Contacts of the helix formed by residues 58 - 67 (chain B) in PDB entry 3VZC
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 58 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56B ARG 3.7 0.6 + - - -
57B ARG* 1.3 111.4 + - - +
59B HIS* 1.3 54.0 + - - +
60B ALA 3.4 2.5 - - - -
61B ARG* 3.2 16.8 + - + +
62B GLU* 2.7 57.4 + - + +
65B ARG* 6.3 0.2 - - - +
86B GLU* 3.7 24.9 + - - +
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Residues in contact with HIS 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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53B LEU 3.6 21.3 - - - -
54B THR* 3.2 19.0 + - - +
55B GLU 3.9 4.8 + - - -
56B ARG* 3.2 64.2 + - + +
57B ARG 2.9 3.2 + - - -
58B ASN* 1.3 78.1 - - - +
60B ALA* 1.3 58.9 + - - +
62B GLU* 3.3 6.7 + - + +
63B LEU* 2.9 36.2 + - + +
49C PHE* 3.9 5.4 - + - -
50C THR* 2.9 35.1 - - + +
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Residues in contact with ALA 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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20B LEU* 4.2 13.5 - - + -
54B THR* 3.2 19.5 + - + +
56B ARG 4.8 0.6 + - - -
58B ASN 3.4 0.2 - - - -
59B HIS* 1.3 75.9 - - - +
61B ARG* 1.3 65.2 + - - +
63B LEU* 3.3 6.6 + - - +
64B VAL* 3.0 31.9 + - - +
83B LEU* 3.5 31.9 - - + -
86B GLU* 4.4 8.7 - - + -
87B VAL* 4.7 2.5 - - + -
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Residues in contact with ARG 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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58B ASN* 3.2 24.9 + - + +
60B ALA* 1.3 79.5 - - - +
62B GLU* 1.3 56.5 + - - +
64B VAL* 3.7 0.6 - - - +
65B ARG* 2.9 42.8 + - - +
85B HIS* 4.5 10.1 - - - -
86B GLU* 2.6 67.0 + - + +
89B ASN* 3.6 26.7 - - - +
90B GLY* 3.7 14.1 - - - -
93B GLU* 3.0 26.9 + - - -
161B LEU* 6.4 0.2 - - - +
163B LEU* 5.0 9.5 - - - +
343B GLU* 5.0 4.4 + - - -
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Residues in contact with GLU 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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56B ARG* 4.8 8.2 + - - -
57B ARG 4.9 1.4 - - - +
58B ASN* 2.7 44.3 + - + +
59B HIS* 3.7 5.3 - - + +
61B ARG* 1.3 71.3 - - + +
63B LEU* 1.3 66.9 + - + +
65B ARG* 3.5 31.5 + - - +
66B SER* 3.2 24.7 + - - -
16C ARG* 4.0 27.3 + - - -
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Residues in contact with LEU 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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20B LEU* 5.5 4.0 - - + -
52B MET* 3.5 39.0 - - + -
54B THR* 4.0 12.3 - - - +
59B HIS* 2.9 45.2 + - + +
60B ALA* 3.3 6.9 + - - +
62B GLU* 1.3 77.5 - - + +
64B VAL* 1.3 59.1 + - + +
66B SER* 3.2 2.8 + - - +
67B GLU* 2.9 14.9 + - - +
50C THR* 3.9 5.8 - - + -
71C ARG* 2.8 34.2 + - - +
72C TRP* 3.8 33.7 - - + -
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Residues in contact with VAL 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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18B LEU* 6.0 2.7 - - + -
20B LEU* 3.9 24.9 - - + -
60B ALA 3.0 19.9 + - - +
61B ARG 3.7 3.4 - - - +
63B LEU* 1.3 74.0 - - + +
65B ARG* 1.3 66.1 + - - +
67B GLU* 3.3 11.5 + - + +
69B LEU* 4.6 2.2 - - + +
75B LEU* 4.6 9.6 - - + -
87B VAL* 3.3 40.4 - - + +
90B GLY* 3.8 0.7 - - - -
91B LEU* 3.5 29.6 - - + +
94B ARG* 3.0 19.8 + - - -
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Residues in contact with ARG 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 ARG* 2.9 35.9 + - - +
62B GLU* 3.7 31.0 + - - +
63B LEU 3.3 0.2 - - - -
64B VAL* 1.3 76.9 - - - +
66B SER* 1.3 57.0 + - - +
90B GLY 3.6 15.3 - - - +
93B GLU* 3.0 48.3 + - - +
94B ARG* 3.2 32.6 + - + +
95B PRO* 5.7 2.0 - - + +
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Residues in contact with SER 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 GLU 3.2 17.7 + - - -
63B LEU* 4.0 1.6 - - - +
65B ARG* 1.3 77.0 - - - +
67B GLU* 1.3 63.8 + - - +
68B GLU 3.7 1.2 + - - -
94B ARG* 4.0 0.2 - - - -
68C GLU* 3.9 15.0 - - - +
71C ARG* 3.1 41.3 + - - +
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Residues in contact with GLU 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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18B LEU* 4.1 12.6 - - + +
52B MET* 3.8 13.9 - - - +
63B LEU* 2.9 13.2 + - - +
64B VAL* 3.3 16.6 + - + +
66B SER* 1.3 77.4 - - - +
68B GLU* 1.3 71.3 + - - +
69B LEU* 3.2 16.3 + - + -
71B ARG* 2.6 34.2 + - - -
72B TRP* 2.8 25.2 + - + +
75B LEU* 5.6 0.4 - - + -
94B ARG* 2.8 27.4 + - - +
71C ARG* 2.8 34.1 + - - +
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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