Contacts of the strand formed by residues 78 - 83 (chain E) in PDB entry 3T30
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 VAL 78 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A LEU* 4.0 28.0 - - + +
19A TRP* 3.3 36.3 - - - +
20A GLY* 3.9 10.8 - - - +
115A LEU 4.3 0.4 - - - +
116A SER* 3.5 26.5 - - - -
63E GLU* 3.1 2.5 - - - -
64E ILE* 2.7 41.2 + - + +
76E GLN 4.0 7.6 - - - +
77E PRO* 1.3 77.0 - - - +
79E THR* 1.3 61.4 + - - +
80E ILE* 3.4 6.9 + - + +
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Residues in contact with THR 79 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A THR* 4.0 2.1 + - - -
50A CYS* 3.9 26.9 - - + -
114A PHE* 3.5 29.7 - - + +
115A LEU 4.6 3.8 + - - -
116A SER* 3.4 21.1 + - - -
61E ARG* 2.9 53.5 + - + +
62E VAL 3.6 6.1 - - - +
63E GLU* 4.0 6.1 + - - +
77E PRO 4.0 2.2 + - - -
78E VAL* 1.3 72.2 - - - +
80E ILE* 1.3 62.3 + - - +
81E ALA 4.0 3.4 - - - +
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Residues in contact with ILE 80 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LEU* 5.7 2.2 - - + -
48A THR* 2.9 32.1 + - + +
50A CYS* 3.8 1.8 - - - -
90A MET* 3.5 2.3 - - - +
116A SER* 4.3 13.0 - - - +
46E LEU* 3.9 11.0 - - + -
49E ILE* 3.8 22.0 - - + -
62E VAL* 2.8 29.9 + - + +
64E ILE* 3.8 28.0 - - + -
78E VAL* 3.4 7.4 + - + +
79E THR* 1.3 78.2 - - - +
81E ALA* 1.3 61.0 + - - +
93E MET* 3.6 9.6 - - - +
104E PHE* 3.7 33.4 - - + -
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Residues in contact with ALA 81 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A CYS* 3.6 7.3 - - - -
90A MET* 3.6 14.8 - - + -
49E ILE* 3.7 33.2 - - + -
61E ARG* 3.4 5.4 - - - +
62E VAL* 3.0 34.9 + - + +
79E THR* 4.5 0.2 - - - -
80E ILE* 1.3 83.5 - - + +
82E SER* 1.3 62.8 + - - +
83E LEU* 4.3 5.4 - - + -
91E VAL* 4.2 5.6 - - + -
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Residues in contact with SER 82 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A CYS* 3.3 19.7 - - - +
51A LEU 2.8 21.5 + - - -
89A PRO* 3.6 19.6 - - - +
90A MET* 3.4 26.3 - - - +
59E MET* 3.1 26.3 - - - +
60E HIS 3.2 4.5 - - - -
61E ARG* 3.7 6.9 - - - -
81E ALA* 1.3 74.0 + - - +
83E LEU* 1.3 62.0 + - - +
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Residues in contact with LEU 83 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A PRO* 4.4 3.8 - - - -
90A MET* 4.1 2.5 - - - -
49E ILE* 3.6 41.5 - - + +
50E CYS 4.3 1.6 - - - +
51E LEU* 3.9 25.1 - - + -
59E MET* 3.5 4.0 - - - +
60E HIS* 2.7 36.7 + - + +
62E VAL* 5.9 1.3 - - + -
81E ALA* 4.7 4.9 - - + -
82E SER* 1.3 83.5 - - - +
84E GLN* 1.3 62.2 + - - +
88E LEU* 3.5 23.1 - - + +
89E PRO 4.1 8.1 - - - +
90E MET* 3.5 28.0 - - - +
91E VAL* 3.9 9.4 - - + +
113E VAL* 4.7 2.2 - - + -
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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