Contacts of the helix formed by residues 64 - 74 (chain u) in PDB entry 4B2Q
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 GLY 64 (chain u).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63u ALA* 1.3 78.4 - - - +
65u LEU* 1.3 59.2 + - - +
66u VAL 3.4 0.9 - - - -
67u ASP* 3.8 24.1 - - - +
68u ASP* 2.8 32.0 + - - +
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Residues in contact with LEU 65 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155t LEU* 4.5 12.6 - - + -
158t HIS* 3.6 35.4 - - + +
60u VAL* 4.6 10.3 - - + -
62u LYS* 3.9 27.4 - - + +
63u ALA 2.8 6.3 + - - -
64u GLY* 1.3 75.3 - - - +
66u VAL* 1.3 52.4 + - + +
68u ASP* 3.0 9.7 - - - +
69u PHE* 2.7 63.7 + - + -
57v ASN* 3.3 32.3 - - + +
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Residues in contact with VAL 66 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155t LEU* 5.1 11.2 - - + -
53u TRP* 3.7 43.3 - - + +
56u TYR* 4.0 13.7 - - + -
57u LYS* 3.7 33.4 - - + +
60u VAL* 4.0 25.4 - - + -
63u ALA 4.3 1.1 + - - +
64u GLY* 5.9 0.4 - - - -
65u LEU* 1.3 75.7 - - + +
67u ASP* 1.3 55.0 + - - +
69u PHE* 3.0 7.2 + - - +
70u GLU* 2.6 35.7 + - + +
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Residues in contact with ASP 67 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57u LYS* 3.7 29.5 + - - +
64u GLY* 3.6 20.9 + - - +
65u LEU 3.3 0.4 - - - -
66u VAL* 1.3 74.3 - - - +
68u ASP* 1.3 64.8 + - - +
70u GLU* 4.0 6.0 - - - +
71u LYS* 3.0 45.1 + - - +
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Residues in contact with ASP 68 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64u GLY 2.8 24.3 + - - +
65u LEU* 3.0 12.4 - - - +
67u ASP* 1.3 71.7 - - - +
69u PHE* 1.3 70.3 + - - +
71u LYS* 3.6 7.0 - - - +
72u LYS* 2.9 71.8 + - - +
57v ASN 5.7 0.2 - - - +
59v PHE 5.4 0.3 + - - -
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Residues in contact with PHE 69 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151t VAL* 4.6 9.2 - - + -
154t ARG* 4.3 17.0 - - + -
155t LEU* 3.6 28.0 - - + -
53u TRP* 3.6 14.6 - - + -
65u LEU* 2.7 52.0 + - + +
66u VAL* 3.5 5.2 - - - +
68u ASP* 1.3 84.0 - - - +
70u GLU* 1.3 55.8 - - - +
72u LYS* 3.1 0.3 + - - +
73u PHE* 2.6 37.9 + - - +
56v MET 4.8 2.2 - - - -
57v ASN 4.5 1.3 - - - -
58v THR 3.4 27.6 - - - -
59v PHE* 3.6 41.0 - + + -
60v PRO* 5.2 0.7 - - + -
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Residues in contact with GLU 70 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53u TRP* 3.2 64.0 + - + +
66u VAL* 2.6 18.2 + - - +
67u ASP* 4.0 5.7 - - - +
69u PHE* 1.3 70.5 - - - +
71u LYS* 1.3 68.2 + - - +
73u PHE* 3.4 0.7 - - - +
74u ASN* 2.8 43.7 + - - +
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Residues in contact with LYS 71 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67u ASP* 3.0 32.0 + - - +
68u ASP* 3.6 5.8 - - - +
70u GLU* 1.3 79.6 - - - +
72u LYS* 1.3 55.0 + - + +
74u ASN* 2.4 36.5 + - - +
75u ALA* 4.9 0.7 - - - +
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Residues in contact with LYS 72 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68u ASP* 2.9 55.1 + - - +
69u PHE 3.6 2.7 - - - +
71u LYS* 1.3 71.8 - - + +
73u PHE* 1.3 62.8 + - - +
74u ASN 3.0 6.0 - - - +
75u ALA 4.4 0.5 - - - +
76u LEU* 3.2 17.8 + - - +
59v PHE* 3.7 47.7 - - + +
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Residues in contact with PHE 73 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147t VAL* 4.3 26.5 - - + -
148t TYR* 4.6 10.3 - + + -
151t VAL* 4.6 13.2 - - + -
48u PRO* 6.1 4.5 - - + -
49u PRO 5.7 2.5 - - - -
50u ALA* 6.1 3.1 - - - -
51u ILE* 4.0 25.8 - - + -
53u TRP* 3.5 26.2 - + + -
69u PHE 2.6 20.8 + - - +
70u GLU 3.4 4.0 - - - +
71u LYS 2.8 1.0 + - - -
72u LYS* 1.3 72.3 - - - +
74u ASN* 1.3 88.2 + - - +
76u LEU* 3.2 20.2 + - - +
59v PHE* 3.6 10.7 - + + -
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Residues in contact with ASN 74 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53u TRP* 4.7 2.9 + - - -
70u GLU* 2.8 42.3 + - - +
71u LYS* 2.4 23.8 + - - +
72u LYS* 3.0 3.3 - - - +
73u PHE* 1.3 91.4 - - - +
75u ALA* 1.3 64.6 - - + +
76u LEU 2.8 12.1 + - - -
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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