Contacts of the strand formed by residues 17 - 23 (chain C) in PDB entry 3QOQ
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 ASP 17 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11C TYR* 3.0 23.7 + - - +
15C THR 4.6 2.2 - - - +
16C ALA* 1.3 71.5 - - - +
18C LYS* 1.3 59.6 + - - +
21D VAL 3.4 0.3 - - - +
22D ARG* 3.3 2.6 - - - -
23D LEU* 2.8 37.8 + - + +
24D PRO 4.3 2.1 - - - +
25D GLU 3.7 15.1 - - - +
28D ARG* 3.9 36.3 - - - +
29D GLU* 4.9 2.3 - - - +
3E T 5.4 5.6 + - - +
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Residues in contact with LYS 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C ARG 5.6 4.5 + - - +
15C THR 6.0 0.2 - - - -
16C ALA 3.4 14.9 + - - +
17C ASP* 1.3 73.4 - - - +
19C PHE* 1.3 60.5 + - - +
20D VAL* 4.3 10.8 - - + -
21D VAL 3.2 4.0 - - - +
22D ARG* 3.8 34.3 - - + +
23D LEU* 4.6 0.4 - - - -
28D ARG* 4.9 7.8 + - - -
2E C 5.0 8.5 + - - +
3E T 3.8 50.7 + - + +
4E G 2.8 50.3 + - - -
5E G 2.9 20.6 + - - -
32F C 4.0 7.9 - - - +
33F C 4.7 0.7 - - - +
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Residues in contact with PHE 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C LYS* 1.3 74.3 - - - +
20C VAL* 1.3 76.8 + - - +
21C VAL* 3.4 21.7 + - + -
20D VAL* 4.3 0.9 - - - -
21D VAL* 2.8 36.6 + - + +
23D LEU* 3.8 21.9 - - + +
28D ARG* 4.2 16.2 - - - +
42D MSE 3.5 34.5 - - + -
43D ASN* 3.8 33.9 - - + -
46D ILE* 3.7 19.5 - - + -
1E A 4.6 9.6 - - - -
2E C 4.3 11.9 - - - -
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Residues in contact with VAL 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C PHE* 1.3 86.3 - - - +
21C VAL* 1.3 61.2 + - - +
22C ARG* 3.6 22.1 + - - +
18D LYS* 3.7 44.4 - - + +
19D PHE 4.0 8.1 - - - +
20D VAL* 4.1 18.2 - - + +
43D ASN* 4.3 0.7 - - - +
1E A 6.6 0.2 - - - +
2E C 4.8 9.6 - - + -
3E T 4.1 27.4 - - + +
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Residues in contact with VAL 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C PHE* 3.6 22.0 - - + -
20C VAL* 1.3 70.8 - - - +
22C ARG* 1.3 69.8 + - - +
23C LEU* 3.5 16.9 + - + +
46C ILE* 6.0 1.6 - - + -
18D LYS* 3.4 3.6 - - - -
19D PHE* 2.9 37.0 + - + +
21D VAL* 3.7 24.9 - - + -
43D ASN* 3.6 11.7 - - - +
46D ILE* 3.9 32.5 - - + -
47D ILE* 4.1 9.9 - - + -
50D LEU* 5.1 3.6 - - + -
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Residues in contact with ARG 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C VAL* 3.9 25.6 + - - +
21C VAL* 1.3 69.2 - - - +
23C LEU* 1.3 55.9 + - - +
16D ALA* 4.5 17.9 - - + +
17D ASP 3.6 7.6 - - - +
18D LYS* 3.2 43.9 - - + +
43D ASN* 2.7 22.7 + - - +
47D ILE* 2.8 32.9 - - - +
1E A 5.1 20.2 + - - -
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Residues in contact with LEU 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C VAL* 3.6 16.4 - - + +
22C ARG* 1.3 72.8 - - - +
24C PRO* 1.3 75.1 - - + +
27C MSE 4.1 15.9 - - + -
28C ARG* 4.3 15.7 - - + +
31C ILE* 3.8 29.6 - - + -
46C ILE* 5.4 4.3 - - + -
16D ALA* 3.6 9.3 - - - +
17D ASP* 2.9 49.5 + - - +
18D LYS 3.9 2.0 - - - +
19D PHE* 3.4 34.5 - - + +
47D ILE* 4.1 1.6 - - + -
50D LEU* 5.2 3.1 - - + -
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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