Contacts of the strand formed by residues 64 - 68 (chain A) in PDB entry 1MUG
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 64 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A LEU* 3.8 4.7 - - - +
11A ARG* 4.9 3.6 - - - -
12A VAL* 3.2 15.5 - - - +
14A PHE* 4.1 15.9 - - + -
46A PHE* 4.0 38.4 - - - -
59A LEU* 3.1 46.4 + - + +
60A LEU* 3.5 12.6 + - - +
62A TYR 3.8 11.2 - - - -
63A ARG* 1.3 81.6 - - - +
65A GLY* 1.3 58.9 + - - +
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Residues in contact with GLY 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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5A ILE* 3.0 17.5 - - - -
10A LEU* 3.7 12.7 - - - +
12A VAL 2.8 9.8 + - - -
13A VAL* 4.0 5.6 - - - -
14A PHE* 2.9 30.0 + - - -
59A LEU* 4.7 0.7 - - - -
64A CYS* 1.3 75.0 - - - +
66A VAL* 1.3 68.1 + - - +
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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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3A GLU 5.9 1.3 - - - +
4A ASP* 3.6 3.8 - - - +
5A ILE* 2.9 40.7 + - + +
6A LEU* 4.2 3.1 - - - +
13A VAL* 4.7 0.2 - - - -
14A PHE* 3.3 7.6 - - + +
29A PRO* 3.7 35.9 - - + -
30A PHE* 3.9 22.4 - - + -
37A PHE* 4.5 6.5 - - + -
38A TRP* 5.3 0.2 - - + -
59A LEU* 3.4 26.5 - - + -
65A GLY* 1.3 79.2 - - - +
67A THR* 1.3 77.4 + - - +
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Residues in contact with THR 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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4A ASP* 2.7 30.5 + - - +
6A LEU* 4.6 7.0 - - + -
13A VAL* 3.7 22.7 - - + -
14A PHE 3.0 7.6 + - - +
15A CYS* 3.9 9.6 - - + -
16A GLY 3.3 16.3 + - - -
30A PHE* 5.5 0.3 - - - -
66A VAL* 1.3 84.4 - - - +
68A LYS* 1.3 70.7 + - - +
92A LEU* 3.9 25.5 - - + +
95A LYS* 3.4 18.2 + - + +
96A ILE* 5.6 0.4 - - + -
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Residues in contact with LYS 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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2A VAL* 3.0 35.2 + - + +
3A GLU 5.3 0.2 - - - -
4A ASP* 4.6 9.4 + - - +
15A CYS* 3.6 7.4 - - - -
16A GLY* 3.4 13.9 - - - +
17A ILE 4.3 2.2 - - - +
18A ASN* 4.3 5.4 - - - -
19A PRO* 3.5 35.4 - - + -
67A THR* 1.3 88.0 + - - +
69A LEU* 1.3 63.9 + - - +
70A VAL 3.6 11.7 - - - +
71A ASP* 3.2 37.1 + - - +
92A LEU* 5.3 3.6 - - - +
95A LYS* 4.8 6.3 + - - +
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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