Contacts of the helix formed by residues 4 - 15 (chain D) in PDB entry 5WYF
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 4 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D LYS* 1.3 94.0 - - + +
5D ASP* 1.3 64.6 + - - +
6D LYS 3.5 1.8 - - - -
7D ALA* 4.4 9.2 - - + -
8D SER* 3.0 29.2 + - - +
28D ASN* 3.9 24.5 - - + +
41D ASP* 3.9 19.5 - - - +
43D ASP* 3.5 7.6 - - - +
45D ASN* 5.2 0.4 - - - +
47D TYR* 3.9 9.0 - - - +
393D PHE* 3.9 23.8 - - + -
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Residues in contact with ASP 5 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D LYS 3.7 6.6 + - - -
4D LEU* 1.3 79.5 - - - +
6D LYS* 1.3 65.0 + - + +
8D SER* 3.9 3.3 - - - -
9D LYS* 3.5 39.2 + - - +
43D ASP* 3.5 6.4 + - - +
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Residues in contact with LYS 6 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D ASP* 1.3 74.7 - - + +
7D ALA* 1.3 65.5 + - - +
8D SER 3.4 0.2 + - - -
9D LYS* 3.4 13.7 + - - +
10D LEU* 3.1 30.1 + - + +
42D VAL* 4.0 25.2 + - + +
43D ASP* 2.8 26.0 + - - +
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Residues in contact with ALA 7 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D LEU* 3.9 13.0 - - + +
6D LYS* 1.3 72.6 - - - +
8D SER* 1.3 51.5 + - - +
10D LEU* 3.0 8.4 + - - +
11D ILE* 2.8 37.0 + - - +
28D ASN* 3.8 24.0 - - + +
30D VAL* 3.9 25.1 - - + +
41D ASP* 5.9 2.0 - - + -
42D VAL* 3.9 6.5 - - + +
43D ASP* 2.9 18.4 + - - +
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Residues in contact with SER 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D LEU* 3.0 20.5 + - - +
5D ASP* 3.9 3.4 - - - -
7D ALA* 1.3 72.7 - - - +
9D LYS* 1.3 61.2 + - - +
11D ILE* 4.0 3.3 - - - +
12D ASP* 2.9 35.8 + - - +
28D ASN* 3.2 28.4 + - - +
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Residues in contact with LYS 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D ASP* 3.5 34.3 + - - +
6D LYS* 3.4 15.0 + - - +
8D SER* 1.3 77.6 - - - +
10D LEU* 1.3 62.3 + - + +
12D ASP* 3.6 6.1 - - - +
13D GLU* 3.2 27.9 + - - +
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Residues in contact with LEU 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C VAL* 4.6 15.3 - - + -
91C MET* 3.6 23.9 - - + +
6D LYS* 3.1 23.7 + - + +
7D ALA 3.0 6.5 + - - +
9D LYS* 1.3 75.1 - - + +
11D ILE* 1.3 60.9 + - - +
13D GLU* 3.1 7.8 + - + +
14D GLU* 2.9 28.2 + - - +
30D VAL* 4.3 10.8 - - + -
42D VAL* 3.8 30.7 - - + -
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Residues in contact with ILE 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C HIS* 3.2 45.1 - - + +
91C MET* 3.9 5.2 - - + -
7D ALA 2.8 20.3 + - - +
8D SER* 4.0 4.9 - - - +
10D LEU* 1.3 69.4 - - - +
12D ASP* 1.3 58.7 + - - +
14D GLU* 3.3 4.3 + - - +
15D ASN* 2.9 47.7 + - - +
25D ASN* 6.1 0.2 - - - +
28D ASN* 3.4 46.9 - - + +
30D VAL* 3.6 21.1 - - + -
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Residues in contact with ASP 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D SER* 2.9 21.3 + - - +
9D LYS* 3.6 9.4 - - - +
11D ILE* 1.3 77.2 - - - +
13D GLU* 1.3 63.5 + - + +
15D ASN* 3.8 15.4 + - - +
16D LYS* 3.8 19.3 - - - +
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Residues in contact with GLU 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C GLU* 4.9 7.4 - - - +
1010C CD 3.3 22.2 - - - -
9D LYS 3.2 13.4 + - - +
10D LEU* 3.1 11.0 + - + +
12D ASP* 1.3 78.6 - - + +
14D GLU* 1.3 64.9 + - - +
15D ASN 3.2 1.8 - - - -
16D LYS* 2.9 52.0 + - - +
17D TYR* 3.3 27.4 + - - -
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Residues in contact with GLU 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C HIS* 2.4 35.3 + - - +
87C HIS 5.2 0.3 - - - +
90C GLY 5.3 1.2 - - - -
91C MET* 3.4 38.6 + - + +
94C SER* 4.3 11.2 + - - +
10D LEU 2.9 15.0 + - - +
11D ILE* 3.6 6.3 - - - +
13D GLU* 1.3 70.4 - - - +
15D ASN* 1.3 54.4 + - - +
17D TYR* 2.7 30.7 + - - +
18D TYR* 2.9 33.4 + - + +
23D ARG* 2.6 32.4 + - - +
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Residues in contact with ASN 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C HIS* 5.2 1.0 - - - -
108C MET* 3.5 17.7 - - - +
295C LYS* 5.1 1.2 + - - -
11D ILE* 2.9 36.7 + - - +
12D ASP* 3.8 12.6 + - - +
13D GLU 3.2 0.4 - - - -
14D GLU* 1.3 77.1 - - - +
16D LYS* 1.3 59.3 + - - +
18D TYR 4.0 7.1 - - - +
23D ARG* 4.8 11.6 + - - -
25D ASN* 5.7 2.9 + - - +
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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