Contacts of the helix formed by residues 61 - 73 (chain A) in PDB entry 4WUR
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 THR 61 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A ARG* 3.4 22.8 + - - +
59A ASN 3.8 0.8 + - - -
60A LEU* 1.3 72.7 - - - +
62A ALA* 1.3 70.9 + - + +
63A ASP* 3.0 33.9 - - + +
64A GLU* 3.0 33.5 + - + +
65A THR* 2.7 30.8 + - - -
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Residues in contact with ALA 62 (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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61A THR* 1.3 76.8 - - - +
63A ASP* 1.3 67.5 + - - +
65A THR* 3.5 6.8 + - - -
66A LYS* 3.3 19.4 + - - +
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Residues in contact with ASP 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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61A THR* 3.0 14.7 - - + +
62A ALA* 1.3 80.9 - - - +
64A GLU* 1.3 66.4 + - + +
66A LYS* 3.1 17.7 + - - +
67A ALA* 3.1 12.6 + - - +
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Residues in contact with GLU 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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8A VAL* 3.9 16.3 - - - +
9A THR* 4.6 2.8 - - - -
10A VAL* 3.8 19.9 - - + +
14A ASN* 5.5 4.2 - - + +
16A ARG* 2.8 50.5 + - - +
56A LEU* 3.9 1.5 - - - +
60A LEU* 3.7 21.3 - - + +
61A THR* 3.0 28.0 + - + +
63A ASP* 1.3 74.8 - - + +
65A THR* 1.3 61.0 + - - +
67A ALA* 3.1 10.6 + - - +
68A LEU* 2.8 28.1 + - - +
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Residues in contact with THR 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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60A LEU* 3.4 18.7 + - + +
61A THR 2.7 23.3 + - - -
62A ALA* 3.5 8.4 - - - -
63A ASP 3.2 0.2 - - - -
64A GLU* 1.3 74.0 - - - +
66A LYS* 1.3 65.7 + - - +
68A LEU* 3.1 13.7 + - + +
69A LYS* 3.0 25.3 + - + +
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Residues in contact with LYS 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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62A ALA 3.3 9.6 + - - +
63A ASP* 3.1 14.4 + - - +
65A THR* 1.3 79.9 - - - +
67A ALA* 1.3 60.4 + - - +
69A LYS* 3.5 5.4 + - - +
70A GLU* 3.1 33.3 + - - +
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Residues in contact with ALA 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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10A VAL* 4.3 9.2 - - + -
11A ASP* 3.9 23.8 - - + +
14A ASN* 5.4 2.7 - - + +
63A ASP 3.1 11.0 + - - +
64A GLU* 3.1 11.9 + - - +
66A LYS* 1.3 74.2 - - - +
68A LEU* 1.3 58.7 + - - +
70A GLU* 3.6 12.4 - - - +
71A LEU* 2.8 34.5 + - - +
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Residues in contact with LEU 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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10A VAL* 4.7 8.9 - - + +
60A LEU* 3.9 22.9 - - + -
64A GLU 2.8 15.5 + - - +
65A THR* 3.1 15.5 + - + +
67A ALA* 1.3 72.9 - - - +
69A LYS* 1.3 55.7 + - - +
71A LEU* 4.7 0.4 - - - -
72A TYR* 2.8 72.4 + - + +
73A GLY 3.8 0.4 - - - +
75A VAL* 4.2 24.7 - - + +
76A ASP 5.9 0.4 - - - +
77A PRO* 6.5 1.1 - - + -
79A PHE* 5.1 0.7 - - + -
80A LEU* 3.6 31.6 - - + -
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Residues in contact with LYS 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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65A THR* 3.0 17.3 + - + +
66A LYS* 3.8 6.3 - - - +
68A LEU* 1.3 78.4 - - - +
70A GLU* 1.3 58.0 + - - +
73A GLY* 2.6 45.7 + - - +
74A PRO* 4.4 28.9 - - + +
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Residues in contact with GLU 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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66A LYS* 3.1 22.2 + - - +
67A ALA* 3.3 13.9 + - - +
69A LYS* 1.3 77.7 - - - +
71A LEU* 1.3 63.6 + - - +
73A GLY 4.3 0.7 + - - -
131A PRO* 3.4 20.9 - - - +
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Residues in contact with LEU 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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10A VAL 4.4 0.7 - - - +
11A ASP* 3.8 37.7 - - + +
67A ALA 2.8 17.8 + - - +
68A LEU* 6.1 0.2 - - - -
70A GLU* 1.3 78.4 - - - +
72A TYR* 1.3 80.7 + - + +
130A ILE* 3.3 4.5 - - - +
131A PRO* 3.4 14.2 - - + +
132A ALA* 2.9 54.2 + - + +
135A HIS* 6.4 0.2 - - + -
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Residues in contact with TYR 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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10A VAL 4.4 12.9 + - - -
68A LEU* 2.8 46.5 + - + +
71A LEU* 1.3 98.5 - - + +
73A GLY* 1.3 62.9 + - - +
75A VAL* 3.7 14.2 - - + +
79A PHE* 3.6 22.9 - + + -
80A LEU* 4.7 5.2 - - + -
83A PHE* 3.5 33.8 - + - -
84A TYR* 4.8 5.7 - - - -
130A ILE* 3.5 14.1 - - - +
132A ALA* 3.4 24.9 - - + -
151A LEU* 4.1 8.3 - - + -
155A TYR* 2.6 29.6 + - - +
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Residues in contact with GLY 73 (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 LEU 3.8 2.1 - - - +
69A LYS* 2.6 39.9 + - - -
70A GLU 4.3 1.4 + - - -
71A LEU 3.7 0.8 - - - -
72A TYR* 1.3 76.3 - - - +
74A PRO* 1.3 75.8 - - - +
75A VAL* 3.3 9.7 + - - +
130A ILE* 4.4 7.7 - - - +
131A PRO* 5.5 0.4 - - - +
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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