Contacts of the helix formed by residues 65 - 83 (chain B) in PDB entry 1U5Q
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 GLN 65 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63B GLY 3.2 4.0 + - - -
64B LYS* 1.3 97.3 - - + +
66B SER* 1.3 66.8 - - - +
67B ASN 2.8 5.8 + - - -
68B GLU* 2.9 54.1 + - + +
69B LYS* 3.2 12.5 + - + +
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Residues in contact with SER 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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61B TYR* 3.1 40.6 + - - +
62B SER 5.1 0.7 - - - -
63B GLY 3.4 11.9 + - - -
64B LYS 3.5 0.4 - - - -
65B GLN* 1.3 73.7 - - - +
67B ASN* 1.3 64.2 + - - +
70B TRP* 3.1 29.7 + - - +
99B HIS* 5.5 2.4 + - - -
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Residues in contact with ASN 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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65B GLN 2.8 5.7 + - - -
66B SER* 1.3 82.6 + - - +
68B GLU* 1.3 76.8 + - - +
69B LYS 3.2 0.9 - - - -
70B TRP* 4.1 6.8 - - - +
71B GLN* 3.1 32.7 + - - +
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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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65B GLN* 2.9 64.4 + - + +
67B ASN* 1.3 84.7 + - - +
69B LYS* 1.3 66.0 + - + +
71B GLN* 3.3 7.4 + - - +
72B ASP* 3.2 27.9 + - - +
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Residues in contact with LYS 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B MET* 5.4 0.2 - - - +
60B SER* 3.8 11.3 - - - +
61B TYR* 3.3 31.6 - - + +
62B SER* 2.6 25.5 + - - +
64B LYS* 2.6 42.6 + - - +
65B GLN* 3.2 12.7 + - + +
68B GLU* 1.3 77.3 - - + +
70B TRP* 1.3 63.4 + - - +
72B ASP* 3.0 18.4 + - - +
73B ILE* 3.1 17.8 + - - +
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Residues in contact with TRP 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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14B ASP* 4.6 14.5 + - + +
15B VAL* 3.7 21.1 - - + -
19B PHE* 3.7 19.7 - + - -
61B TYR* 3.3 52.2 - + + +
66B SER 3.1 17.8 + - - +
67B ASN* 4.1 7.2 - - - +
69B LYS* 1.3 77.5 - - - +
71B GLN* 1.3 73.0 + - - +
73B ILE* 3.0 16.0 + - + +
74B ILE* 3.0 49.8 + - + +
96B LEU* 3.6 26.5 - - + -
101B ALA* 5.2 0.4 - - + -
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Residues in contact with GLN 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ASP* 5.9 1.2 + - - -
67B ASN* 3.1 26.4 + - - +
68B GLU* 3.4 8.3 - - - +
69B LYS 3.2 0.2 - - - -
70B TRP* 1.3 86.3 - - - +
72B ASP* 1.3 60.8 + - - +
74B ILE* 3.3 13.5 + - - +
75B LYS* 3.0 30.3 + - + +
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Residues in contact with ASP 72 (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 MET* 4.6 9.5 - - + +
68B GLU* 3.2 13.4 + - - +
69B LYS* 3.0 11.6 + - - +
71B GLN* 1.3 76.1 - - - +
73B ILE* 1.3 67.7 + - - +
75B LYS* 3.3 12.5 + - - +
76B GLU* 2.9 26.7 + - - +
171B GLY 6.2 0.7 - - - +
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Residues in contact with ILE 73 (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 PHE* 4.3 15.5 - - + -
59B MET* 3.5 54.5 - - + +
60B SER 4.1 4.9 - - - +
61B TYR* 3.9 22.2 - - + -
69B LYS 3.1 14.7 + - - +
70B TRP* 3.3 15.5 - - + +
72B ASP* 1.3 78.1 - - - +
74B ILE* 1.3 60.4 + - + +
76B GLU* 3.3 1.9 + - - +
77B VAL* 2.9 38.8 + - + +
101B ALA* 3.6 24.7 - - + -
103B LEU* 4.7 4.0 - - + +
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Residues in contact with ILE 74 (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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14B ASP* 4.5 13.0 - - + +
18B LEU* 3.6 15.9 - - + -
19B PHE* 4.0 18.4 - - + -
70B TRP* 3.0 60.4 + - + +
71B GLN* 3.6 15.5 - - - +
73B ILE* 1.3 78.2 - - + +
75B LYS* 1.3 56.5 + - - +
77B VAL* 3.3 2.1 + - - +
78B ARG* 2.9 58.1 + - - +
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Residues in contact with LYS 75 (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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71B GLN* 3.0 18.2 + - + +
72B ASP* 3.3 13.4 + - - +
74B ILE* 1.3 77.0 - - - +
76B GLU* 1.3 57.8 + - - +
78B ARG* 4.0 6.4 - - - +
79B PHE* 3.2 26.0 + - - +
150B ARG* 4.3 1.8 - - - +
172B SER 6.1 0.2 - - - -
