Contacts of the helix formed by residues 64 - 80 (chain B) in PDB entry 5VBL
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 ALA 64 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B ARG* 3.2 2.4 - - + +
63B SER* 1.3 78.4 + - - +
65B ASP* 1.4 62.2 + - - +
66B ILE 3.3 2.9 - - - -
67B PHE* 3.1 16.3 + - - -
68B ILE* 3.2 22.8 + - + +
123B LEU* 3.6 25.7 - - + +
126B ASP* 4.5 9.0 - - + +
127B ARG* 5.2 0.4 - - - +
246B LEU* 3.8 26.5 - - + -
250B ILE* 4.6 7.0 - - + -
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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
----------------------------------------------------------
53B VAL* 3.8 27.8 - - + +
61B ARG* 3.7 14.2 - - + +
62B ARG* 2.8 59.9 + - - +
64B ALA* 1.4 76.9 - - - +
66B ILE* 1.3 55.8 + - - +
68B ILE* 3.8 12.4 - - - +
69B ALA* 3.1 31.7 + - - +
315B ARG* 3.4 18.4 + - - -
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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
----------------------------------------------------------
62B ARG 4.4 1.8 + - - +
63B SER 3.7 17.9 + - - +
65B ASP* 1.3 76.6 - - - +
67B PHE* 1.3 79.8 + - + +
69B ALA* 3.9 5.0 + - - +
70B SER* 3.3 24.9 + - - +
143B ARG 5.9 0.7 - - - +
146B GLY* 4.1 12.3 - - - +
147B ALA* 4.4 14.8 - - + +
150B THR* 3.8 29.5 + - + +
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Residues in contact with PHE 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B SER 4.1 11.7 - - - -
64B ALA* 3.1 9.4 + - - +
66B ILE* 1.3 87.9 - - + +
68B ILE* 1.4 59.3 + - - +
70B SER* 4.0 3.8 - - - -
71B LEU* 3.0 29.0 + - - +
119B CYS* 3.5 27.2 - - - +
122B GLY* 3.7 41.7 - - - -
123B LEU* 3.7 12.3 - - + -
126B ASP* 4.6 8.1 - - + -
146B GLY* 3.6 33.7 - - - -
149B ALA* 4.3 10.1 - - + -
150B THR* 4.3 10.3 - - - -
153B LEU* 4.1 26.7 - - + -
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Residues in contact with ILE 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B VAL* 3.9 21.4 - - + +
53B VAL* 4.5 9.4 - - + -
62B ARG* 4.7 14.4 - - - +
64B ALA* 3.2 35.1 + - + +
65B ASP* 3.4 19.9 + - - +
67B PHE* 1.4 73.5 - - - +
69B ALA* 1.4 59.1 + - - +
71B LEU* 3.3 9.0 + - - +
72B ALA* 3.0 27.0 + - - +
123B LEU* 3.9 14.4 - - + -
246B LEU* 5.8 0.2 - - + -
249B ILE* 5.7 3.4 - - + -
253B LEU* 5.6 0.7 - - + -
309B TYR* 3.7 35.8 - - + +
313B ASP* 5.1 2.0 - - - +
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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
----------------------------------------------------------
49B VAL* 5.5 0.7 - - - -
50B LEU* 3.5 5.8 - - + +
53B VAL* 4.1 21.3 - - + +
54B PHE* 4.3 20.2 - - + -
65B ASP 3.1 17.5 + - - +
66B ILE* 4.1 5.8 - - - +
68B ILE* 1.4 77.2 - - - +
70B SER* 1.4 56.6 + - - +
72B ALA* 3.3 9.2 + - - +
73B VAL* 3.1 32.1 + - - +
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Residues in contact with SER 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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66B ILE* 3.3 17.8 + - - +
67B PHE* 4.0 0.7 - - - -
68B ILE 3.4 0.2 - - - -
69B ALA* 1.4 75.4 - - - +
71B LEU* 1.4 60.0 + - - +
73B VAL* 3.2 7.7 + - - -
74B ALA* 2.9 27.2 + - - +
119B CYS* 3.7 19.3 - - - -
150B THR* 3.4 12.8 + - - -
153B LEU* 5.1 0.2 - - - -
154B TRP* 3.2 36.1 + - - -
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Residues in contact with LEU 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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67B PHE 3.0 19.1 + - - +
68B ILE* 3.3 6.0 + - - +
70B SER* 1.4 73.9 - - - +
72B ALA* 1.3 58.5 + - - +
74B ALA* 3.7 3.9 + - - +
75B ASP* 3.2 36.5 + - - +
116B SER* 3.6 42.8 - - - +
119B CYS* 3.7 11.2 - - + -
120B LEU* 3.9 18.8 - - + -
123B LEU* 4.8 8.1 - - + -
253B LEU* 4.6 3.1 - - + -
305B ASN* 3.5 27.8 - - + +
309B TYR* 3.4 26.0 - - + +
