Contacts of the strand formed by residues 44 - 51 (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 LEU 44 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E TRP* 3.3 48.5 - - + +
32E PHE* 3.3 57.2 - - + -
43E ARG* 1.3 71.4 - - - +
45E LEU* 1.3 63.4 + - - +
46E LEU* 3.5 2.5 + - + -
97E GLN* 3.4 1.2 - - - -
98E LEU* 2.8 51.3 + - + +
100E PRO* 4.9 0.4 - - + +
102E VAL* 4.3 9.0 - - + -
104E PHE* 3.9 26.0 - - + -
118E GLN 4.5 1.1 - - - -
119E GLU* 4.3 1.1 - - + -
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Residues in contact with LEU 45 (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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19E TRP* 3.4 3.4 + - - -
43E ARG* 4.4 1.8 - - + -
44E LEU* 1.3 73.5 - - - +
46E LEU* 1.3 57.9 + - - +
47E HIS* 3.9 18.6 - - + +
95E GLY* 6.3 1.6 - - - +
96E VAL 3.4 5.8 - - - +
97E GLN* 3.5 42.4 - - + +
117E GLY* 2.9 26.5 - - - -
118E GLN* 3.0 37.4 + - + +
120E ARG* 3.9 31.9 - - + +
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Residues in contact with LEU 46 (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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19E TRP* 4.0 15.5 - - + -
44E LEU 3.5 2.2 + - - +
45E LEU* 1.3 71.3 - - - +
47E HIS* 1.3 62.5 + - - +
48E THR 4.5 4.9 - - - +
49E ILE* 4.3 4.0 - - + -
64E ILE* 5.4 0.7 - - + -
80E ILE* 3.9 24.0 - - + -
93E MET* 3.1 52.7 - - + +
94E VAL* 4.0 0.9 - - - -
95E GLY 4.3 0.2 + - - -
96E VAL* 2.9 29.0 + - + +
98E LEU* 4.3 19.3 - - + -
104E PHE* 4.4 3.8 - - + -
115E LEU* 4.0 25.6 - - + -
116E SER 3.8 13.5 - - - +
117E GLY* 4.5 0.2 - - - -
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Residues in contact with HIS 47 (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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95D GLY 5.3 0.8 + - - -
96D VAL* 3.6 34.9 - - + +
18E LEU* 5.5 2.0 - - - +
45E LEU* 3.7 18.7 + - + +
46E LEU* 1.3 79.5 - - - +
48E THR* 1.3 69.3 + - + +
92E SER* 3.4 1.4 + - - -
93E MET* 2.8 31.1 + - - -
94E VAL* 3.6 25.0 + - + +
95E GLY 4.9 2.2 - - - -
116E SER* 2.9 22.2 + - - +
117E GLY* 3.8 10.6 + - - -
118E GLN* 2.9 46.4 + - + +
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Residues in contact with THR 48 (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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79D THR 3.9 0.3 + - - -
80D ILE* 3.1 32.7 + - + +
93D MET* 4.6 11.2 - - + -
96D VAL* 6.0 0.9 - - + -
46E LEU* 4.5 0.9 - - - +
47E HIS* 1.3 91.9 - - + +
49E ILE* 1.3 68.3 + - - +
50E CYS* 3.8 4.4 - - - -
90E MET* 3.8 14.8 - - + -
91E VAL 3.4 9.9 - - - +
92E SER* 4.1 10.5 - - - +
93E MET* 4.8 0.4 - - - +
94E VAL* 5.1 2.5 - - + -
115E LEU* 3.4 3.6 - - - +
116E SER* 2.7 47.5 + - - +
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Residues in contact with ILE 49 (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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46E LEU* 4.3 8.1 - - + -
48E THR* 1.3 81.5 - - - +
50E CYS* 1.3 63.0 + - - +
62E VAL* 4.5 9.4 - - + -
80E ILE* 3.8 26.5 - - + -
81E ALA* 3.7 23.6 - - + -
83E LEU* 3.6 13.2 - - + +
90E MET* 3.2 3.6 - - - +
91E VAL* 2.9 36.7 + - + -
93E MET* 3.9 17.5 - - + -
113E VAL* 3.5 25.6 - - + -
114E PHE 3.2 6.7 - - - +
115E LEU* 4.0 18.8 - - + -
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Residues in contact with CYS 50 (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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79D THR* 3.9 16.8 - - + -
80D ILE 3.8 4.9 - - - -
81D ALA* 3.6 34.8 - - - -
82D SER* 3.4 17.7 - - - +
48E THR* 3.8 7.4 - - - -
49E ILE* 1.3 80.5 - - - +
51E LEU* 1.3 62.6 + - - +
52E GLY 3.7 0.2 + - - -
83E LEU* 4.5 0.4 - - - -
89E PRO 3.6 5.2 - - - -
90E MET* 3.7 16.4 - - - -
113E VAL* 3.5 4.4 - - - -
114E PHE* 2.8 39.3 + - - +
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Residues in contact with LEU 51 (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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59D MET* 3.6 9.8 - - + +
82D SER* 2.7 29.3 + - - -
50E CYS* 1.3 73.2 - - - +
52E GLY* 1.3 66.6 + - - +
55E ALA* 4.5 4.5 - - + -
60E HIS* 3.6 40.8 - - + +
83E LEU* 3.9 14.6 - - + +
84E GLN* 3.5 17.5 - - - +
85E ALA* 3.2 37.5 - - + +
89E PRO* 2.8 23.1 + - + +
112E PRO 3.8 2.5 - - - +
113E VAL* 3.7 18.2 - - + -
114E PHE* 4.5 1.1 - - - -
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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