Contacts of the helix formed by residues 81 - 94 (chain L) in PDB entry 1J0B
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 81 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76L VAL 4.9 0.5 + - - -
77L GLY* 4.4 4.9 - - - -
78L ALA* 3.6 31.4 - - - +
79L VAL 3.2 3.2 - - - +
80L HIS* 1.3 79.7 + - - +
82L ASN* 1.3 65.7 + - - +
83L HIS* 3.6 9.2 - - - +
84L ALA* 3.7 14.9 + - - +
85L PHE* 3.7 8.0 + - - +
102L LEU* 5.3 1.4 - - - +
111L ASN* 4.1 4.1 - - - +
115L ASP* 5.4 1.7 - - - +
256L TYR* 5.0 2.2 - - - -
282L TYR* 5.3 2.0 - - - -
1121L 5PA 2.5 37.5 + - - -
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Residues in contact with ASN 82 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50L ILE* 3.8 15.1 - - + +
54L LYS* 5.7 2.5 - - + -
80L HIS 3.0 3.1 + - - +
81L SER* 1.3 69.8 - - - +
83L HIS* 1.3 56.4 + - - +
85L PHE* 2.6 35.7 + - - +
86L VAL* 3.2 7.9 + - + +
111L ASN* 2.4 43.8 + - - +
279L ASP* 4.8 0.3 - - - +
281L VAL* 5.5 0.7 - - - +
282L TYR* 3.8 10.8 - - - -
310L GLY* 3.4 29.1 - - - +
312L SER* 3.6 10.3 - - - +
313L GLY* 4.4 2.7 + - - +
1121L 5PA 3.3 27.1 + - + +
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Residues in contact with HIS 83 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54L LYS* 3.8 33.9 - - + +
58L LEU* 5.6 0.6 - - - +
61L LEU* 5.5 3.0 - - - +
75L THR* 2.9 28.0 - - - -
76L VAL 4.6 3.6 + - - -
81L SER* 3.6 3.1 - - - +
82L ASN* 1.3 79.0 - - - +
84L ALA* 1.3 70.3 + - - +
85L PHE 2.8 1.4 + - - -
86L VAL* 3.1 2.7 + - - +
87L THR* 2.9 38.9 + - + -
154L ILE* 4.6 4.8 - - + +
155L PRO 4.6 0.7 - - - -
157L GLY* 3.0 35.8 + - - -
158L GLY* 3.1 22.8 + - - -
1121L 5PA 3.2 22.4 + - - +
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Residues in contact with ALA 84 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75L THR* 3.8 16.8 - - + +
76L VAL 4.7 7.2 - - - +
78L ALA 5.3 0.2 - - - +
81L SER* 3.7 15.1 + - - +
82L ASN 3.4 0.6 - - - -
83L HIS* 1.3 87.4 + - - +
85L PHE* 1.3 57.7 + - - +
87L THR* 3.7 1.1 - - - -
88L GLY 3.0 20.6 + - - -
100L LEU* 2.9 35.5 - - + +
102L LEU* 3.7 17.5 - - + -
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Residues in contact with PHE 85 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277K ILE* 4.1 14.6 - - + -
50L ILE* 3.7 43.1 - - + -
81L SER 3.7 5.0 + - - +
82L ASN* 2.6 20.2 + - - +
84L ALA* 1.3 70.0 - - - +
86L VAL* 1.3 64.6 + - + +
88L GLY* 3.0 2.8 + - - -
89L LEU* 2.7 62.0 + - + +
100L LEU* 3.8 7.7 - - - +
111L ASN* 4.4 9.6 - - + +
114L LEU* 3.4 43.7 - - + -
115L ASP* 4.3 6.7 - - - +
118L MET* 4.5 9.4 - - + -
120L ILE* 3.5 25.9 - - + +
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Residues in contact with VAL 86 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48L LEU* 4.2 11.8 - - + +
50L ILE* 3.5 37.7 - - + -
51L GLY 4.0 2.7 - - - +
54L LYS* 4.1 11.9 - - + +
55L ILE* 3.2 36.8 - - + -
58L LEU* 3.5 17.0 - - + -
82L ASN* 4.0 7.0 - - + +
83L HIS 3.1 5.3 + - - +
85L PHE* 1.3 77.9 - - + +
87L THR* 1.3 62.0 + - - +
89L LEU* 4.2 4.2 - - - +
90L ALA* 3.0 29.3 + - + +
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Residues in contact with THR 87 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58L LEU* 3.3 26.9 - - + +
62L LEU* 4.9 3.0 - - + +
73L VAL* 3.7 15.0 - - + -
75L THR* 3.4 22.4 - - + -
83L HIS* 2.9 37.2 + - - -
84L ALA 3.7 3.4 - - - -
86L VAL* 1.3 76.7 - - - +
88L GLY* 1.3 60.4 + - - +
90L ALA* 3.7 0.9 - - - +
91L ALA* 2.9 32.7 + - + +