173B ALA 4.1 19.0 + - - -
174B SER* 5.6 1.2 - - - +
175B ILE* 5.0 23.5 - - + +
181B SEP 3.8 20.6 + - - -
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Residues in contact with GLU 76 (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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57B LYS* 2.8 39.8 + - - +
59B MET* 3.6 17.8 - - + +
72B ASP* 2.9 16.8 + - - +
73B ILE* 3.7 4.3 - - - +
75B LYS* 1.3 75.4 - - - +
77B VAL* 1.3 59.5 + - - +
79B PHE* 3.2 5.7 + - - +
80B LEU* 2.8 54.0 + - + +
103B LEU* 4.2 6.1 - - + -
169B ASP* 5.2 0.7 - - - -
170B PHE* 4.3 11.4 + - + +
171B GLY* 3.5 29.6 + - - +
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Residues in contact with VAL 77 (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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18B LEU* 4.0 26.2 - - + -
19B PHE* 4.8 4.3 - - + -
73B ILE* 2.9 27.9 + - + +
74B ILE* 3.3 4.9 + - - +
76B GLU* 1.3 75.2 - - - +
78B ARG* 1.3 63.6 + - - +
80B LEU* 3.2 9.8 + - - +
81B GLN* 3.0 28.3 + - - +
91B TYR* 3.5 19.5 - - + +
94B CYS* 3.9 19.1 - - - -
103B LEU* 4.0 29.8 - - + -
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Residues in contact with ARG 78 (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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14B ASP* 2.7 31.9 + - - -
17B GLU* 2.7 37.8 + - - -
18B LEU* 3.6 21.2 - - + +
74B ILE* 2.9 30.4 + - - +
75B LYS* 4.0 6.7 - - - +
77B VAL* 1.3 79.0 - - - +
79B PHE* 1.3 64.3 + - - +
81B GLN* 3.3 15.7 + - - +
82B LYS* 3.2 21.8 - - + +
175B ILE* 6.1 1.6 - - + -
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Residues in contact with PHE 79 (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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75B LYS 3.2 17.1 + - - +
76B GLU* 3.5 6.7 - - - +
78B ARG* 1.3 80.2 - - - +
80B LEU* 1.3 63.5 + - + +
82B LYS* 3.1 24.2 + - - +
83B LEU* 3.7 23.1 - - + +
142B LEU* 4.1 6.7 - - + -
147B MET* 3.6 30.5 - - + -
148B ILE 5.0 1.1 - - - -
170B PHE* 3.3 41.5 - + + +
173B ALA* 3.4 31.2 - - + -
174B SER 3.8 19.5 - - - -
175B ILE* 3.9 21.2 - - + +
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Residues in contact with LEU 80 (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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227A ASN* 4.9 0.9 - - - +
76B GLU* 2.8 35.2 + - + +
77B VAL 3.6 4.3 - - - +
79B PHE* 1.3 74.5 - - - +
81B GLN* 1.3 62.0 + - - +
82B LYS 3.1 1.0 + - - -
83B LEU* 3.2 26.0 + - + +
89B ILE* 5.0 8.7 - - + +
91B TYR* 3.7 47.4 - - + +
103B LEU* 3.8 26.5 - - + -
105B MET* 5.3 10.1 - - + -
170B PHE* 3.7 35.7 - - + +
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Residues in contact with GLN 81 (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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225A LEU* 5.8 1.6 - - - +
227A ASN* 4.4 15.4 + - - +
228A MET* 3.7 44.4 - - + +
232A SER* 5.9 0.2 - - - -
17B GLU 4.7 2.0 + - - -
18B LEU* 3.7 44.4 + - - +
77B VAL* 3.0 20.4 + - - +
78B ARG* 3.5 13.8 + - - +
79B PHE 3.3 0.2 - - - -
80B LEU* 1.3 76.2 - - - +
82B LYS* 1.3 61.1 + - + +
83B LEU 3.5 3.5 + - - +
84B ARG* 5.7 1.6 - - - +
91B TYR* 3.6 21.0 - - + -
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Residues in contact with LYS 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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236A HIS* 5.4 8.5 + - - -
78B ARG* 3.2 20.2 - - + +
79B PHE* 3.6 11.9 - - - +
80B LEU 3.1 1.0 - - - -
81B GLN* 1.3 78.4 - - + +
83B LEU* 1.3 66.7 + - + +
84B ARG* 3.5 4.5 + - - +
141B TYR* 3.5 9.7 + - - -
147B MET* 5.2 14.3 - - + +
175B ILE* 4.8 16.2 - - + -
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Residues in contact with LEU 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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227A ASN* 5.4 3.6 - - - +
79B PHE* 3.7 27.6 - - + +
80B LEU* 3.2 24.5 + - + +
81B GLN 4.5 2.8 - - - +
82B LYS* 1.3 77.4 - - - +
84B ARG* 1.3 65.9 - - - +
85B HIS 4.0 0.9 - - - -
88B THR* 4.0 17.9 - - - +
89B ILE 4.8 8.3 - - - +
91B TYR* 5.8 3.5 + - + +
141B TYR* 3.7 10.5 - - + -
142B LEU* 3.6 29.2 - - + -
147B MET* 4.2 9.2 - - + -
170B PHE* 3.7 36.8 - - + -
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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