Contacts of the helix formed by residues 56 - 69 (chain B) in PDB entry 5VT2
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 ASN 56 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83A TYR* 2.9 31.9 + - - -
103A ASP* 3.4 22.3 + - - +
204A EDO 3.2 24.5 + - - +
54B ALA* 3.3 2.9 + - - +
55B ALA* 1.3 81.6 - - - +
57B MET* 1.3 66.3 + - - +
58B HIS* 3.3 4.2 + - - +
59B ALA* 3.0 28.1 + - - +
60B GLN* 3.4 22.3 + - - +
112B ILE* 3.7 11.2 - - - +
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Residues in contact with MET 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A TRP* 4.0 26.5 - - + -
32A TRP* 4.3 15.9 - - + -
88A LEU* 6.4 0.2 - - - -
101A TYR* 3.8 24.5 - - + +
103A ASP* 3.2 28.8 + - - +
104A LEU* 3.9 26.0 - - + -
56B ASN* 1.3 75.5 - - - +
58B HIS* 1.3 64.1 + - - +
60B GLN* 3.0 44.6 + - - +
61B ILE* 3.0 13.4 + - + +
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Residues in contact with HIS 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A VAL* 4.9 6.5 - - + +
42A THR 3.2 22.4 + - - -
43A MET* 3.7 22.5 - - + +
44A CYS* 4.7 1.1 - - + -
80A PRO* 3.9 22.1 - - + +
83A TYR* 4.1 11.2 - + + +
103A ASP 2.9 16.7 + - - +
104A LEU* 2.8 30.0 - - - +
106A ALA* 3.9 7.3 - - - +
56B ASN* 3.4 11.4 - - - +
57B MET* 1.3 74.4 - - - +
59B ALA* 1.3 57.1 + - - +
61B ILE* 3.3 8.6 + - + +
62B LYS* 2.9 46.6 + - + +
112B ILE* 4.2 9.1 - - + +
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Residues in contact with ALA 59 (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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54B ALA* 4.0 8.7 - - + +
55B ALA 3.5 15.7 - - - +
56B ASN* 3.0 15.3 + - - +
57B MET 3.2 0.4 - - - -
58B HIS* 1.3 76.1 + - - +
60B GLN* 1.3 55.9 + - - +
62B LYS* 3.4 7.6 + - - +
63B THR* 3.1 30.3 + - - -
76B PRO* 4.4 3.5 - - + +
111B CYS* 3.3 28.0 - - + +
112B ILE* 3.8 13.6 - - - +
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Residues in contact with GLN 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A TRP* 5.7 3.1 + - - +
51B GLN* 6.3 4.3 - - + -
54B ALA* 4.1 17.6 - - + +
56B ASN* 3.4 21.7 + - - +
57B MET* 3.0 35.3 + - - +
59B ALA* 1.3 73.2 - - - +
61B ILE* 1.3 66.7 + - + +
63B THR* 3.3 11.2 + - - +
64B SER* 3.0 27.0 + - - +
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Residues in contact with ILE 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU* 4.0 16.2 - - + +
29A TRP* 3.6 42.0 - - + +
39A VAL* 6.1 0.4 - - + -
41A VAL* 4.0 21.3 - - + -
43A MET* 4.8 1.8 - - + -
104A LEU* 3.9 32.3 - - + +
57B MET* 3.0 14.3 + - + +
58B HIS* 3.5 8.5 - - + +
60B GLN* 1.3 75.4 - - + +
62B LYS* 1.3 59.1 + - - +
64B SER* 3.2 6.3 + - - -
65B LEU* 2.9 51.0 + - + +
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Residues in contact with LYS 62 (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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43A MET* 4.0 24.2 - - - -
44A CYS* 4.6 13.3 + - - +
78A CYS 5.2 3.8 + - - -
79A VAL* 6.3 0.2 - - - +
58B HIS* 2.9 40.8 + - + +
59B ALA* 3.5 9.2 - - - +
60B GLN 3.3 0.2 - - - -
61B ILE* 1.3 78.2 - - - +
63B THR* 1.3 56.5 + - - +
