Contacts of the helix formed by residues 51 - 68 (chain B) in PDB entry 2VN9
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 51 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B LYS 3.7 2.2 + - - -
50B LEU* 1.3 76.4 - - - +
52B ALA* 1.3 59.8 + - - +
53B ARG* 3.6 10.5 + - - +
54B ASP* 3.0 36.3 + - - +
55B HIS* 2.8 27.8 + - - +
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Residues in contact with ALA 52 (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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50B LEU 4.0 0.4 + - - -
51B SER* 1.3 71.7 - - - +
53B ARG* 1.3 52.5 + - - +
55B HIS* 3.1 8.2 + - - +
56B GLN* 2.8 53.8 + - - +
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Residues in contact with ARG 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B SER* 3.1 9.3 + - - +
52B ALA* 1.3 80.0 - - - +
54B ASP* 1.3 63.6 + - - +
56B GLN* 3.3 25.9 + - + +
57B LYS* 3.3 28.3 + - - +
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Residues in contact with ASP 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B LEU* 3.9 29.7 - - + +
51B SER* 3.0 29.4 + - - +
53B ARG* 1.3 76.0 - - - +
55B HIS* 1.3 66.5 + - - +
57B LYS* 3.1 34.0 + - - +
58B LEU* 3.2 10.7 + - - +
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Residues in contact with HIS 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B THR* 4.2 14.6 - - + -
50B LEU* 4.1 10.9 - - + +
51B SER 2.8 14.7 + - - +
52B ALA* 3.6 10.3 - - - +
54B ASP* 1.3 77.9 - - - +
56B GLN* 1.3 55.9 + - - +
58B LEU* 3.1 22.3 + - + +
59B GLU* 2.7 60.0 + - + +
86B HIS* 5.0 4.9 - + - -
1311B PO4 2.5 37.8 + - - -
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Residues in contact with GLN 56 (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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52B ALA* 2.8 35.5 + - - +
53B ARG* 3.4 17.7 + - + +
54B ASP 3.2 0.2 - - - -
55B HIS* 1.3 75.1 - - - +
57B LYS* 1.3 56.4 + - - +
59B GLU* 3.5 25.1 + - - +
60B ARG* 3.1 28.2 + - - +
63B ARG* 5.3 1.2 + - - -
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Residues in contact with LYS 57 (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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53B ARG* 3.3 27.0 + - - +
54B ASP* 3.1 25.9 + - - +
56B GLN* 1.3 73.8 - - - +
58B LEU* 1.3 65.7 + - - +
60B ARG* 3.4 11.9 + - - +
61B GLU* 3.1 22.9 + - - +
159B GLY 5.3 9.5 - - - +
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Residues in contact with LEU 58 (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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45B ILE* 3.6 36.3 - - + -
47B THR* 3.9 10.1 - - + -
50B LEU* 4.8 4.0 - - + -
54B ASP 3.2 4.9 + - - +
55B HIS* 3.1 39.4 + - + +
57B LYS* 1.3 77.2 - - - +
59B GLU* 1.3 65.6 + - - +
60B ARG 3.2 0.2 + - - -
61B GLU* 3.2 10.7 + - - +
62B ALA* 2.9 25.1 + - + +
86B HIS* 3.9 33.4 - - + +
88B LEU* 4.3 14.6 - - + -
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Residues in contact with GLU 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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55B HIS* 2.7 53.1 + - + +
56B GLN* 3.6 25.3 + - - +
57B LYS 3.3 0.2 - - - -
58B LEU* 1.3 72.1 - - + +
60B ARG* 1.3 57.0 + - - +
62B ALA* 3.5 6.8 + - - +
63B ARG* 2.9 43.1 + - - +
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Residues in contact with ARG 60 (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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56B GLN 3.1 15.2 + - - +
57B LYS* 3.5 14.2 - - - +
59B GLU* 1.3 76.7 - - - +
61B GLU* 1.3 57.8 + - - +
63B ARG* 3.2 24.8 + - - +
64B ILE* 2.9 42.0 + - + +
161B ALA 3.5 22.4 - - - -
162B ILE* 4.6 7.9 - - - +
163B GLU* 3.0 41.0 + - - +