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Residues in contact with ALA 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ASN* 3.6 29.0 - - - +
49B VAL* 3.9 16.6 - - + -
50B LEU* 3.8 20.4 - - + +
68B ILE 3.0 13.0 + - - +
69B ALA* 3.4 10.8 - - - +
70B SER 3.3 0.2 - - - -
71B LEU* 1.3 74.0 - - - +
73B VAL* 1.4 57.7 + - - +
76B LEU* 3.0 31.9 + - - +
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Residues in contact with VAL 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B LEU* 3.7 24.7 - - + -
54B PHE* 5.9 0.9 - - + -
69B ALA 3.1 19.9 + - - +
70B SER* 3.2 10.3 + - - +
72B ALA* 1.4 72.9 - - - +
74B ALA* 1.4 61.3 + - - +
76B LEU* 3.4 3.3 + - - +
77B THR* 2.9 41.9 + - + +
154B TRP* 3.9 20.6 - - + -
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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
----------------------------------------------------------
70B SER 2.9 15.7 + - - +
71B LEU* 3.8 8.1 - - - +
73B VAL* 1.4 76.7 - - - +
75B ASP* 1.3 60.0 + - - +
77B THR* 3.2 16.9 + - - -
78B PHE* 3.5 8.8 + - - +
111B VAL* 6.0 1.1 - - - -
112B ASN* 3.0 27.2 - - - +
115B ALA* 4.0 27.4 - - + -
116B SER* 4.5 6.5 - - - +
154B TRP* 4.1 8.5 - - + -
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Residues in contact with ASP 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ASN* 3.5 25.6 - - - +
71B LEU* 3.2 18.6 + - - +
74B ALA* 1.3 74.4 - - - +
76B LEU* 1.4 59.2 - - - +
78B PHE* 3.5 2.1 + - - +
79B VAL* 3.0 33.6 + - - +
112B ASN* 3.0 18.3 - - - +
116B SER* 4.4 11.6 - - - -
301B ASN* 4.1 2.9 + - - +
302B SER* 3.0 34.1 + - - +
305B ASN* 3.0 25.4 + - - -
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Residues in contact with LEU 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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42B GLY 3.9 4.3 - - - +
43B THR* 3.4 42.2 - - + +
46B ASN* 4.2 5.5 - - + +
47B GLY* 4.1 12.3 - - - +
50B LEU* 4.1 19.7 - - + -
72B ALA 3.0 19.1 + - - +
73B VAL* 3.8 4.7 - - - +
75B ASP* 1.4 75.9 - - - +
77B THR* 1.4 65.3 + - + +
79B VAL* 3.4 6.5 + - - +
80B VAL* 3.3 32.2 + - + +
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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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73B VAL* 2.9 30.3 + - + +
74B ALA* 3.2 13.3 + - - -
76B LEU* 1.4 80.4 - - + +
78B PHE* 1.3 59.3 + - - +
80B VAL* 4.0 10.3 + - - +
81B THR* 3.9 15.9 - - - +
108B LEU* 4.1 28.5 + - + +
111B VAL* 5.6 3.6 - - - +
154B TRP* 5.6 1.6 - - - -
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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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74B ALA 3.5 15.1 + - - +
75B ASP 3.9 0.7 - - - +
76B LEU 3.3 0.6 - - - -
77B THR* 1.3 79.5 + - - +
79B VAL* 1.3 60.9 + - - +
80B VAL 3.2 0.7 - - - -
81B THR* 2.7 37.2 + - - -
82B LEU* 3.5 24.5 + - + +
85B TRP* 5.2 2.5 - + - -
108B LEU* 3.8 7.6 + - - +
109B ILE* 3.7 41.3 - - + -
112B ASN* 3.7 23.8 - - + -
299B TYR* 3.5 50.3 - + + -
302B SER* 3.3 28.0 - - - -
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Residues in contact with VAL 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B VAL* 3.6 17.7 - - + +
39B PHE* 3.2 41.8 - - - +
42B GLY* 3.7 10.5 - - - +
43B THR* 3.6 25.1 - - + +
75B ASP 3.0 21.0 + - - +
76B LEU* 3.4 5.8 + - - +
78B PHE* 1.3 76.1 - - + +
80B VAL* 1.4 60.2 + - - +
82B LEU* 3.2 29.2 + - + +
302B SER* 3.9 22.0 - - - -
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Residues in contact with VAL 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B PHE* 3.9 12.8 - - + -
43B THR* 4.2 18.4 - - + -
76B LEU* 3.3 21.5 + - + +
77B THR* 4.1 9.2 - - - +
78B PHE 3.2 0.6 - - - -
79B VAL* 1.4 74.8 - - - +
81B THR* 1.4 59.5 + - + +
83B PRO* 3.2 15.6 - - - +
84B LEU* 4.6 5.8 - - - +
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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