65B LEU* 3.8 3.7 - - - -
66B HIS* 2.9 33.3 + - - +
73B VAL* 3.8 12.4 - - + +
74B PRO* 3.6 26.1 - - + +
75B ALA 4.9 1.6 + - - +
76B PRO* 3.8 22.2 - - + +
77B CYS* 5.1 1.6 - - - +
112B ILE* 3.3 26.3 + - - +
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Residues in contact with THR 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B CYS 4.6 1.0 + - - -
49B PRO 4.5 2.6 + - - -
50B SER* 3.2 45.9 + - - +
51B GLN* 4.3 7.4 + - - +
59B ALA 3.1 13.8 + - - -
60B GLN* 3.4 12.3 - - - +
62B LYS* 1.3 75.9 - - - +
64B SER* 1.3 66.6 + - - +
66B HIS* 4.0 4.6 + - - +
67B ARG* 3.2 24.9 + - - +
76B PRO* 3.6 18.7 - - - +
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Residues in contact with SER 64 (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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26A ASP 4.0 18.1 - - - +
27A LEU* 4.0 19.3 + - - -
28A GLY* 5.7 0.2 - - - -
60B GLN* 3.0 14.9 + - - +
61B ILE* 3.2 8.5 + - - -
63B THR* 1.3 80.9 - - - +
65B LEU* 1.3 59.3 + - - +
67B ARG* 3.6 11.1 - - - +
68B LEU* 3.2 26.9 + - - +
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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
----------------------------------------------------------
20A VAL* 4.7 11.0 - - + -
22A ALA* 4.1 18.4 - - + -
26A ASP* 4.2 16.2 - - + +
27A LEU* 3.6 26.5 - - + -
41A VAL* 4.4 6.3 - - + -
43A MET* 3.7 18.4 - - + -
61B ILE* 2.9 34.8 + - + +
64B SER* 1.3 77.7 - - - +
66B HIS* 1.3 55.6 + - - +
68B LEU* 3.8 8.9 - - + +
69B LYS* 2.7 40.1 + - + +
73B VAL* 3.7 21.3 - - + +
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Residues in contact with HIS 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B LYS 2.9 18.8 + - - +
63B THR* 4.0 4.6 + - - +
65B LEU* 1.3 73.6 - - - +
67B ARG* 1.3 67.9 + - - +
69B LYS 4.6 0.2 - - - -
70B PRO* 3.1 41.6 + - + +
73B VAL* 2.9 32.5 - - + +
74B PRO* 3.4 9.4 - - + +
75B ALA* 3.3 37.6 + - + +
76B PRO* 4.9 2.6 - - - +
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Residues in contact with ARG 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B SER* 3.0 33.5 + - - +
63B THR* 3.2 16.3 + - - +
64B SER* 3.6 9.1 - - - +
66B HIS* 1.3 81.2 + - - +
68B LEU* 1.3 59.9 + - - +
70B PRO* 4.0 8.9 - - - +
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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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26A ASP* 3.5 47.8 - - + +
64B SER 3.2 15.2 + - - +
65B LEU* 3.8 12.3 - - + +
66B HIS 3.1 0.4 - - - -
67B ARG* 1.3 80.4 - - + +
69B LYS* 1.3 76.5 + - + +
70B PRO* 3.5 7.3 - - - +
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Residues in contact with LYS 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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20A VAL* 4.3 21.3 - - + -
21A ARG 4.8 8.2 + - - -
26A ASP* 5.1 5.7 + - - -
65B LEU* 2.7 18.3 + - + +
66B HIS 3.6 3.1 - - - -
68B LEU* 1.3 93.8 - - + +
70B PRO* 1.4 62.8 - - - +
71B ASP* 3.0 6.3 - - + +
72B THR* 3.0 37.1 + - - +
73B VAL* 3.0 15.9 + - + +
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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