* 3.6 12.3 + - - -
457B PHE 3.0 28.5 + - - -
458B SER* 3.4 15.5 - - - -
461B GLU* 3.3 46.0 - - + +
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Residues in contact with ALA 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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29B TYR* 3.3 12.4 - - - +
30B GLY* 3.5 37.5 - - - +
53B PHE* 3.5 29.2 - - + -
55B HIS 3.6 3.8 + - - +
56B GLU* 3.3 11.0 + - - +
58B HIS* 1.3 77.5 - - - +
60B GLY* 1.3 55.7 + - - +
62B ALA* 3.4 0.7 - - - +
63B ALA* 3.1 23.6 + - - +
76B CYS* 4.0 5.7 - - - -
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Residues in contact with GLY 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 GLU 2.8 14.3 + - - -
57B GLN 3.4 5.2 - - - -
58B HIS 3.1 0.2 - - - -
59B ALA* 1.3 72.3 - - - +
61B TYR* 1.3 63.2 + - - +
62B ALA 3.1 1.3 - - - -
63B ALA* 3.0 14.4 + - - +
64B SER* 3.0 11.6 + - - -
76B CYS* 3.7 14.1 - - - -
87B GLY 5.0 0.4 - - - -
90B SER* 3.5 17.9 - - - -
101B MET* 3.7 11.2 - - - +
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Residues in contact with TYR 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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82A PRO* 5.8 1.6 - - - +
86A ASN* 4.9 2.4 + - - -
57B GLN* 2.9 61.0 + - + +
58B HIS* 3.5 9.6 + - - +
60B GLY* 1.3 70.6 - - - +
62B ALA* 1.3 60.7 + - - +
64B SER* 2.6 20.0 + - - -
65B ILE 3.2 6.1 + - - -
89B THR* 4.7 5.0 + - - -
90B SER* 3.5 12.4 - - - -
93B HIS* 3.5 41.2 - + + +
427B VAL* 3.5 19.6 - - + +
428B MET 5.1 0.5 + - - -
429B GLY* 3.3 32.3 - - - -
430B ILE* 3.8 14.6 - - + +
433B GLY* 4.9 2.2 - - - -
434B TYR* 3.3 22.6 - - + -
1563B TPP 6.1 0.2 - - - +
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Residues in contact with ALA 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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29B TYR* 3.8 13.0 - - + -
53B PHE* 3.6 18.6 - - + -
58B HIS 3.0 18.6 + - - +
59B ALA 3.4 6.5 - - - +
61B TYR* 1.3 77.1 - - - +
63B ALA* 1.3 62.3 + - - +
65B ILE* 3.4 0.4 + - - -
66B ALA* 3.1 12.1 + - - +
433B GLY 3.3 25.1 + - - +
434B TYR 4.6 0.2 - - - +
437B ALA* 3.1 24.1 - - + +
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Residues in contact with ALA 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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29B TYR* 3.9 11.3 - - + -
59B ALA 3.1 13.2 + - - +
60B GLY 3.0 9.4 + - - +
62B ALA* 1.3 76.0 - - - +
64B SER* 1.3 62.8 + - - +
66B ALA* 3.3 1.2 + - - +
67B GLY* 3.1 10.2 + - - -
74B GLY* 3.1 42.8 + - - -
75B VAL 4.0 2.2 - - - +
76B CYS* 4.0 11.9 - - + +
100B PRO 4.2 0.5 - - - +
101B MET* 3.9 17.9 - - + -
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Residues in contact with SER 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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60B GLY 3.0 9.3 + - - -
61B TYR* 2.6 27.8 + - - -
63B ALA* 1.3 76.1 - - - +
65B ILE* 1.3 60.6 + - - +
67B GLY* 3.2 2.8 + - - -
68B TYR 3.2 16.5 + - - -
90B SER 4.8 0.7 - - - -
93B HIS* 3.8 15.6 + - - -
94B ALA* 3.9 24.5 - - - -
99B PHE* 3.4 19.7 - - - +
101B MET* 3.9 13.9 - - - -
434B TYR* 3.8 8.3 + - - -
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Residues in contact with ILE 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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61B TYR 3.2 3.0 + - - -
