Contacts of the helix formed by residues 62 - 72 (chain A) in PDB entry 2PU1
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 CYS 62 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A GLU* 2.7 16.1 + - + +
18A PRO* 3.8 11.8 - - - +
19A THR* 3.9 18.4 - - - +
20A VAL* 3.8 16.2 - - + -
49A LEU 4.2 8.3 - - - -
50A ARG* 3.7 28.7 - - - -
51A ASP* 4.0 1.3 - - - -
61A GLY* 1.3 75.0 - - - -
63A LEU* 1.3 57.1 + - - +
64A GLN 3.3 2.7 - - - -
65A ALA* 3.3 5.1 + - + +
66A VAL* 2.9 33.1 + - + +
107A ASN* 3.9 19.3 - - - -
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Residues in contact with LEU 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A GLU* 3.6 28.7 - - + +
51A ASP* 2.8 13.6 + - - +
56A ARG* 3.4 39.3 - - - +
62A CYS* 1.3 77.4 - - - +
64A GLN* 1.3 56.3 + - - +
66A VAL* 3.3 7.8 + - + +
67A LYS* 2.8 30.9 + - - +
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Residues in contact with GLN 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A LEU* 3.9 23.8 - - + -
50A ARG 5.5 0.4 - - - +
51A ASP* 2.8 25.7 + - - +
63A LEU* 1.3 73.0 - - - +
65A ALA* 1.3 57.2 + - - +
67A LYS* 3.1 27.7 + - - +
68A ASN* 2.8 58.4 + - - +
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Residues in contact with ALA 65 (chain A).
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* 3.7 23.8 - - + -
49A LEU* 4.1 14.7 + - + +
51A ASP* 4.6 0.2 + - - -
62A CYS* 3.3 6.0 + - + +
64A GLN* 1.3 76.5 - - - +
66A VAL* 1.3 57.8 + - - +
68A ASN* 3.2 8.0 + - - +
69A VAL* 3.0 25.6 + - - +
107A ASN* 3.8 26.0 - - - +
108A ALA* 3.4 22.9 - - + +
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Residues in contact with VAL 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A GLY 3.3 27.4 - - - +
9A ARG* 3.5 31.9 - - - +
10A GLU* 3.6 10.3 - - + +
20A VAL* 4.1 15.3 - - + -
62A CYS 2.9 22.3 + - - +
63A LEU* 3.7 10.1 - - + +
65A ALA* 1.3 75.9 - - - +
67A LYS* 1.3 57.2 + - - +
69A VAL* 3.2 10.2 + - - +
70A ASN* 2.8 34.1 + - - +
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Residues in contact with LYS 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A LEU 2.8 20.4 + - - +
64A GLN* 3.5 27.7 + - - +
66A VAL* 1.3 74.4 - - - +
68A ASN* 1.3 54.3 + - - +
70A ASN* 4.4 6.1 - - - +
71A GLU* 2.7 77.1 + - + +
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Residues in contact with ASN 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A LEU* 3.5 14.6 - - - +
64A GLN* 2.8 40.3 + - - +
65A ALA 3.4 7.4 - - - +
67A LYS* 1.3 71.8 - - - +
69A VAL* 1.3 60.0 + - - +
72A VAL* 3.0 18.4 + - - +
73A ILE* 2.9 29.3 + - - +
103A LYS 3.7 4.6 + - - -
104A LEU* 2.9 54.7 + - + +
108A ALA* 4.2 3.4 - - + -
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Residues in contact with VAL 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A VAL* 4.1 20.6 - - + -
8A GLY* 3.6 27.1 - - - +
20A VAL* 4.5 4.9 - - + -
22A VAL* 4.0 15.3 - - + -
65A ALA 3.0 18.7 + - - +
66A VAL* 3.2 8.7 + - - +
68A ASN* 1.3 76.2 - - - +
70A ASN* 1.3 61.8 + - - +
73A ILE* 4.3 6.5 - - - -
74A GLY* 2.8 30.8 + - - -
108A ALA* 3.5 32.8 - - + +
112A CYS* 4.1 9.2 - - - -
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Residues in contact with ASN 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A LYS* 5.6 0.6 - - - +
6A VAL 4.0 6.1 + - - +
7A HIS* 3.3 25.3 + - - +
8A GLY 2.7 44.7 - - - +
66A VAL* 2.8 29.0 + - - +
67A LYS* 4.0 4.6 - - - +
69A VAL* 1.3 73.5 - - - +
71A GLU* 1.3 64.2 + - + +
74A GLY* 5.0 0.2 - - - -
75A PRO* 3.4 16.9 - - - +
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Residues in contact with GLU 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A LYS* 2.7 57.9 + - + +
70A ASN* 1.3 82.0 - - + +
72A VAL* 1.3 66.6 + - + +
75A PRO* 3.7 15.0 - - - +
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Residues in contact with VAL 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A ASN* 3.0 19.4 + - - +
70A ASN 3.7 0.2 - - - -
71A GLU* 1.3 90.0 - - + +
73A ILE* 1.3 68.6 + - - +
74A GLY 3.5 0.7 - - - -
75A PRO* 3.6 3.1 - - - +
76A ALA* 3.6 18.9 + - - +
95A LEU* 4.2 22.3 - - + +
103A LYS* 6.2 2.5 - - - +
104A LEU* 4.2 30.5 - - + -
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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