Contacts of the helix formed by residues 63 - 70 (chain A) in PDB entry 1UPD
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 63 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A HIS* 4.3 1.6 - - - -
54A ASP* 3.4 7.8 - - - +
57A ALA* 2.5 32.0 + - - -
58A LYS 3.6 0.5 - - - -
59A LYS 3.5 16.4 + - - -
60A GLY 2.9 14.1 + - - -
61A GLU 3.1 0.2 - - - -
62A LYS* 1.4 78.7 - - - +
64A LEU* 1.3 61.7 + - - +
65A TYR* 3.3 1.7 + - - +
66A TYR* 3.0 21.6 + - - +
67A VAL* 3.1 24.1 + - - +
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Residues in contact with LEU 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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11A VAL* 4.5 9.6 - - + -
12A LYS 3.5 24.9 - - - +
46A CYS* 3.8 30.3 - - + -
47A GLY* 4.2 8.5 - - - +
52A HIS* 3.6 18.1 + - + +
54A ASP 3.1 8.2 + - - +
55A LEU* 3.8 20.2 - - + -
62A LYS 3.5 3.4 + - - -
63A SER* 1.3 70.8 - - - +
65A TYR* 1.3 63.7 + - - +
67A VAL* 3.3 14.8 + - + +
68A VAL* 3.1 34.1 + - + +
1108A HEC 6.0 0.4 - - - +
1109A HEC 5.9 0.2 - - + -
1111A HEC 3.7 27.1 - - + +
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Residues in contact with TYR 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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54A ASP 4.7 0.8 + - - -
55A LEU* 5.7 3.0 - - - +
56A THR 5.5 0.9 - - - +
57A ALA 3.6 10.0 + - - +
58A LYS* 3.3 54.8 + - + -
63A SER* 3.3 8.8 + - - +
64A LEU* 1.3 77.2 - - - +
66A TYR* 1.3 58.7 + - - +
68A VAL 3.3 0.2 + - - -
69A HIS* 2.7 65.6 + + + +
1111A HEC 3.4 86.7 + + + +
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Residues in contact with TYR 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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58A LYS 3.5 18.6 - - - +
59A LYS* 4.0 8.7 - - + -
60A GLY* 3.3 38.1 - - - +
61A GLU* 4.3 1.6 - - - -
63A SER* 3.0 20.7 + - - +
65A TYR* 1.3 80.3 - - - +
67A VAL* 1.3 64.2 + - + +
70A ALA* 2.9 54.1 + - + +
72A GLY* 5.9 1.6 - - - -
73A GLU 4.2 3.8 + - - -
74A LEU* 3.3 34.6 - - + +
1109A HEC 3.7 13.9 - - - -
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Residues in contact with VAL 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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52A HIS* 3.5 40.8 - - + +
61A GLU 3.9 5.8 - - - +
63A SER 3.1 9.8 + - - +
64A LEU* 3.4 27.6 - - + +
66A TYR* 1.3 79.7 - - + +
68A VAL* 1.3 58.1 + - + +
74A LEU* 4.4 3.4 - - - -
78A SER* 3.0 25.8 - - - -
79A CYS* 4.1 1.0 + - - -
1109A HEC 3.7 56.0 - - + +
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Residues in contact with VAL 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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11A VAL* 5.2 2.7 - - + -
64A LEU* 3.1 26.8 + - + +
66A TYR 3.1 0.4 - - - -
67A VAL* 1.3 83.4 - - + +
69A HIS* 1.3 86.0 + - + +
70A ALA 3.7 0.7 - - - -
78A SER* 3.7 1.1 - - - -
79A CYS* 3.3 25.1 + - + +
80A LEU* 3.1 25.5 + - + +
1109A HEC 5.7 3.4 - - + -
1110A HEC 5.0 3.8 - - + -
1111A HEC 3.6 46.4 - - + +
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Residues in contact with HIS 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 TYR* 2.7 51.9 + + + +
68A VAL* 1.3 84.3 - - + +
70A ALA* 1.3 69.0 + - - +
71A ARG* 3.2 4.2 + - - +
80A LEU* 3.5 19.7 - - + +
1111A HEC 2.0 110.6 + + + +
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Residues in contact with ALA 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 TYR* 2.9 44.5 + - + +
68A VAL 3.7 0.6 - - - -
69A HIS* 1.3 77.2 - - - +
71A ARG* 1.3 60.6 + - - +
72A GLY* 4.1 6.4 - - - +
74A LEU* 3.5 24.6 - - + +
78A SER* 2.6 28.6 + - - -
80A LEU* 4.7 0.2 - - - -
81A ALA* 3.9 4.3 + - - +
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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
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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