62B ALA 3.7 1.6 - - - +
64B SER* 1.3 77.8 + - - +
66B ALA* 1.3 62.7 + - - +
68B TYR* 4.1 5.4 - - + -
69B ILE* 2.9 41.4 + - + +
99B PHE* 3.8 16.8 - - + -
249B MET* 4.0 20.4 - - + -
420B LEU* 3.8 25.1 - - + -
434B TYR* 3.5 62.8 - - + +
437B ALA* 3.6 23.1 - - + -
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Residues in contact with ALA 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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29B TYR* 3.7 27.6 - - + +
62B ALA 3.1 17.1 + - - +
63B ALA 3.6 5.2 - - - +
65B ILE* 1.3 79.2 - - - +
67B GLY* 1.3 57.7 + - - +
69B ILE* 4.7 4.9 - - - -
70B GLU* 3.1 38.5 + - - +
72B LYS 4.0 1.4 - - - +
74B GLY* 4.4 5.8 - - - -
437B ALA* 4.3 2.2 - - + -
441B VAL* 4.1 15.0 - - + -
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Residues in contact with GLY 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 ALA 3.1 10.3 + - - -
64B SER 3.6 0.4 - - - -
65B ILE 3.2 0.4 - - - -
66B ALA* 1.3 73.4 - - - +
68B TYR* 1.3 56.5 + - - +
71B GLY* 2.7 34.8 + - - -
72B LYS 3.2 18.2 - - - -
74B GLY 3.8 1.1 - - - +
100B PRO* 3.4 31.1 - - - +
226B TYR* 3.6 0.2 - - - -
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Residues in contact with TYR 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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64B SER 3.2 8.9 + - - +
65B ILE* 3.5 14.6 - - + +
67B GLY* 1.3 76.6 - - - +
69B ILE* 1.3 73.5 + - + +
71B GLY 3.6 2.6 + - - -
99B PHE* 3.3 41.1 - + + -
100B PRO* 4.0 2.2 - - - +
222B LYS* 3.7 24.0 + - + -
225B ALA* 3.4 14.2 - - - +
226B TYR* 3.3 38.1 - + + +
228B GLN* 5.2 0.7 - - - +
249B MET* 3.3 50.4 + - + +
417B ARG* 3.8 32.3 - - + +
419B ARG 4.8 0.6 + - - -
420B LEU* 4.0 10.3 - - + -
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Residues in contact with ILE 69 (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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65B ILE* 2.9 29.0 + - + +
66B ALA 4.2 2.7 - - - +
68B TYR* 1.3 89.5 - - + +
70B GLU* 1.3 61.3 + - + +
228B GLN* 3.4 16.3 - - - +
395B SER* 5.4 1.1 - - - +
417B ARG* 4.2 25.6 + - + +
420B LEU* 4.1 24.0 - - + -
438B ALA* 4.1 17.7 - - + -
441B VAL* 4.0 31.2 - - + -
442B THR* 4.6 12.8 - - + -
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Residues in contact with GLU 70 (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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66B ALA* 3.1 25.6 + - - +
69B ILE* 1.3 80.6 - - + +
71B GLY* 1.3 61.4 + - - +
72B LYS* 3.6 41.0 + - + +
228B GLN* 3.8 6.9 - - - +
441B VAL* 3.9 39.6 - - + +
1567B PGE 3.2 16.6 + - - -
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Residues in contact with GLY 71 (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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67B GLY 2.7 19.8 + - - -
68B TYR 3.6 2.6 + - - -
69B ILE 3.6 1.6 - - - -
70B GLU* 1.3 74.6 - - - +
72B LYS* 1.3 58.8 + - - +
100B PRO* 4.5 0.4 - - - -
157B VAL* 4.3 6.9 - - - +
226B TYR* 3.7 24.4 + - - -
228B GLN* 5.0 0.2 - - - -
1567B PGE 3.7 28.1 + - - +
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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