Contacts of the strand formed by residues 29 - 34 (chain E) in PDB entry 6B0B
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 29 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4E LEU* 4.5 26.5 - - + -
8E THR* 4.7 13.0 - - + +
9E PHE* 6.3 0.4 - - - -
12E GLN* 3.9 33.0 - - + +
13E PHE* 5.0 6.7 - - + -
27E LYS* 5.0 7.4 - - + +
28E ALA* 1.3 84.5 - - - +
30E LEU* 1.3 64.3 + - - +
31E CYS* 5.2 2.2 - - - -
46E TYR* 5.2 7.2 - - + -
47E PHE 3.7 3.1 - - - -
48E GLU* 3.7 26.2 - - + +
55E ALA* 4.9 2.2 - - - -
56E GLU* 5.7 0.5 - - - +
80E LEU* 3.5 6.5 - - - +
81E THR* 2.8 42.2 + - + -
82E TRP 4.3 2.3 + - - +
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Residues in contact with LEU 30 (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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29E LEU* 1.3 75.9 - - - +
31E CYS* 1.3 69.8 + - - +
32E TYR* 3.8 20.9 - - + +
46E TYR* 3.3 4.9 - - - +
47E PHE* 2.9 36.2 + - + +
55E ALA* 3.7 28.7 - - + +
56E GLU* 3.9 29.6 - - + +
59E PHE* 3.7 31.0 - - + -
78E CYS* 3.6 24.0 - - - -
80E LEU* 4.0 11.4 - - + +
106E ILE* 6.1 0.2 - - + -
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Residues in contact with CYS 31 (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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4E LEU* 4.7 5.6 - - - -
13E PHE* 4.1 14.4 - - - -
29E LEU* 5.2 2.7 - - - -
30E LEU* 1.3 87.0 - - - +
32E TYR* 1.3 61.8 - - - +
33E GLN 3.8 0.3 + - - -
45E GLY 3.4 5.2 - - - -
46E TYR* 4.3 8.5 - - - -
77E THR 4.4 0.2 - - - -
78E CYS* 3.2 5.8 - - - -
79E TYR 3.1 41.2 + - - +
144E CYS* 3.8 16.8 - - - -
148E PHE* 3.5 39.0 - - + -
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Residues in contact with TYR 32 (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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30E LEU* 3.8 10.5 - - + +
31E CYS* 1.3 73.4 - - - +
33E GLN* 1.3 58.9 + - - +
34E LEU* 4.7 10.8 - - + -
43E THR* 5.0 5.2 - - - -
44E ARG* 3.5 10.5 + - - -
45E GLY* 2.9 74.9 + - - -
46E TYR 4.2 1.2 + - - -
47E PHE* 3.3 35.8 - + - -
59E PHE* 3.7 31.6 - + + -
62E GLU* 4.0 24.2 + - + +
63E ILE* 5.0 11.7 - - + -
76E VAL* 4.9 4.3 - - + -
77E THR 3.7 4.5 - - - +
78E CYS* 4.5 3.6 - - - +
148E PHE* 3.2 3.9 - - - -
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Residues in contact with GLN 33 (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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31E CYS 3.8 0.4 + - - +
32E TYR* 1.3 71.4 - - - +
34E LEU* 1.3 59.9 + - - +
35E THR* 3.4 18.4 + - + +
42E PRO* 5.0 8.4 - - - +
43E THR 3.4 5.3 - - - +
44E ARG* 3.1 54.2 + - - +
76E VAL* 4.2 2.0 - - - +
77E THR* 2.8 56.3 + - + +
79E TYR* 6.3 0.9 - - + -
147E ASN* 5.0 7.4 - - - +
148E PHE* 3.8 17.5 - - + -
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Residues in contact with LEU 34 (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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32E TYR* 3.9 9.9 - - + -
33E GLN* 1.3 72.9 - - - +
35E THR* 1.3 59.6 + - - +
36E PRO* 3.3 14.1 - - + +
42E PRO* 3.3 2.1 - - - +
43E THR* 2.9 52.6 + - - +
63E ILE* 4.4 22.9 - - + -
66E MET* 4.7 13.2 - - + -
68E LEU* 5.2 9.4 - - + -
74E TYR* 3.7 39.0 - - + -
76E VAL* 3.7 22.4 - - + +
102E LEU* 4.3 7.2 - - + -
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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