Contacts of the helix formed by residues 77 - 92 (chain B) in PDB entry 5JLH
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 ASN 77 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36B ARG* 5.2 2.4 - - - +
67B LYS* 4.0 17.0 - - - +
69B PRO* 3.6 8.0 + - + +
75B VAL* 4.8 2.4 - - - +
76B THR* 1.3 86.2 + - - +
78B TRP* 1.3 65.5 + - - +
79B ASP* 2.5 36.6 + - - +
80B ASP* 2.8 28.7 + - + +
81B MET* 3.3 17.2 + - - +
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Residues in contact with TRP 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B VAL* 2.9 42.1 + - + +
76B THR 4.7 6.3 - - - -
77B ASN* 1.3 72.1 + - - +
79B ASP* 1.3 67.5 + - - +
80B ASP 3.1 2.2 - - - -
81B MET* 3.0 14.5 + - + +
82B GLU* 2.8 23.6 + - - +
85B TRP* 4.8 3.6 - + - -
113B ALA* 4.5 1.1 - - + -
114B ASN* 3.8 19.9 + - - -
117B LYS* 3.4 47.1 - - + +
118B MET* 3.8 19.3 - - + -
121B ILE* 3.4 32.0 - - + +
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Residues in contact with ASP 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ARG* 5.3 2.9 + - - -
77B ASN* 2.5 30.3 + - - +
78B TRP* 1.3 75.7 - - - +
80B ASP* 1.3 85.2 + - - +
82B GLU* 3.3 13.2 + - - +
83B LYS* 2.9 37.3 + - + +
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Residues in contact with ASP 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B VAL* 3.9 21.3 - - + +
36B ARG* 3.1 26.7 + - - -
67B LYS* 4.0 16.1 - - - +
69B PRO* 3.7 15.9 - - + +
77B ASN* 2.8 32.8 + - - +
78B TRP 3.1 0.4 - - - -
79B ASP* 1.3 100.7 + - - +
81B MET* 1.3 63.2 + - - +
83B LYS* 3.0 9.6 + - - +
84B ILE* 2.9 25.9 + - - +
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Residues in contact with MET 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ASN* 3.5 25.6 - - - +
69B PRO* 4.0 13.8 - - + +
70B ILE* 3.3 41.1 - - + -
75B VAL* 4.2 15.7 - - + -
77B ASN 3.3 9.7 + - - +
78B TRP* 3.0 19.8 + - + +
80B ASP* 1.3 73.6 - - - +
82B GLU* 1.3 68.5 + - - +
84B ILE* 3.0 14.7 + - + +
85B TRP* 2.9 53.9 + - + +
118B MET* 6.4 0.2 - - - -
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Residues in contact with GLU 82 (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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78B TRP 2.8 12.3 + - - +
79B ASP* 3.5 16.3 - - - +
81B MET* 1.3 77.9 - - - +
83B LYS* 1.3 68.0 + - - +
85B TRP* 3.3 13.5 + - - +
86B HIS* 2.9 48.3 + - - +
121B ILE* 4.8 12.1 - - + +
125B THR* 3.8 29.3 - - + +
126B PHE* 3.8 8.4 - - + -
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Residues in contact with LYS 83 (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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34B VAL* 4.7 8.5 - - + -
36B ARG* 3.4 35.2 - - - +
50B ASP* 3.9 10.9 + - - +
51B SER* 3.9 11.5 - - - +
53B VAL* 4.2 19.4 - - + +
79B ASP* 2.9 24.4 + - + +
80B ASP* 3.0 17.0 + - - +
82B GLU* 1.3 85.1 - - - +
84B ILE* 1.3 57.3 + - - +
86B HIS* 3.2 9.6 - - - +
87B HIS* 2.9 28.2 + - - +
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Residues in contact with ILE 84 (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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11B ASN* 4.7 4.3 - - - +
16B CYS* 3.3 32.5 - - - -
30B PHE* 4.0 11.7 - - + -
32B SER* 3.6 30.1 - - - +
33B ILE 3.9 1.8 - - - +
34B VAL* 4.1 6.3 - - + -
53B VAL* 3.8 20.4 - - + -
69B PRO* 3.5 31.6 - - + -
80B ASP 2.9 14.9 + - - +
81B MET* 3.0 13.7 + - + +
83B LYS* 1.3 75.8 - - - +
85B TRP* 1.3 58.8 + - - +
87B HIS* 3.2 4.7 + - - +
88B THR* 3.0 25.1 + - - +
