Contacts of the strand formed by residues 21 - 28 (chain D) in PDB entry 1XSK
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 GLN 21 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19D PRO 3.8 1.2 - - - -
20D LEU* 1.3 80.7 - - - +
22D VAL* 1.3 74.8 + - - +
23D PHE* 5.3 0.4 - - - +
36D ALA* 3.3 1.2 - - - -
37D ALA* 2.9 29.0 + - + +
39D ARG 4.0 11.0 - - - +
40D ASP* 2.8 32.0 + - - +
41D VAL* 3.1 40.2 - - - +
42D ARG* 3.7 18.1 + - - +
115D GLY* 4.1 21.8 - - - +
116D GLU* 5.6 2.5 - - - -
118D TRP* 3.8 8.1 - - - -
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Residues in contact with VAL 22 (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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21D GLN* 1.3 89.6 + - - +
23D PHE* 1.3 63.9 + - - +
24D GLU* 3.7 11.7 - - - +
25D VAL* 3.7 29.4 - - + -
34D VAL* 4.1 7.4 - - + -
35D TYR 3.8 3.4 - - - -
101D ALA* 6.3 0.2 - - + -
112D VAL* 3.5 32.1 - - + -
113D SER 3.8 13.2 + - - +
114D LYS* 4.2 24.1 - - + +
115D GLY 4.9 4.5 + - - +
118D TRP* 3.6 11.6 - - + -
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Residues in contact with PHE 23 (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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312C ALA* 4.1 17.0 - - + -
313C PHE* 3.6 37.0 - + + -
353C LYS* 4.2 11.4 - - - -
21D GLN* 3.5 2.4 + - - +
22D VAL* 1.3 75.7 - - - +
24D GLU* 1.3 90.6 + - + +
35D TYR* 2.8 20.1 + - + +
36D ALA 5.2 0.2 - - - -
37D ALA* 5.0 4.7 - - + +
41D VAL* 3.6 31.0 - - + -
47D GLN* 4.0 23.1 - - - -
52D LEU* 5.2 1.3 - - + -
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Residues in contact with GLU 24 (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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311C LYS* 4.2 14.7 + - - -
353C LYS* 3.3 31.0 + - - -
22D VAL* 3.7 3.5 - - - +
23D PHE* 1.3 102.5 - - + +
25D VAL* 1.3 79.4 + - - +
26D GLU* 4.2 15.8 - - - +
34D VAL* 3.7 0.2 - - - -
35D TYR* 2.9 38.6 + - + +
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Residues in contact with VAL 25 (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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22D VAL* 3.7 20.2 - - + -
24D GLU* 1.3 87.9 - - - +
26D GLU* 1.3 67.8 + - - +
32D MET* 4.0 21.5 - - + -
33D VAL 3.4 8.1 - - - +
34D VAL* 4.3 9.6 - - + -
94D ILE* 6.2 0.4 - - + -
96D ASN* 3.6 38.8 + - + +
101D ALA* 4.0 14.6 - - + -
114D LYS* 3.8 20.4 - - - +
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Residues in contact with GLU 26 (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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353C LYS* 5.4 1.0 + - - -
24D GLU* 4.2 11.9 - - - +
25D VAL* 1.3 79.6 - - - +
27D GLN* 1.3 69.2 + - - +
28D GLN* 3.0 30.7 + - + +
32D MET* 3.6 6.3 - - - +
33D VAL* 2.8 41.8 + - + +
35D TYR* 3.7 25.2 + - + -
96D ASN* 5.4 1.3 - - - +
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Residues in contact with GLN 27 (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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26D GLU* 1.3 81.9 - - - +
28D GLN* 1.3 65.2 + - - +
29D ASP 3.4 24.2 + - - +
31D GLU 3.6 7.9 - - - +
32D MET* 4.8 0.2 - - - +
94D ILE* 3.3 43.5 + - + +
96D ASN* 6.0 3.0 - - + +
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Residues in contact with GLN 28 (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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26D GLU* 3.0 32.2 + - + +
27D GLN* 1.3 75.7 - - - +
29D ASP* 1.3 76.8 + - - +
31D GLU* 2.9 26.6 + - - +
33D VAL* 3.6 24.3 - - + +
35D TYR* 4.5 5.9 + - - -
56D ARG* 2.8 34.3 + - - +
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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