Contacts of the strand formed by residues 34 - 40 (chain E) in PDB entry 3V62
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 GLY 34 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29E GLN 4.0 0.3 - - - +
31E LYS* 3.0 33.6 + - - +
32E GLU 3.6 0.6 - - - -
33E ASP* 1.3 79.5 + - - +
35E ILE* 1.3 64.8 + - - -
36E ILE* 5.6 1.1 - - - -
52E ILE 3.3 12.1 - - - -
53E GLY 4.4 0.4 - - - -
54E VAL* 4.4 6.3 - - - -
57E PHE* 4.7 2.2 - - - -
60E TYR* 3.4 10.9 + - - -
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Residues in contact with ILE 35 (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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2E LEU* 5.8 0.4 - - + -
4E ALA* 4.3 6.7 - - + -
6E PHE* 5.5 2.5 - - + -
28E PHE* 3.8 39.5 - - + -
29E GLN 3.4 11.0 - - - +
30E CYS* 3.8 15.3 - - - -
34E GLY* 1.3 77.9 - - - -
36E ILE* 1.3 69.3 + - - +
37E ALA 3.8 1.5 + - - +
50E LEU 3.6 0.7 - - - +
51E GLU* 3.6 2.4 - - - +
52E ILE* 2.8 48.9 + - + +
57E PHE* 3.3 31.0 - - + -
60E TYR* 3.7 19.3 - - + +
68E LEU* 6.0 0.7 - - + -
90E LEU* 5.8 6.7 - - + -
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Residues in contact with ILE 36 (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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27E ASN 3.4 2.1 - - - +
29E GLN* 2.9 38.3 + - + +
31E LYS* 4.5 26.2 - - + -
34E GLY 5.5 1.1 - - - +
35E ILE* 1.3 76.2 - - - +
37E ALA* 1.3 60.5 + - - +
38E GLN* 3.5 31.4 + - + +
49E SER* 4.1 11.9 - - - +
50E LEU 3.3 7.6 - - - +
51E GLU* 3.8 29.2 - - + +
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Residues in contact with ALA 37 (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 PHE* 3.7 28.3 - - + -
26E VAL* 4.1 4.5 - - + -
27E ASN 3.4 6.3 - - - -
28E PHE* 3.9 28.9 - - + -
35E ILE* 3.8 2.2 - - - +
36E ILE* 1.3 72.7 - - - +
38E GLN* 1.3 59.0 + - - +
48E VAL 3.8 0.5 - - - +
49E SER* 3.3 4.5 - - - -
50E LEU* 2.8 43.7 + - + +
52E ILE* 4.7 3.5 - - + +
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Residues in contact with GLN 38 (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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26E VAL* 3.6 2.7 - - - +
27E ASN* 2.8 41.0 + - - +
29E GLN* 2.9 23.5 + - - +
36E ILE* 3.5 28.2 - - + +
37E ALA* 1.3 78.2 - - - +
39E ALA* 1.3 62.6 + - - +
48E VAL 3.4 4.3 - - - -
49E SER* 4.4 7.3 + - - -
123E ALA* 3.3 25.5 + - - +
124E ASP 4.0 6.5 + - - -
126E LEU* 3.4 44.4 + - + +
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Residues in contact with ALA 39 (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 PHE* 4.0 3.1 - - + -
23E VAL* 3.4 33.7 - - + -
25E LEU 3.5 13.0 - - - +
26E VAL* 4.0 6.7 - - + -
38E GLN* 1.3 76.9 - - - +
40E VAL* 1.3 60.1 + - - +
47E LEU* 3.5 5.7 - - - +
48E VAL* 2.9 41.9 + - + +
123E ALA* 3.9 8.2 - - - +
126E LEU* 4.5 1.5 - - - +
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Residues in contact with VAL 40 (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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23E VAL* 3.6 10.7 - - - +
24E GLN 5.5 0.5 + - - -
25E LEU 5.0 1.8 + - - +
39E ALA* 1.3 73.9 - - - +
41E ASP* 1.3 78.0 + - - +
42E ASP* 3.9 0.5 + - - -
44E ARG* 3.8 27.4 - - + +
46E LEU 3.4 11.7 - - - +
47E LEU* 4.2 12.1 - - + -
121E ILE* 5.4 3.1 - - + -
122E ASP* 5.0 1.8 - - + -
123E ALA* 3.6 28.0 - - + +
1153F PHE* 4.0 23.1 - - + -
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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