Contacts of the helix formed by residues 62 - 74 (chain B) in PDB entry 1B3U
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 62 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60B ASP 5.3 0.2 - - - +
61B GLU* 1.3 74.8 + - - +
63B GLU* 1.3 59.8 + - + +
65B LEU* 4.1 17.7 - - - +
66B LEU* 2.8 31.8 + - - +
98B VAL* 4.4 5.9 - - - +
99B GLU* 6.1 0.2 - - - +
100B GLU* 3.5 36.0 + - + +
102B VAL* 5.8 1.6 - - + -
103B VAL* 3.6 12.3 - - + +
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Residues in contact with GLU 63 (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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24B VAL* 5.3 11.6 - - + +
28B LEU* 4.5 21.3 - - + +
61B GLU* 3.1 10.7 + - + -
62B ASP* 1.3 77.1 - - + +
64B VAL* 1.3 63.6 + - + +
66B LEU* 3.7 11.5 - - - +
67B ALA* 3.6 17.8 + - - +
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Residues in contact with VAL 64 (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 3.1 - - + -
24B VAL* 4.4 18.8 - - + -
27B ARG* 4.6 12.3 - - + +
28B LEU* 4.7 10.8 - - + +
31B ILE* 3.7 28.4 - - + +
58B ILE* 6.0 3.1 - - + -
60B ASP* 2.9 41.3 - - + +
61B GLU* 2.9 8.5 + - + +
63B GLU* 1.3 76.1 - - + +
65B LEU* 1.3 68.3 + - + +
66B LEU 3.1 1.3 - - - -
67B ALA* 3.0 16.9 + - - +
68B LEU* 3.0 13.4 + - + +
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Residues in contact with LEU 65 (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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58B ILE* 3.5 33.4 - - + +
59B TYR 3.6 11.7 - - - +
60B ASP* 3.9 16.4 - - + +
61B GLU 3.1 12.4 + - - +
62B ASP* 3.7 22.9 - - - +
64B VAL* 1.3 76.2 - - + +
66B LEU* 1.3 62.3 + - - +
68B LEU* 3.3 9.3 + - + +
69B ALA* 3.0 23.4 + - - +
95B LEU* 4.0 16.5 - - + +
98B VAL* 4.2 25.6 - - + -
103B VAL* 4.0 14.5 - - + +
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Residues in contact with LEU 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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62B ASP 2.8 17.7 + - - +
63B GLU* 3.7 11.7 - - - +
64B VAL 3.1 0.2 - - - -
65B LEU* 1.3 76.6 - - - +
67B ALA* 1.3 62.1 + - - +
69B ALA* 3.2 8.2 + - - +
70B GLU* 3.2 19.1 + - - +
102B VAL* 3.8 31.2 - - + +
103B VAL* 4.1 7.5 - - + +
106B LYS* 3.5 41.4 - - + +
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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
----------------------------------------------------------
28B LEU* 4.3 20.9 - - + -
31B ILE* 3.7 17.5 - - + +
32B LYS* 4.9 8.3 - - + -
63B GLU 3.6 9.7 + - - +
64B VAL* 3.0 10.1 + - - +
66B LEU* 1.3 76.5 - - - +
68B LEU* 1.3 65.0 + - - +
70B GLU* 3.4 13.7 + - - +
71B GLN* 3.0 26.0 + - - +
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Residues in contact with LEU 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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31B ILE* 3.6 20.1 - - + +
34B LEU* 3.5 30.7 - - + -
54B LEU* 4.2 29.2 - - + +
58B ILE* 4.4 31.0 - - + -
64B VAL* 3.0 12.6 + - + +
65B LEU* 3.5 10.3 - - + +
66B LEU 3.2 0.2 - - - -
67B ALA* 1.3 73.6 - - - +
69B ALA* 1.3 67.0 + - - +
71B GLN* 3.3 2.8 + - - +
72B LEU* 2.9 37.8 + - + +
95B LEU* 4.0 22.7 - - + -
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Residues in contact with ALA 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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65B LEU 3.0 12.4 + - - +
66B LEU* 3.2 10.5 + - - +
68B LEU* 1.3 79.1 - - - +
70B GLU* 1.3 62.4 + - - +
72B LEU* 3.3 9.9 + - - +
73B GLY 3.3 2.3 + - - -
92B LEU* 4.1 3.8 - - - +
95B LEU* 3.9 18.8 - - + +
103B VAL* 4.6 3.4 - - + +
106B LYS* 3.8 16.4 - - + -
107B ALA* 4.1 20.4 - - + +
110B SER* 2.9 20.0 + - - -
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Residues in contact with GLU 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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32B LYS* 5.8 5.5 - - - +
66B LEU 3.2 7.1 + - - +
67B ALA* 3.6 15.0 - - - +
69B ALA* 1.3 79.5 - - - +
71B GLN* 1.3 67.5 + - - +
73B GLY* 3.3 10.9 + - - -
74B THR* 3.7 16.0 - - + +
106B LYS* 3.6 35.2 + - - +
110B SER* 4.0 6.1 + - - -
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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
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31B ILE 3.9 9.2 - - - +
32B LYS* 3.7 23.7 + - - +
34B LEU* 3.9 23.8 - - + -
35B SER* 4.6 12.0 + - - -
67B ALA 3.0 17.6 + - - +
68B LEU* 3.6 7.9 - - - +
70B GLU* 1.3 80.6 - - - +
72B LEU* 1.3 63.2 + - - +
74B THR* 3.0 32.5 + - - +
75B PHE* 2.9 44.0 - - + -
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Residues in contact with LEU 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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34B LEU* 5.1 2.0 - - + -
51B LEU* 5.0 1.8 - - + -
54B LEU* 4.4 23.3 - - + -
68B LEU* 2.9 27.7 + - + +
69B ALA 3.6 4.5 - - - +
71B GLN* 1.3 75.8 - - - +
73B GLY* 1.3 60.7 + - - +
74B THR 3.1 1.3 + - - -
75B PHE* 3.2 26.7 + - + +
88B LEU* 3.6 31.7 - - + +
91B PRO* 4.0 21.5 - - + -
92B LEU* 3.7 28.2 - - + +
95B LEU* 3.6 31.0 - - + -
114B ILE* 4.6 0.9 - - - +
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Residues in contact with GLY 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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69B ALA 3.3 4.4 + - - -
70B GLU 3.3 6.5 + - - -
71B GLN 3.1 1.2 - - - -
72B LEU* 1.3 78.8 - - - +
74B THR* 1.3 61.9 + - - +
75B PHE 3.5 0.2 - - - -
76B THR* 4.8 2.3 + - - -
92B LEU* 5.2 0.2 - - - -
110B SER* 3.5 27.5 + - - -
113B ALA* 4.8 7.7 - - - +
114B ILE* 3.5 24.3 - - - +
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Residues in contact with THR 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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70B GLU* 3.7 17.3 - - + +
71B GLN* 3.0 30.8 + - - +
73B GLY* 1.3 80.5 - - - +
75B PHE* 1.3 63.0 + - - +
76B THR* 3.4 4.5 + - - -
77B THR* 4.7 10.0 - - - +
78B LEU* 4.9 4.0 - - - +
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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