Contacts of the strand formed by residues 7 - 14 (chain E) in PDB entry 3W13
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 7 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6E GLU* 1.3 91.3 + - - +
8E CYS* 1.3 62.0 + - - +
28E VAL* 3.2 10.3 - - + +
30E GLU* 3.8 23.3 - - + +
251E TRP* 4.1 14.6 - - + -
252E ARG* 3.3 46.0 - - - +
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Residues in contact with CYS 8 (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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6E GLU* 3.7 18.2 - - - -
7E VAL* 1.3 74.1 - - - +
9E PRO* 1.3 72.8 - - + +
11E MET* 4.2 10.3 - - + -
22E GLU 4.7 11.7 - - - -
26E CYS* 2.0 46.7 - - - -
28E VAL 3.0 6.5 + - - -
29E ILE* 3.5 3.1 - - + -
30E GLU* 2.8 33.4 + - - +
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Residues in contact with PRO 9 (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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8E CYS* 1.3 100.0 - - + +
10E GLY* 1.3 68.9 + - - +
11E MET* 3.3 29.8 + - + +
29E ILE* 3.5 10.3 - - - +
30E GLU* 3.6 7.2 - - + +
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Residues in contact with GLY 10 (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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9E PRO* 1.3 76.3 - - - +
11E MET* 1.3 61.0 + - - +
29E ILE* 3.9 1.6 - - - -
30E GLU 3.0 12.5 + - - -
31E GLY* 4.1 1.6 - - - -
32E HIS* 3.0 38.3 + - - -
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Residues in contact with MET 11 (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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8E CYS* 4.2 6.3 - - + -
9E PRO* 3.3 38.5 + - + +
10E GLY* 1.3 75.3 - - - +
12E ASP* 1.3 62.9 + - - +
13E ILE* 4.1 9.9 - - + -
19E ARG* 5.8 2.2 - - - +
22E GLU* 3.7 46.7 - - + +
23E LEU* 3.4 30.1 - - + -
32E HIS* 2.9 12.7 + - - +
33E LEU* 3.5 18.9 - - + +
34E GLN 3.0 23.4 + - - -
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Residues in contact with ASP 12 (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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11E MET* 1.3 78.6 - - - +
13E ILE* 1.3 54.5 + - - +
14E ARG* 2.8 37.2 + - - +
19E ARG* 2.6 28.8 + - - +
32E HIS* 5.5 3.8 - - - +
34E GLN* 3.0 31.1 + - - +
36E LEU* 3.5 8.7 - - - +
715F VAL* 5.6 1.6 - - - +
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Residues in contact with ILE 13 (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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11E MET* 4.3 11.0 - - + -
12E ASP* 1.3 78.6 - - - +
14E ARG* 1.3 63.7 + - - +
16E ASN 4.5 0.4 - - - +
19E ARG* 3.8 35.9 - - + +
20E LEU* 3.8 41.7 - - + +
23E LEU* 4.0 19.1 - - + -
33E LEU* 4.1 14.8 - - + -
34E GLN 2.6 13.6 + - - +
35E ILE* 3.3 9.1 - - + -
36E LEU 2.9 27.7 + - - +
38E MET* 3.6 20.8 - - + +
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Residues in contact with ARG 14 (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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21A ASN* 4.6 8.7 + - - -
12E ASP* 2.8 38.2 + - - +
13E ILE* 1.3 81.7 - - - +
15E ASN* 1.3 81.9 + - - +
16E ASN 3.0 14.4 + - - +
19E ARG* 4.3 16.4 - - - +
34E GLN* 5.0 2.0 - - - +
36E LEU* 3.4 38.9 - - + +
37E LEU* 4.5 9.4 - - + +
38E MET* 3.7 4.0 - - - -
712F VAL 4.8 1.4 + - - -
713F VAL* 3.5 43.4 + - - +
714F PHE* 3.7 4.4 - - - +
715F VAL* 4.4 28.4 - - - +
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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