Contacts of the helix formed by residues 64 - 80 (chain B) in PDB entry 3B1D
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 SER 64 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A HIS* 3.4 42.7 - - - -
62B TYR* 3.4 12.0 + - - -
63B ALA* 1.3 75.6 - - - +
65B ASP* 1.3 64.4 + - - +
66B GLU* 3.3 9.4 + - - +
67B LEU* 3.0 27.3 + - - +
68B LEU* 3.0 24.0 + - - +
274B TYR* 5.9 0.4 - - - +
278B GLU* 3.9 5.0 + - - -
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Residues in contact with ASP 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B TYR* 5.6 0.6 - - - -
63B ALA 4.1 0.2 + - - -
64B SER* 1.3 72.9 - - - +
66B GLU* 1.3 67.4 + - - +
68B LEU* 3.3 18.1 + - - +
69B GLN* 2.8 30.5 + - - +
85B LYS* 3.9 26.3 + - - +
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Residues in contact with GLU 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A HIS* 3.5 15.7 + - + -
64B SER* 3.4 20.7 - - - +
65B ASP* 1.3 84.0 + - - +
67B LEU* 1.3 58.5 + - - +
69B GLN* 3.4 6.5 + - - +
70B ALA* 3.0 27.9 + - - +
278B GLU* 3.3 22.5 - - - +
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Residues in contact with LEU 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ALA* 4.0 7.6 - - + -
64B SER* 3.0 19.9 + - - +
66B GLU* 1.3 75.2 - - - +
68B LEU* 1.3 64.3 + - - +
70B ALA* 3.1 2.3 + - + +
71B VAL* 3.1 22.4 + - + +
90B PHE* 3.5 30.7 - - + -
243B ASN* 4.4 0.2 - - - +
274B TYR* 3.4 47.1 - - + +
277B THR* 3.9 17.7 - - + -
278B GLU* 3.7 41.8 + - + +
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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
----------------------------------------------------------
63B ALA* 4.5 9.4 - - + +
64B SER 3.0 21.4 + - - +
65B ASP* 3.7 23.1 - - - +
67B LEU* 1.3 75.6 - - - +
69B GLN* 1.3 58.0 + - - +
71B VAL 3.3 1.9 + - - -
72B LEU* 3.0 24.8 + - - +
85B LYS* 3.7 31.9 - - + +
88B ILE* 3.5 41.6 - - + +
90B PHE* 3.6 26.9 - - + -
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Residues in contact with GLN 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ASP 2.8 17.6 + - - +
66B GLU* 3.7 7.6 - - - +
68B LEU* 1.3 77.5 - - - +
70B ALA* 1.3 55.4 + - - +
72B LEU* 3.3 19.8 + - - +
73B ASP* 2.8 68.0 + - - +
85B LYS* 4.0 20.1 + - - +
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Residues in contact with ALA 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B GLU 3.0 14.7 + - - +
67B LEU* 3.1 9.4 + - + +
69B GLN* 1.3 76.4 - - - +
71B VAL* 1.3 58.4 + - - +
73B ASP* 3.9 6.4 - - - +
74B TRP* 3.0 30.5 + - - +
278B GLU* 4.0 31.2 - - + +
281B TYR* 4.0 13.2 - - + +
282B ARG* 5.2 6.3 - - + +
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Residues in contact with VAL 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LEU* 3.1 19.2 + - + +
68B LEU 3.7 6.7 - - - +
70B ALA* 1.3 73.8 - - - +
72B LEU* 1.3 65.3 + - - +
74B TRP* 3.3 1.2 + - - +
75B GLU* 3.0 29.0 + - + +
83B PHE* 4.5 0.7 - - + -
88B ILE* 3.9 18.2 - - + -
90B PHE* 3.9 25.4 - - + -
245B TYR* 3.9 38.1 - - + -
247B ILE* 4.5 1.6 - - + -
277B THR* 4.5 1.8 - - + -
281B TYR* 4.0 22.0 - - + -
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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
----------------------------------------------------------
68B LEU 3.0 16.9 + - - +
69B GLN* 3.5 26.2 - - - +
