Contacts of the helix formed by residues 62 - 82 (chain B) in PDB entry 1U56
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 62 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B SER* 3.7 2.9 - - - -
60B GLY 3.6 2.2 + - - -
61B LYS* 1.3 75.1 - - - +
63B VAL* 1.3 68.4 + - - +
64B ASN* 2.9 36.8 + - - +
65B GLU* 2.8 61.2 + - - +
66B ILE* 3.1 10.0 + - - +
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Residues in contact with VAL 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B PHE* 4.6 11.4 - - + +
53B ALA* 4.5 14.6 - - + -
56B SER* 3.6 20.9 + - - +
62B ASN* 1.3 75.5 - - - +
64B ASN* 1.3 72.1 + - - +
66B ILE* 2.9 18.7 + - - +
67B TRP* 3.0 37.5 + - + +
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Residues in contact with ASN 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ASN* 2.9 21.5 + - - +
63B VAL* 1.3 80.3 - - - +
65B GLU* 1.3 61.8 + - - +
67B TRP* 3.4 5.2 + - - -
68B ARG* 3.1 23.4 + - - +
139B ASP* 2.6 38.6 + - - +
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Residues in contact with GLU 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LYS* 4.1 20.6 + - + +
62B ASN* 2.8 43.9 + - - +
64B ASN* 1.3 76.3 - - - +
66B ILE* 1.3 62.9 + - - +
68B ARG* 3.3 8.3 + - - +
69B GLU* 3.0 33.0 + - - +
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Residues in contact with ILE 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LEU* 4.2 3.8 - - + -
17B TYR* 3.7 33.2 - - + +
52B PHE* 3.8 30.3 - - + +
55B VAL* 3.7 12.6 - - + -
56B SER* 3.3 45.3 - - - +
59B THR* 3.9 5.2 - - - +
61B LYS* 4.0 12.6 - - + +
62B ASN 3.1 7.8 + - - +
63B VAL* 2.9 9.9 + - - +
65B GLU* 1.3 75.2 - - - +
67B TRP* 1.3 59.5 + - - +
69B GLU* 3.1 3.0 + - - +
70B VAL* 2.8 29.7 + - + +
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Residues in contact with TRP 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B TRP* 3.8 31.4 - + - -
48B VAL* 4.2 8.5 - - + -
49B ARG* 6.0 1.7 - - - +
52B PHE* 3.3 55.7 - + + +
63B VAL* 3.0 38.1 + - + +
64B ASN* 3.8 8.7 - - - +
65B GLU 3.4 0.2 - - - -
66B ILE* 1.3 76.9 - - - +
68B ARG* 1.3 56.9 + - - +
70B VAL* 3.4 6.0 + - + +
71B GLY 2.9 23.4 + - - -
137B MET* 3.6 33.2 - - + -
139B ASP* 4.1 12.1 - - + -
140B TYR* 3.6 38.1 - + + +
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Residues in contact with ARG 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 ASN 3.1 14.8 + - - +
65B GLU* 3.4 12.1 - - - +
67B TRP* 1.3 76.4 - - - +
69B GLU* 1.3 61.7 + - + +
71B GLY 3.4 0.9 + - - -
72B ARG* 3.2 49.3 + - - +
139B ASP* 3.3 37.0 + - + +
142B LEU* 3.9 20.5 - - - +
143B GLY* 3.6 16.3 - - - +
146B GLU* 2.8 37.5 + - - -
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Residues in contact with GLU 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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16B LEU* 3.6 22.5 - - + +
17B TYR* 2.9 39.7 + - - +
61B LYS* 3.1 35.1 + - - +
65B GLU* 3.0 19.5 + - - +
66B ILE 3.1 1.8 + - - +
68B ARG* 1.3 75.4 - - + +
70B VAL* 1.3 63.8 + - - +
72B ARG* 3.3 21.2 + - - +
73B GLN* 3.0 19.4 + - - +
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Residues in contact with VAL 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B TRP* 4.0 29.6 - - + -
12B THR* 3.8 13.8 - - + +
13B LEU* 3.7 30.1 - - + -
16B LEU* 4.0 13.2 - - + -
52B PHE* 3.8 12.1 - - + -
66B ILE* 2.8 21.9 + - + +
67B TRP* 3.7 13.0 - - + +
69B GLU* 1.3 74.1 - - - +
71B GLY* 1.3 56.5 + - - +
74B ASN* 2.7 39.2 + - + +
140B TYR* 4.0 8.5 - - + -
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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
----------------------------------------------------------
67B TRP 2.9 13.8 + - - -
68B ARG 3.9 1.3 - - - -
69B GLU 3.3 0.2 - - - -
70B VAL* 1.3 78.3 - - - +
72B ARG* 1.3 61.3 + - - +
74B ASN 3.5 3.3 + - - -
75B ILE* 3.8 2.8 + - - +
140B TYR* 3.6 26.4 - - - -
143B GLY 3.5 7.0 - - - -
144B LEU* 3.1 35.3 - - - +
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Residues in contact with ARG 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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68B ARG* 3.2 40.5 + - - +
69B GLU* 3.6 20.7 - - - +
71B GLY* 1.3 77.2 - - - +
73B GLN* 1.3 61.1 + - - +
75B ILE* 3.9 7.1 + - - +
76B LYS* 4.6 1.6 + - - +
143B GLY* 3.2 20.3 + - - +
146B GLU* 2.6 41.8 + - + +
147B GLY* 3.5 21.6 - - - +
150B LYS* 4.6 20.6 + - - +
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Residues in contact with GLN 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LYS* 5.5 1.4 + - - -
12B THR* 3.5 29.4 - - + +
15B ASP* 4.3 17.9 - - + +
16B LEU* 4.0 25.2 - - + +
69B GLU 3.0 13.7 + - - +
