Contacts of the helix formed by residues 62 - 74 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A GLU* 1.3 74.4 + - - +
63A GLU* 1.3 64.6 + - - +
65A LEU* 3.4 18.8 + - - +
66A LEU* 3.1 24.0 + - - +
98A VAL* 4.1 7.6 - - - +
100A GLU* 3.7 33.9 - - + +
103A VAL* 3.7 12.4 - - + +
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Residues in contact with GLU 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A VAL* 5.0 14.4 - - + +
25A GLN* 5.0 7.0 - - - +
28A LEU* 3.8 28.3 - - + +
61A GLU* 3.3 4.0 - - + +
62A ASP* 1.3 79.4 - - - +
64A VAL* 1.3 62.8 + - + +
66A LEU* 3.5 14.8 - - + +
67A ALA* 3.4 18.7 + - - +
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Residues in contact with VAL 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LEU* 5.3 2.9 - - + -
24A VAL* 4.4 18.8 - - + -
27A ARG* 4.9 4.7 - - + +
28A LEU* 4.9 17.5 - - + +
31A ILE* 3.5 30.2 - - + +
58A ILE* 5.7 4.3 - - + -
60A ASP* 3.3 41.7 - - + +
61A GLU* 3.3 8.3 + - + +
62A ASP 3.1 0.4 - - - -
63A GLU* 1.3 75.0 - - + +
65A LEU* 1.3 67.9 + - + +
66A LEU 3.0 1.6 - - - -
67A ALA* 2.8 10.6 + - - +
68A LEU* 2.8 21.4 + - + +
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Residues in contact with LEU 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A ILE* 4.1 27.1 - - + -
59A TYR* 4.9 4.5 - - - +
60A ASP* 4.1 16.8 - - + +
61A GLU 3.1 17.5 - - - +
62A ASP* 3.4 24.0 + - - +
64A VAL* 1.3 76.4 - - + +
66A LEU* 1.3 52.3 + - - +
68A LEU* 3.0 9.7 + - + +
69A ALA* 2.7 36.4 + - - +
95A LEU* 4.0 22.9 - - + +
98A VAL* 4.5 21.5 - - + -
103A VAL* 4.0 9.0 - - + -
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Residues in contact with LEU 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ASP 3.1 17.9 + - - +
63A GLU* 3.5 16.4 - - + +
64A VAL 3.0 0.2 - - - -
65A LEU* 1.3 75.9 - - - +
67A ALA* 1.3 56.1 + - - +
69A ALA* 3.3 6.1 + - - +
70A GLU* 3.0 28.2 + - - +
102A VAL* 3.7 35.7 - - + +
103A VAL* 4.1 11.2 - - + +
106A LYS* 3.3 34.6 - - + +
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Residues in contact with ALA 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A LEU* 4.3 22.7 - - + -
31A ILE* 3.7 17.4 - - + +
32A LYS* 5.1 7.0 - - + -
63A GLU 3.4 9.7 + - - +
64A VAL* 2.8 11.3 + - - +
66A LEU* 1.3 77.0 - - - +
68A LEU* 1.3 61.4 + - - +
70A GLU* 3.5 15.1 + - - +
71A GLN* 3.0 30.1 + - - +
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Residues in contact with LEU 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ILE* 3.6 17.2 - - + +
34A LEU* 3.9 27.4 - - + -
54A LEU* 4.4 15.9 - - + +
58A ILE* 3.4 36.1 - - + -
64A VAL* 2.8 12.6 + - + +
65A LEU* 3.0 12.8 + - + +
67A ALA* 1.3 75.2 - - - +
69A ALA* 1.3 65.8 + - - +
71A GLN* 3.0 3.2 + - - +
72A LEU* 3.0 45.5 + - + +
95A LEU* 4.0 24.7 - - + -
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Residues in contact with ALA 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A LEU 2.7 19.7 + - - +
66A LEU* 3.5 7.4 - - - +
68A LEU* 1.3 74.0 - - - +
70A GLU* 1.3 61.0 + - - +
72A LEU* 3.6 8.3 + - - +
73A GLY 3.6 1.4 + - - -
92A LEU* 4.1 3.0 - - - +
95A LEU* 3.5 22.9 - - + -
103A VAL* 4.6 3.8 - - + +
106A LYS* 3.9 20.9 - - + -
107A ALA* 4.0 13.7 - - + +
110A SER* 2.8 23.3 + - - -
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Residues in contact with GLU 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LYS* 5.6 8.1 - - - +
66A LEU* 3.0 16.4 + - + +
67A ALA* 3.7 14.0 - - - +
68A LEU 3.2 0.2 - - - -
69A ALA* 1.3 76.0 - - - +
71A GLN* 1.3 68.2 + - - +
73A GLY* 3.2 14.0 + - - -
74A THR* 4.0 9.9 + - + +
106A LYS* 3.9 33.8 + - + +
110A SER* 4.2 4.8 + - - -
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Residues in contact with GLN 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ILE 3.1 26.0 - - - +
32A LYS* 3.4 24.7 + - - +
34A LEU* 3.7 13.7 - - + -
35A SER* 4.6 9.9 + - - +
67A ALA 3.0 16.2 + - - +
68A LEU* 3.2 12.6 - - - +
70A GLU* 1.3 80.2 - - - +
72A LEU* 1.3 57.2 + - - +
73A GLY 3.0 0.2 - - - -
74A THR* 2.8 37.6 + - - -
75A PHE* 3.1 38.0 - - + -
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Residues in contact with LEU 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LEU* 4.7 4.5 - - + -
51A LEU* 5.1 2.2 - - + -
54A LEU* 4.5 15.0 - - + -
68A LEU* 3.0 35.1 + - + +
69A ALA 4.0 0.4 - - - +
70A GLU 3.4 0.2 - - - -
71A GLN* 1.3 75.2 - - - +
73A GLY* 1.3 58.9 + - - +
74A THR 3.1 1.8 + - - -
75A PHE* 3.6 22.1 + - + -
88A LEU* 3.9 34.8 - - + +
91A PRO* 3.9 31.9 - - + -
92A LEU* 4.0 27.2 - - + +
95A LEU* 4.1 20.2 - - + -
114A ILE* 4.3 3.3 - - - +
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Residues in contact with GLY 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A ALA 3.6 4.0 + - - -
70A GLU 3.2 7.4 + - - -
71A GLN 3.0 2.4 + - - -
72A LEU* 1.3 78.1 - - - +
74A THR* 1.3 64.3 + - - +
75A PHE 3.7 1.1 + - - -
76A THR* 5.2 1.2 + - - -
110A SER* 3.6 25.8 + - - -
113A ALA* 4.7 8.4 - - - +
114A ILE* 4.0 19.4 - - - +
314B ALA 5.2 0.2 - - - +
315B ASP 5.1 2.4 - - - +
319B ASN* 5.1 8.8 + - - +
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Residues in contact with THR 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A GLU* 4.1 8.6 + - + +
71A GLN* 2.8 32.3 + - - -
73A GLY* 1.3 84.9 - - - +
75A PHE* 1.3 62.4 + - - +
76A THR 3.7 2.2 - - - +
77A THR* 4.9 8.2 - - - +
78A LEU* 5.0 4.5 - - - +
314B ALA* 3.8 35.9 - - + +
315B ASP* 5.3 1.3 - - - -
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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
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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