71B VAL* 1.3 77.2 - - - +
73B ASP* 1.3 56.6 + - - +
75B GLU* 3.4 2.3 + - - +
76B LYS* 2.9 30.4 + - - +
81B TYR 4.6 1.4 - - - +
83B PHE* 3.0 65.1 - - + +
84B ASP* 3.9 7.2 - - - -
85B LYS* 3.5 29.4 - - + +
88B ILE* 4.0 2.7 - - + -
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Residues in contact with ASP 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B GLN* 2.8 60.0 + - - +
70B ALA* 3.9 6.1 - - - +
72B LEU* 1.3 71.1 - - - +
74B TRP* 1.3 61.6 + - - +
76B LYS* 3.9 5.6 - - - +
77B SER* 2.9 35.3 + - - -
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Residues in contact with TRP 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 ALA 3.0 19.4 + - - +
71B VAL 3.7 3.4 - - - +
73B ASP* 1.3 76.7 - - - +
75B GLU* 1.3 73.0 + - - +
77B SER* 3.9 6.1 - - - -
78B GLU* 2.8 63.9 + - + +
79B HIS* 4.1 1.0 + + - -
203B GLN* 4.6 0.6 - - - +
204B ASP* 3.1 41.0 + - - -
236B PHE* 3.7 24.0 - + - -
245B TYR* 4.7 0.4 - - - -
281B TYR* 3.3 66.0 - + + -
285B LYS* 4.5 21.8 - - + -
288B LEU* 4.0 16.8 - - + -
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Residues in contact with GLU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B VAL* 3.0 24.0 + - + +
72B LEU 3.7 1.3 - - - +
74B TRP* 1.3 78.5 - - + +
76B LYS* 1.3 58.6 + - - +
79B HIS* 3.0 35.0 + - - +
80B GLN 3.1 6.9 + - - -
81B TYR* 3.1 31.9 + - + +
83B PHE* 3.4 31.9 - - + -
203B GLN* 2.9 31.7 + - - +
214B SER* 4.6 3.6 + - - -
228B VAL* 5.0 4.7 - - - +
245B TYR* 3.4 21.6 + - + +
247B ILE* 4.7 3.5 - - - +
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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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72B LEU 2.9 17.6 + - - +
73B ASP* 3.9 6.3 - - - +
74B TRP 3.2 0.2 - - - -
75B GLU* 1.3 76.8 - - - +
77B SER* 1.3 60.7 + - - +
80B GLN* 3.0 26.9 + - - +
81B TYR 3.4 13.0 + - - +
82B SER* 4.0 22.0 - - - +
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Residues in contact with SER 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 ASP* 2.9 27.5 + - - -
74B TRP* 3.6 5.4 + - - -
76B LYS* 1.3 75.7 - - - +
78B GLU* 1.3 74.0 + - - +
80B GLN* 3.3 14.0 + - - -
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Residues in contact with GLU 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B TRP* 2.8 56.1 + - + +
77B SER* 1.3 87.7 + - - +
79B HIS* 1.3 82.9 + - + +
80B GLN* 3.7 9.7 + - - +
204B ASP* 5.0 1.2 - - - +
285B LYS* 2.9 48.6 + - - +
288B LEU* 4.8 2.9 - - - +
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Residues in contact with HIS 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B TRP* 4.2 3.1 - + - -
75B GLU* 3.0 25.7 + - - +
78B GLU* 1.3 94.9 + - + +
80B GLN* 1.3 79.5 + - - +
81B TYR* 3.1 5.1 + - + -
203B GLN* 3.2 53.9 - - - +
204B ASP* 2.7 24.8 + - - -
212B HIS* 3.5 23.6 + + + +
214B SER* 4.6 15.3 + - - +
217B THR* 3.9 12.1 + - - +
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Residues in contact with GLN 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B LYS* 3.0 18.6 + - - +
77B SER 3.3 24.2 + - - -
78B GLU 3.7 8.3 + - - +
79B HIS* 1.3 88.3 - - - +
81B TYR* 1.3 57.8 + - - +
82B SER* 4.0 5.4 + - - -
212B HIS 5.6 1.6 - - - +
217B THR* 3.7 11.2 - - + +
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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