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Residues in contact with TRP 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ILE* 4.1 20.7 - - + +
11B ASN* 3.1 27.6 - - + +
78B TRP* 4.8 2.2 - + - -
81B MET* 2.9 42.7 + - + -
82B GLU* 3.7 4.9 - - - +
84B ILE* 1.3 72.7 - - - +
86B HIS* 1.3 65.1 + - - +
88B THR* 2.5 28.6 + - + -
89B PHE* 2.9 12.8 + - + -
104B LEU* 3.9 30.5 - - + +
118B MET* 3.8 35.9 - - + -
121B ILE* 3.6 32.1 - - + -
122B MET* 3.9 13.0 - - + -
126B PHE* 3.4 29.4 - + + -
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Residues in contact with HIS 86 (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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82B GLU* 2.9 30.0 + - - +
83B LYS* 3.2 13.2 - - - +
85B TRP* 1.3 74.8 - - - +
87B HIS* 1.3 60.3 + - - +
89B PHE* 3.3 0.8 + - - -
90B TYR* 2.9 76.1 + + + +
91B ASN* 5.1 5.2 + - - -
126B PHE* 3.7 13.4 - + + -
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Residues in contact with HIS 87 (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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30B PHE* 3.7 19.7 - + - -
53B VAL* 3.6 40.4 + - + +
54B GLY* 4.3 10.1 - - - -
55B ASP* 4.8 6.2 + - - -
56B GLU* 5.2 6.8 + - - +
83B LYS 2.9 13.4 + - - +
84B ILE 3.2 8.5 + - - +
86B HIS* 1.3 75.7 + - - +
88B THR* 1.3 66.0 + - - +
91B ASN* 2.9 61.0 + - - +
92B GLU* 3.0 43.2 + - - +
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Residues in contact with THR 88 (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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9B ILE* 4.0 17.4 - - + +
16B CYS* 4.3 14.6 - - + -
18B ALA* 4.7 12.1 - - + -
28B ALA* 6.2 0.2 - - - -
30B PHE* 3.4 29.8 - - + -
84B ILE 3.0 16.6 + - - +
85B TRP* 2.5 17.8 + - + +
87B HIS* 1.3 80.2 + - - +
89B PHE* 1.3 86.8 + - - +
92B GLU* 3.4 11.9 + - - +
93B LEU* 3.0 27.1 + - - +
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Residues in contact with PHE 89 (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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7B LEU* 3.6 22.4 - - + -
9B ILE* 3.7 25.4 - - + -
85B TRP* 2.9 30.7 + - + +
86B HIS 4.1 1.6 - - - +
88B THR* 1.3 88.4 + - - +
90B TYR* 1.3 63.1 + - + +
93B LEU* 3.5 5.1 + - + -
94B ARG* 2.6 35.2 + - - -
95B VAL* 3.4 31.6 + - + +
97B PRO* 3.7 25.8 - - + -
102B VAL* 4.5 8.7 - - + -
122B MET* 4.2 13.7 - - + -
126B PHE* 3.7 33.2 - + - -
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Residues in contact with TYR 90 (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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86B HIS* 2.9 69.1 + + + +
89B PHE* 1.3 77.0 - - + +
91B ASN* 1.3 71.1 + - - +
94B ARG* 3.7 18.8 + - - +
95B VAL 3.8 21.8 - - - -
96B ALA* 5.1 2.7 - - - -
97B PRO* 4.4 15.4 - - + +
98B GLU* 5.5 1.9 + - - -
126B PHE* 4.7 15.1 - + - +
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Residues in contact with ASN 91 (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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86B HIS* 5.1 4.8 + - - -
87B HIS* 2.9 61.1 + - + +
90B TYR* 1.3 82.4 + - - +
92B GLU* 1.3 63.9 + - - +
94B ARG* 4.4 11.4 + - - -
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Residues in contact with GLU 92 (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 ALA* 3.5 31.6 - - + -
30B PHE* 4.1 9.5 - - - +
55B ASP* 4.6 7.1 - - - +
87B HIS* 3.0 48.8 + - - +
88B THR* 3.6 8.9 - - - +
91B ASN* 1.3 80.6 - - - +
93B LEU* 1.3 68.8 + - + +
94B ARG* 3.4 11.7 + - - +
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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