Contacts of the helix formed by residues 64 - 80 (chain B) in PDB entry 1UZL
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 ASP 64 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B ASP* 3.0 18.8 + - + +
62B VAL 3.2 0.8 - - - -
63B THR* 1.3 79.7 + - - +
65B SER* 1.3 57.5 + - - +
66B ASP* 3.1 20.6 + - - +
67B ALA* 3.1 22.2 + - + +
68B VAL* 2.9 29.3 + - - +
70B ARG* 4.1 7.1 + - - -
118B ARG* 4.2 2.2 - - - -
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Residues in contact with SER 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B THR 4.1 0.4 + - - -
64B ASP* 1.3 73.4 + - - +
66B ASP* 1.3 62.0 + - - +
68B VAL* 3.6 6.3 + - - +
69B ASP* 3.1 24.3 + - - +
117B PHE* 6.1 0.3 - - - -
118B ARG* 3.1 35.7 + - - +
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Residues in contact with ASP 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ASP* 3.1 7.3 + - - +
65B SER* 1.3 78.8 - - - +
67B ALA* 1.3 58.3 + - - +
69B ASP* 3.3 9.1 + - - +
70B ARG* 3.1 56.8 + - - +
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Residues in contact with ALA 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B GLU 4.6 3.3 - - - +
60B CYS* 3.4 13.9 - - - +
61B ASP* 4.2 17.0 - - + +
64B ASP* 3.1 33.2 + - + +
66B ASP* 1.3 74.1 - - - +
68B VAL* 1.3 64.9 + - - +
70B ARG* 3.5 17.7 + - + +
71B ALA* 3.1 18.5 + - - +
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Residues in contact with VAL 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B CYS* 3.6 21.3 - - - -
62B VAL* 3.9 18.2 - - - +
64B ASP 2.9 18.7 + - - +
65B SER* 3.7 9.6 - - - +
67B ALA* 1.3 75.7 - - - +
69B ASP* 1.3 62.7 + - - +
71B ALA* 3.3 2.1 + - - +
72B PHE* 3.1 28.9 + - + -
118B ARG* 3.8 37.5 - - + +
119B VAL* 3.9 20.0 - - + -
122B ARG* 3.9 13.5 - - + -
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Residues in contact with ASP 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B SER 3.1 14.6 + - - +
66B ASP* 3.3 13.3 + - - +
68B VAL* 1.3 78.1 - - - +
70B ARG* 1.3 62.3 + - - +
72B PHE 3.5 0.5 + - - -
73B THR* 3.1 29.8 + - - -
122B ARG* 2.9 41.5 + - - +
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Residues in contact with ARG 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B GLU 5.9 2.2 - - - +
64B ASP* 4.1 8.9 + - - -
66B ASP* 3.1 52.8 + - - +
67B ALA* 3.5 17.4 - - - +
69B ASP* 1.3 77.9 - - - +
71B ALA* 1.3 65.4 + - - +
73B THR* 3.9 9.2 - - + +
74B ALA* 3.2 23.2 + - - +
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Residues in contact with ALA 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LEU* 5.5 0.9 - - + -
45B THR* 4.5 5.2 - - + -
58B VAL* 3.7 26.3 - - + +
59B GLU 4.3 4.0 - - - +
60B CYS* 3.9 20.4 - - + -
67B ALA 3.1 19.4 + - - +
68B VAL 3.3 4.2 + - - +
70B ARG* 1.3 75.4 - - - +
72B PHE* 1.3 68.4 + - + +
74B ALA* 3.3 5.2 + - - +
75B VAL* 3.0 28.2 + - + +
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Residues in contact with PHE 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LEU* 3.9 14.4 - - + -
68B VAL* 3.1 28.7 + - + +
71B ALA* 1.3 78.5 - - + +
73B THR* 1.3 56.7 + - - +
75B VAL* 3.1 8.6 + - - +
76B GLU* 2.8 30.5 + - - +
82B VAL* 3.8 34.3 - - + +
85B LEU* 4.0 16.8 - - + -
119B VAL* 3.4 35.0 - - + -
122B ARG* 3.4 49.8 - - + +
123B ALA* 3.6 24.0 - - + -
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Residues in contact with THR 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B ASP* 3.1 24.9 + - - -
70B ARG* 3.9 9.9 - - + +
72B PHE* 1.3 74.1 - - - +
74B ALA* 1.3 64.8 + - - +
76B GLU* 3.4 9.3 + - + +
77B GLU* 3.1 24.0 + - + +
122B ARG* 3.2 16.2 + - - +
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Residues in contact with ALA 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B PHE* 4.1 7.4 - - + -
58B VAL* 3.9 21.1 - - + -
70B ARG 3.2 17.4 + - - +
71B ALA* 3.6 4.5 - - - +
73B THR* 1.3 79.7 - - - +
75B VAL* 1.3 63.4 + - - +
77B GLU* 3.4 7.5 + - - +
78B HIS* 3.1 22.7 + - - +
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Residues in contact with VAL 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LEU* 3.9 18.2 - - + -
43B ALA* 3.9 21.3 - - + -
56B PHE* 4.3 9.4 - - + -
58B VAL* 4.3 10.8 - - + -
71B ALA 3.0 20.1 + - - +
72B PHE* 3.1 8.5 + - - +
74B ALA* 1.3 77.4 - - - +
76B GLU* 1.3 57.6 + - - +
78B HIS* 3.1 2.0 + - - +
79B GLN* 3.0 54.7 + - + +
80B GLY 4.4 1.6 - - - +
82B VAL* 3.5 26.5 - - + -
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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
----------------------------------------------------------
72B PHE 2.8 18.9 + - - +
73B THR* 3.8 9.2 - - + +
75B VAL* 1.3 72.7 - - - +
77B GLU* 1.3 62.7 + - + +
80B GLY* 3.0 33.8 + - - -
81B PRO* 3.7 34.7 - - + +
82B VAL* 5.3 1.5 - - + +
122B ARG* 5.6 3.0 + - - +
125B ARG* 4.0 19.4 + - - -
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Residues in contact with GLU 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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73B THR* 3.1 18.1 + - + +
74B ALA* 3.7 7.0 - - - +
75B VAL 3.3 0.2 - - - -
76B GLU* 1.3 79.8 - - + +
78B HIS* 1.3 63.2 + - - +
80B GLY 4.9 0.2 + - - -
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Residues in contact with HIS 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B PHE* 3.2 62.2 - + + +
74B ALA 3.1 13.2 + - - +
75B VAL 3.1 7.7 + - - +
77B GLU* 1.3 80.3 - - - +
79B GLN* 1.3 78.4 + - + +
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Residues in contact with GLN 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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17B SER* 2.7 24.7 + - - +
18B VAL 3.2 23.6 + - - +
41B LYS* 3.2 65.4 + - + +
42B VAL 3.8 2.4 + - - +
43B ALA* 3.8 12.5 + - - +
75B VAL* 3.0 30.4 + - + +
78B HIS* 1.3 98.7 + - + +
80B GLY* 1.3 59.3 + - - +
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Residues in contact with GLY 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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17B SER* 2.9 13.7 + - - -
41B LYS* 5.2 0.9 - - - -
75B VAL* 3.8 2.9 - - - +
76B GLU* 3.0 27.7 + - - -
77B GLU 4.7 0.2 - - - -
79B GLN* 1.3 78.9 - - - +
81B PRO* 1.3 78.8 - - - +
82B VAL 3.3 1.4 + - - -
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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
------------------------------------------------------------
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