154L ILE* 3.7 20.9 - - + -
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Residues in contact with GLY 88 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73L VAL* 5.8 0.9 - - - -
75L THR* 5.6 0.2 - - - -
84L ALA 3.0 13.3 + - - -
85L PHE 3.5 2.7 - - - -
87L THR* 1.3 85.3 - - - +
89L LEU* 1.3 58.2 + - - +
91L ALA* 3.8 2.0 + - - +
92L LYS* 3.6 16.5 + - - +
98L ALA* 3.5 32.1 - - - +
99L ILE 5.6 0.2 - - - -
100L LEU* 4.5 3.1 - - - -
120L ILE* 3.9 13.3 - - - +
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Residues in contact with LEU 89 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271K GLY 3.0 32.1 - - - +
272K THR* 3.7 18.7 - - + -
275K GLY* 3.7 26.0 - - - +
277K ILE* 4.9 4.5 - - + -
48L LEU* 3.9 10.5 - - + -
49L GLY* 4.2 8.1 - - - -
85L PHE* 2.7 42.1 + - + +
86L VAL* 4.2 2.9 - - - +
88L GLY* 1.3 70.8 - - - +
90L ALA* 1.3 64.0 + - - +
92L LYS* 3.4 7.3 + - - +
93L LYS* 3.3 17.5 + - - +
118L MET* 3.9 13.7 - - + -
120L ILE* 3.9 11.6 - - + +
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Residues in contact with ALA 90 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17L LEU* 5.6 0.4 - - + -
48L LEU* 3.4 33.8 - - + +
58L LEU* 4.3 4.0 - - + -
62L LEU* 3.8 19.5 - - + -
86L VAL 3.0 20.6 + - - +
87L THR 3.7 1.8 - - - +
89L LEU* 1.3 73.9 - - - +
91L ALA* 1.3 60.7 + - - +
92L LYS 3.0 1.8 - - - -
93L LYS* 2.8 24.5 + - - +
94L LEU* 3.0 17.0 + - + +
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Residues in contact with ALA 91 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62L LEU* 3.7 17.6 - - + +
73L VAL* 3.3 35.7 - - + -
87L THR 2.9 19.0 + - - +
88L GLY* 3.9 6.5 - - - +
89L LEU 3.4 0.2 - - - -
90L ALA* 1.3 75.9 - - - +
92L LYS* 1.3 58.5 + - - +
94L LEU* 3.5 5.0 + - - +
96L LEU* 2.9 33.5 + - + +
97L ASP 4.0 7.2 - - - +
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Residues in contact with LYS 92 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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272K THR* 3.7 37.9 - - + +
273K ARG* 5.0 1.4 - - - +
88L GLY 3.6 13.4 + - - +
89L LEU* 3.4 9.5 + - - +
90L ALA 3.0 0.8 - - - -
91L ALA* 1.3 73.8 - - - +
93L LYS* 1.3 59.8 + - - +
94L LEU 2.8 4.9 - - - -
95L GLY* 2.8 20.1 + - - -
96L LEU 3.4 13.2 + - - +
97L ASP* 3.8 20.4 + - - -
98L ALA* 4.2 15.5 - - + +
118L MET 4.8 0.7 - - - +
119L GLY 3.5 24.7 + - - -
120L ILE* 4.2 12.8 - - + +
121L GLU 5.2 0.9 - - - +
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Residues in contact with LYS 93 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28K PRO* 5.2 8.7 - - - +
29K ASN* 4.4 7.2 + - - -
272K THR 3.9 4.7 + - - +
273K ARG* 3.6 23.1 - - - +
274K GLU* 4.1 18.3 + - - +
275K GLY* 4.0 22.9 - - - +
15L VAL* 6.0 0.2 - - - -
16L GLU 5.7 2.0 - - - -
17L LEU* 4.4 24.0 - - + +
48L LEU* 4.2 19.1 - - + -
89L LEU 3.3 9.1 + - - +
90L ALA* 2.8 12.9 + - + +
92L LYS* 1.3 78.2 - - - +
94L LEU* 1.3 65.7 + - + +
95L GLY 3.3 0.8 + - - -
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Residues in contact with LEU 94 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15L VAL* 3.7 32.3 - - + -
17L LEU* 4.5 8.7 - - + -
62L LEU* 3.3 54.5 - - + -
66L LEU* 4.4 19.4 - - + +
90L ALA 3.0 8.9 + - - +
91L ALA* 3.6 8.1 - - - +
92L LYS 2.8 1.0 - - - -
93L LYS* 1.3 90.3 - - + +
95L GLY* 1.3 54.2 + - - +
96L LEU* 3.3 18.9 + - + +
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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