Contacts of the helix formed by residues 82 - 95 (chain B) in PDB entry 1ULT
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 82 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B SER* 3.5 18.8 - - - +
39B ARG 5.1 2.9 - - - +
40B LEU* 4.4 19.7 - - + -
80B PHE* 3.2 23.7 + - + -
81B ASN* 1.3 73.7 - - - +
83B PHE* 1.3 69.7 + + + +
84B ARG* 3.5 12.0 + - + +
85B HIS* 3.0 40.0 + - + +
86B LEU 3.1 8.5 + - - -
126B ASP* 2.7 36.3 + - - -
149B MET* 3.8 17.9 + - + -
228B MET* 4.3 0.5 - - - +
249B LEU* 3.3 14.5 - - - +
251B GLY* 5.4 2.9 - - - -
252B PRO* 6.1 1.1 - - + -
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Residues in contact with PHE 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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36B VAL* 4.4 5.8 - - + -
38B SER* 2.9 22.6 + - - +
40B LEU* 4.2 13.7 - - + -
46B HIS* 3.5 49.1 - + - -
48B THR* 4.1 21.3 - - + -
53B VAL* 5.1 2.0 - - + +
56B ARG* 3.7 26.5 - - - -
82B HIS* 1.3 76.7 - - + +
84B ARG* 1.3 99.4 - - + +
86B LEU* 3.1 6.7 + - - +
87B GLU* 2.9 46.7 + - - +
249B LEU* 4.1 6.5 - - - -
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Residues in contact with ARG 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LEU* 4.8 10.9 - - - +
82B HIS* 3.3 15.7 + - + +
83B PHE* 1.3 119.5 - - + +
85B HIS* 1.3 62.9 + - - +
87B GLU* 3.3 7.1 + - - -
88B ALA* 3.0 22.3 + - - +
149B MET* 3.7 30.4 + - - -
150B ASP* 3.7 27.3 + - - +
151B GLU* 3.9 13.1 - - - +
160B TYR* 3.4 42.1 + - + -
161B GLU* 3.0 33.0 + - - +
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Residues in contact with HIS 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B THR* 2.9 43.1 + - + +
79B GLY* 3.6 25.0 + - - -
80B PHE 3.0 27.6 + - - +
82B HIS* 3.0 20.3 + + + +
84B ARG* 1.3 79.1 - - - +
86B LEU* 1.3 58.4 + - - +
88B ALA* 3.3 3.2 + - + +
89B TYR* 2.9 45.6 + + - -
101B THR* 4.4 1.8 - - + +
149B MET* 4.5 4.9 - - + -
228B MET* 3.8 32.5 - - + +
229B PHE* 4.8 2.0 - - + -
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Residues in contact with LEU 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU* 6.2 0.2 - - + -
36B VAL* 3.9 35.7 - - + -
50B TYR* 4.8 4.7 - - + -
53B VAL* 4.4 17.5 - - + -
82B HIS 3.1 10.2 + - - +
83B PHE* 3.1 12.0 + - - +
85B HIS* 1.3 76.0 - - - +
87B GLU* 1.3 65.0 + - - +
89B TYR* 3.1 19.6 + - + +
90B PHE* 3.4 33.9 + - + -
228B MET* 3.9 6.9 - - + +
237B PRO* 4.2 29.2 - - + +
241B THR* 4.4 0.4 - - - +
247B GLN* 4.2 16.6 - - - +
249B LEU* 4.5 6.3 - - + -
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Residues in contact with GLU 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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48B THR* 5.5 0.5 + - - -
53B VAL* 3.7 36.2 - - + +
56B ARG* 2.7 54.2 + - - +
57B ALA* 4.1 13.1 - - + +
60B LEU* 4.0 4.7 - - + -
83B PHE* 2.9 28.9 + - - +
84B ARG* 3.3 5.2 + - - +
86B LEU* 1.3 75.8 - - - +
88B ALA* 1.3 56.9 + - - +
90B PHE* 3.2 3.5 + - - +
91B ALA* 2.8 30.7 + - - +
160B TYR* 2.7 33.4 + - - +
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Residues in contact with ALA 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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60B LEU* 3.8 10.7 - - + +
77B THR* 4.4 15.7 - - + -
84B ARG 3.0 13.2 + - - +
85B HIS* 3.6 10.3 - - + +
87B GLU* 1.3 74.2 - - - +
89B TYR* 1.3 67.1 + - - +
90B PHE 3.0 1.4 + - - -
91B ALA* 4.4 1.3 - - - +
92B VAL* 3.2 29.2 + - + +
93B PRO* 3.6 1.9 - - - +
99B LEU* 4.1 7.6 - - + +
124B LEU* 4.0 26.7 - - + -
149B MET* 5.5 0.4 - - - -