72B ARG* 1.3 74.2 - - - +
74B ASN* 1.3 65.6 + - - +
75B ILE 3.1 2.5 - - - -
76B LYS* 3.0 40.2 + - - +
77B THR* 3.3 6.1 + - - +
150B LYS* 4.8 11.7 - - - +
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Residues in contact with ASN 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B THR* 3.3 28.7 + - - +
9B TRP* 3.9 7.6 + - - -
12B THR* 2.7 27.8 + - - +
70B VAL 2.7 23.3 + - - +
71B GLY 3.8 5.6 - - - +
72B ARG 3.4 0.6 - - - -
73B GLN* 1.3 71.8 - - - +
75B ILE* 1.3 58.2 + - - +
77B THR* 3.2 2.0 + - - -
78B PHE* 2.8 55.7 + - - -
140B TYR* 2.9 25.7 + - - +
144B LEU* 4.1 6.7 - - + -
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Residues in contact with ILE 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 GLY 3.9 10.1 - - - +
72B ARG 4.0 6.7 - - - +
73B GLN 3.1 0.2 + - - -
74B ASN* 1.3 73.5 - - - +
76B LYS* 1.3 67.1 + - - +
78B PHE* 3.1 15.9 + - + +
79B SER* 2.9 22.0 + - - -
86B PHE* 3.7 20.5 - - + -
94B PHE* 4.6 6.5 - - + -
144B LEU* 3.5 37.5 - - + +
147B GLY* 3.8 8.1 - - - +
148B SER* 3.5 23.6 - - - +
151B PHE* 3.9 24.0 - - + -
501B HEM 4.3 11.2 - - + -
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Residues in contact with LYS 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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11B LYS* 5.8 1.3 - - - +
72B ARG 4.6 1.7 + - - +
73B GLN* 3.0 35.1 + - - +
75B ILE* 1.3 80.7 - - - +
77B THR* 1.3 62.8 + - - +
79B SER* 2.6 31.7 + - - +
80B GLU* 3.0 37.3 + - - +
151B PHE* 4.8 18.0 - - + -
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Residues in contact with THR 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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8B THR* 4.0 25.8 - - + +
11B LYS* 3.9 32.9 + - + +
12B THR* 2.8 25.4 + - - +
15B ASP* 4.5 1.2 + - - -
73B GLN* 3.3 6.7 + - - +
74B ASN* 3.2 11.3 + - - -
76B LYS* 1.3 80.2 - - - +
78B PHE* 1.3 62.1 + - - +
80B GLU* 3.1 16.2 + - - +
81B TRP* 3.1 31.8 + - + +
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Residues in contact with PHE 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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4B THR* 6.4 0.7 - - + -
5B ILE* 3.8 16.2 - - + -
8B THR* 3.9 24.7 - - + -
74B ASN* 2.8 44.0 + - - -
75B ILE* 3.4 13.7 - - + +
77B THR* 1.3 75.7 - - - +
79B SER* 1.3 56.3 + - - +
82B PHE* 2.7 61.8 + + + +
86B PHE* 3.7 3.8 - - + -
140B TYR* 4.4 1.3 - - - -
144B LEU* 4.3 10.8 - - + -
501B HEM 3.4 67.3 - + + -
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Residues in contact with SER 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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85A TYR* 4.7 1.2 + - - -
75B ILE 2.9 11.8 + - - -
76B LYS* 2.6 27.9 + - - +
78B PHE* 1.3 76.3 - - - +
80B GLU* 1.3 60.3 + - - +
83B PRO* 3.5 23.6 - - - +
86B PHE* 3.5 19.4 - - - -
151B PHE* 3.5 38.3 - - - -
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Residues in contact with GLU 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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85A TYR* 4.2 3.2 + - - -
104A GLN* 3.6 39.1 + - - +
105A LEU* 3.7 15.8 - - - +
11B LYS* 3.2 29.4 + - - -
76B LYS* 3.0 38.4 - - + +
77B THR* 3.1 9.5 + - - +
79B SER* 1.3 86.4 + - - +
81B TRP* 1.3 68.5 + - + +
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Residues in contact with TRP 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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2A LYS* 4.7 2.8 + - - -
104A GLN* 3.7 27.4 - - + +
105A LEU* 3.6 22.9 - - - +
107A LYS* 3.8 32.3 - - + +
108A MET* 3.4 44.9 - - + +
7B GLY 3.7 21.1 - - - -
8B THR* 3.5 29.6 - - + -
11B LYS* 4.1 29.4 - - + +
77B THR* 3.1 23.0 + - + +
78B PHE* 6.1 0.2 - + - -
80B GLU* 1.3 87.7 + - + +
82B PHE* 1.3 88.3 + + + +
83B PRO* 3.5 3.3 - - - +
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Residues in contact with PHE 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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2A LYS* 5.0 0.9 - - - -
39A PRO* 4.1 15.3 - - + -
40A LEU* 3.3 30.7 - - + -
105A LEU 5.9 1.6 - - - -
108A MET* 4.1 21.3 - - + -
109A ILE* 6.2 2.7 - - + -
4B THR* 4.4 8.7 - - + -
8B THR* 4.7 2.2 - - + -
78B PHE* 2.7 54.5 + + + +
81B TRP* 1.3 117.6 - + + +
83B PRO* 1.3 65.7 - - - +
84B SER 3.2 3.8 + - - -
85B TYR* 3.3 34.0 + + + -
86B PHE* 3.7 5.4 - - - -
189B CL 3.8 4.9 - - - -
501B HEM 4.4 12.3 - - + -
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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
------------------------------------------------------------
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