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Residues in contact with GLU 61 (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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43B LYS* 2.9 29.9 + - - +
57B LYS 3.1 12.6 + - - +
58B LEU* 3.7 10.9 - - - +
60B ARG* 1.3 80.3 - - - +
62B ALA* 1.3 56.5 + - - +
64B ILE* 3.8 5.3 - - - +
65B CYS* 2.9 38.5 + - - -
88B LEU* 3.8 20.7 - - + +
90B PHE* 4.4 6.8 - - - -
158B PHE 3.9 25.4 + - - +
159B GLY* 3.3 27.2 + - - -
1310B GVD 5.0 0.3 + - - -
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Residues in contact with ALA 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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58B LEU* 2.9 17.0 + - + +
59B GLU* 3.7 7.4 - - - +
61B GLU* 1.3 76.5 - - - +
63B ARG* 1.3 62.8 + - - +
65B CYS* 4.6 0.7 - - - -
66B ARG* 3.0 25.6 + - - +
76B LEU* 3.7 7.2 - - - +
79B SER* 3.7 25.8 - - - +
86B HIS* 4.8 3.8 - - + +
88B LEU* 3.9 19.0 - - + +
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Residues in contact with ARG 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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56B GLN 5.3 1.2 + - - -
59B GLU* 2.9 37.2 + - - +
60B ARG* 3.5 31.0 - - - +
62B ALA* 1.3 77.6 - - - +
64B ILE* 1.3 61.3 + - - +
66B ARG* 3.5 8.5 + - - +
67B LEU* 3.2 21.0 + - - +
163B GLU* 3.0 39.3 + - - +
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Residues in contact with ILE 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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60B ARG* 2.9 33.1 + - + +
61B GLU* 3.8 7.0 - - - +
63B ARG* 1.3 75.2 - - - +
65B CYS* 1.3 63.5 + - - +
67B LEU* 3.2 22.3 + - - +
68B LEU* 3.3 27.8 - - + +
132B ILE* 3.9 16.1 - - + +
158B PHE* 3.9 20.9 - - + +
161B ALA* 3.6 36.3 - - + +
162B ILE 4.1 2.9 - - - +
163B GLU* 3.7 29.4 - - + -
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Residues in contact with CYS 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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61B GLU* 2.9 32.7 + - - +
62B ALA* 4.6 0.4 - - - -
64B ILE* 1.3 77.5 - - - +
66B ARG* 1.3 64.1 + - - +
68B LEU* 3.3 24.6 + - - +
74B VAL 5.8 1.6 - - - +
75B ARG* 3.6 3.8 + - - -
76B LEU* 3.7 32.0 + - + +
88B LEU* 5.8 0.4 - - + -
90B PHE* 4.0 21.5 - - - -
158B PHE* 3.8 34.3 - - - -
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Residues in contact with ARG 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 ALA 3.0 17.3 + - - +
63B ARG* 3.6 9.2 - - - +
65B CYS* 1.3 76.7 - - - +
67B LEU* 1.3 60.9 + - - +
75B ARG* 3.1 23.3 + - - +
76B LEU* 3.7 13.1 - - + +
79B SER* 6.2 3.6 - - - -
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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
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63B ARG 3.2 11.3 + - - +
64B ILE* 3.2 12.7 + - - +
65B CYS 3.2 0.8 - - - -
66B ARG* 1.3 79.2 - - - +
68B LEU* 1.3 59.4 + - - +
69B LYS* 3.7 6.1 + - - +
126B HIS* 5.3 1.4 + - - -
130B ASN* 3.7 35.2 - - + +
132B ILE* 3.6 25.1 - - + -
163B GLU* 5.8 3.8 - - + +
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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
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64B ILE* 3.3 26.7 - - + +
65B CYS* 3.3 11.6 + - - +
67B LEU* 1.3 75.7 - - - +
69B LYS* 1.3 59.5 + - - +
70B HIS 4.2 0.7 - - - -
73B ILE* 4.1 19.5 - - + +
74B VAL 5.5 0.2 - - - +
75B ARG* 3.0 26.1 + - - -
126B HIS* 4.2 11.9 - - + -
127B CYS* 4.1 17.7 - - - -
130B ASN* 4.1 17.3 - - + +
132B ILE* 3.5 22.2 - - + -
158B PHE* 3.4 41.3 - - + -
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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
------------------------------------------------------------
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