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Residues in contact with TYR 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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85B HIS* 2.9 35.1 + + - +
86B LEU* 3.1 16.8 - - + +
88B ALA* 1.3 77.2 - - - +
90B PHE* 1.3 58.7 + - + +
93B PRO* 3.1 13.7 - - - +
99B LEU* 3.5 22.9 - - + -
101B THR* 4.2 3.3 - - + +
228B MET* 2.4 49.6 + - + +
232B ASN* 3.2 28.7 + - + -
237B PRO* 3.9 30.3 - - + -
238B TYR* 2.6 58.9 + + + +
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Residues in contact with PHE 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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20B LEU* 3.5 29.2 - - + -
21B TRP* 3.4 12.3 + - + +
23B PHE* 3.9 9.4 - - + -
24B LEU* 3.7 40.6 - - + -
53B VAL* 5.2 0.9 - - + -
57B ALA* 4.8 0.2 - - + -
86B LEU* 3.4 36.9 + - + -
87B GLU 3.2 4.8 + - - +
88B ALA 3.0 0.2 - - - -
89B TYR* 1.3 80.9 - - - +
91B ALA* 1.3 55.0 + - - +
92B VAL 3.5 0.7 - - - -
93B PRO* 3.5 1.2 - - - +
94B GLY* 2.7 35.5 + - - -
237B PRO 4.5 0.2 - - - -
238B TYR* 3.5 33.9 - + - -
241B THR* 3.6 40.6 - - + -
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Residues in contact with ALA 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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21B TRP* 4.2 4.0 - - - -
57B ALA* 3.6 21.5 - - - +
60B LEU* 3.8 24.2 - - + -
61B MET* 3.3 24.3 - - + +
64B LEU* 4.8 2.2 - - + -
87B GLU 2.8 21.9 + - - +
88B ALA* 4.3 0.9 - - - +
90B PHE* 1.3 72.7 - - - +
92B VAL* 1.3 63.7 + - - +
94B GLY 3.3 0.2 + - - -
95B MET* 3.0 22.9 + - - +
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Residues in contact with VAL 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B LEU* 4.1 12.1 - - + -
75B VAL* 4.1 22.7 - - + -
88B ALA* 3.2 19.5 + - + +
91B ALA* 1.3 76.0 - - + +
93B PRO* 1.3 68.0 - - + +
95B MET* 3.3 11.5 - - - +
97B ALA* 2.9 45.8 + - + +
98B VAL 3.5 29.2 - - - +
99B LEU* 3.5 21.1 - - + +
124B LEU* 5.7 0.4 - - + -
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Residues in contact with PRO 93 (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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19B ASN* 4.8 0.5 - - - +
20B LEU* 4.1 11.2 - - + -
88B ALA 3.6 2.2 - - - +
89B TYR 3.1 28.9 - - - +
90B PHE* 3.5 5.4 - - - +
92B VAL* 1.3 96.3 - - + +
94B GLY* 1.3 60.6 + - - +
96B GLY* 3.0 12.6 + - - -
97B ALA 3.7 9.6 - - - +
99B LEU* 4.5 4.7 - - + -
171B VAL 4.6 1.7 - - - +
179B CYS* 3.5 24.2 - - + +
198B HIS* 3.4 37.8 + - + +
238B TYR* 3.8 8.7 - - - +
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Residues in contact with GLY 94 (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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19B ASN* 4.8 2.9 + - - -
21B TRP* 3.9 28.6 - - - +
61B MET* 3.5 6.7 - - - -
90B PHE 2.7 24.8 + - - -
91B ALA 3.6 1.6 - - - -
92B VAL 3.2 0.2 - - - -
93B PRO* 1.3 73.6 - - - +
95B MET* 1.3 48.6 + - - +
96B GLY 3.3 0.7 - - - -
170B PRO* 3.3 8.0 - - - +
171B VAL 2.8 34.1 + - - +
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Residues in contact with MET 95 (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 MET* 3.7 32.3 - - + +
64B LEU* 3.7 34.1 - - + -
65B ARG* 3.7 27.0 + - - +
69B VAL* 3.5 39.5 - - + +
70B GLY* 4.9 1.3 - - - +
71B VAL* 3.8 13.5 + - - +
91B ALA 3.0 13.0 + - - +
92B VAL* 3.3 15.5 - - - +
93B PRO 3.1 0.4 - - - -
94B GLY* 1.3 75.9 - - - +
96B GLY* 1.3 58.6 + - - +
97B ALA* 3.8 7.4 - - + +
171B VAL* 3.8 21.7 - - - +
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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