Contacts of the strand formed by residues 3 - 9 (chain D) in PDB entry 1USK
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 ILE 3 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1D ASP* 4.3 5.2 - - + +
2D ASP* 1.3 73.9 - - - +
4D LYS* 1.3 64.8 + - - +
5D VAL* 3.9 3.7 - - + +
39D ILE* 3.8 38.6 - - + -
42D ASP* 3.8 21.5 - - + +
43D LYS 3.1 10.2 + - - +
44D LEU* 3.8 16.8 - - + -
45D VAL* 3.1 23.5 + - - +
72D TYR* 3.7 31.0 - - + -
291D LEU* 4.6 12.1 - - + -
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Residues in contact with LYS 4 (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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2D ASP* 3.9 7.0 + - + +
3D ILE* 1.3 74.4 - - - +
5D VAL* 1.3 64.1 + - - +
6D ALA 4.3 0.2 - - - -
45D VAL* 3.6 13.7 - - + +
47D VAL* 4.4 15.3 - - + -
68D ASP* 4.3 14.5 + - - +
69D GLY 5.8 0.9 - - - +
70D ILE* 3.9 39.4 - - + +
71D LYS 5.0 1.0 + - - -
72D TYR* 3.5 18.4 + - - -
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Residues in contact with VAL 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 ILE* 3.9 5.2 - - + +
4D LYS* 1.3 80.9 - - - +
6D ALA* 1.3 63.9 + - - +
7D VAL* 3.5 5.7 + - + +
30D ILE* 5.4 7.0 - - + -
44D LEU* 3.6 31.2 - - + -
45D VAL 3.0 11.1 + - - +
46D GLY* 3.5 5.7 - - - -
47D VAL* 3.0 24.4 + - - +
72D TYR* 3.6 12.8 - - + +
74D ILE* 3.7 30.3 - - + +
284D VAL* 5.8 3.6 - - + -
287D LEU* 3.7 22.9 - - + -
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Residues in contact with ALA 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 VAL* 1.3 70.6 - - - +
7D VAL* 1.3 61.7 + - - +
8D VAL* 4.1 2.0 - - + -
47D VAL* 3.2 8.7 - - - -
49D TYR* 3.8 26.0 - - + -
65D ILE* 3.9 19.7 - - + -
70D ILE* 3.8 14.3 - - + +
72D TYR 3.1 12.7 + - - +
73D VAL* 3.4 7.7 - - + +
74D ILE* 2.8 28.6 + - - +
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Residues in contact with VAL 7 (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 VAL* 3.5 10.3 + - + +
6D ALA* 1.3 73.9 - - - +
8D VAL* 1.3 64.3 + - - +
22D GLU* 3.9 17.3 - - + +
23D PHE* 3.3 31.3 - - + -
26D ALA* 4.1 28.9 - - + -
30D ILE* 4.7 13.2 - - + -
46D GLY* 4.9 3.6 - - - -
47D VAL 3.1 6.2 + - - +
48D GLU* 3.4 8.1 - - + +
49D TYR 3.0 24.4 + - - -
74D ILE* 3.4 20.2 - - + +
284D VAL* 5.6 0.4 - - + -
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Residues in contact with VAL 8 (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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6D ALA 4.4 0.4 - - - -
7D VAL* 1.3 81.9 - - - +
9D GLY* 1.3 58.4 - - - +
22D GLU* 2.6 24.2 - - - +
23D PHE* 4.1 0.4 - - - -
49D TYR* 3.7 12.6 - - + +
51D ASP* 3.9 11.2 - - + -
61D VAL* 3.9 12.1 - - + -
65D ILE* 3.8 26.9 - - + -
73D VAL* 3.9 17.9 - - + -
74D ILE 3.2 6.5 + - - -
75D GLY* 3.8 1.8 - - - -
76D HIS* 3.1 56.3 - - + +
77D LEU 3.6 0.2 + - - -
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Residues in contact with GLY 9 (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 VAL* 1.3 77.6 - - - +
10D ALA* 1.3 65.1 + - - -
11D MET 3.2 3.8 + - - -
22D GLU* 3.2 15.3 - - - -
23D PHE* 3.6 8.8 - - - -
49D TYR 3.4 10.7 + - - +
50D ASP* 3.6 0.2 - - - +
51D ASP* 3.2 29.9 + - - +
77D LEU* 3.9 8.7 - - - -
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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