Contacts of the strand formed by residues 21 - 28 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A PRO 3.6 1.8 - - - -
20A LEU* 1.3 81.2 - - - +
22A VAL* 1.3 73.0 + - - +
36A ALA* 3.1 3.8 - - - -
37A ALA* 2.9 29.4 + - + +
39A ARG 4.1 13.0 - - - +
40A ASP* 3.2 28.3 + - - +
41A VAL* 2.9 35.3 + - + +
42A ARG* 3.7 24.1 + - - +
115A GLY 3.4 21.1 + - - +
116A GLU* 4.2 10.5 + - - +
118A TRP* 4.1 9.6 - - - -
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Residues in contact with VAL 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A GLN* 1.3 84.7 - - - +
23A PHE* 1.3 63.0 + - - +
24A GLU 3.8 8.1 - - - +
25A VAL* 3.8 28.7 - - + -
34A VAL* 4.0 10.3 - - + -
35A TYR 3.7 3.8 - - - -
36A ALA* 4.5 0.9 - - - +
112A VAL* 3.4 32.5 - - + -
113A SER 3.6 12.5 + - - +
114A LYS* 4.1 22.2 - - + +
115A GLY 4.5 6.6 + - - -
118A TRP* 3.5 13.6 - - + -
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Residues in contact with PHE 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A GLN 3.5 2.8 + - - +
22A VAL* 1.3 76.1 - - - +
24A GLU* 1.3 83.7 + - + +
35A TYR* 2.8 20.8 + - + +
37A ALA 4.9 0.7 - - - +
41A VAL* 4.0 25.6 - - + -
47A GLN* 4.0 21.8 - - - -
52A LEU* 4.8 8.1 - - + -
312F ALA* 4.0 14.1 - - + -
313F PHE* 3.7 39.0 - + - -
353F LYS* 4.0 17.5 - - - -
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Residues in contact with GLU 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A VAL* 3.7 2.7 - - - +
23A PHE* 1.3 102.7 - - + +
25A VAL* 1.3 75.5 + - - +
26A GLU* 3.7 19.7 - - - +
34A VAL* 3.6 1.2 - - - -
35A TYR* 2.9 39.2 + - + +
311F LYS* 4.5 12.8 + - - -
353F LYS* 3.4 27.0 + - - -
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Residues in contact with VAL 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A VAL* 3.8 13.9 - - + -
24A GLU* 1.3 85.4 - - - +
26A GLU* 1.3 65.2 + - - +
27A GLN* 6.3 0.2 - - + -
32A MET* 4.3 14.8 - - + -
33A VAL 3.4 7.2 - - - +
34A VAL* 4.4 8.3 - - + -
94A ILE* 6.0 0.2 - - + -
96A ASN* 3.4 43.5 + - + +
101A ALA* 3.7 21.3 - - + -
114A LYS* 3.4 28.0 - - - +
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Residues in contact with GLU 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A GLU* 3.7 18.5 - - - +
25A VAL* 1.3 79.3 - - - +
27A GLN* 1.3 66.4 + - - +
28A GLN* 2.7 35.2 + - + +
32A MET* 3.7 3.0 - - - +
33A VAL* 2.7 45.6 + - + +
35A TYR* 3.8 22.1 + - + -
353F LYS* 5.1 1.7 + - - -
355F PRO* 6.2 0.5 - - - +
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Residues in contact with GLN 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A VAL* 6.3 0.7 - - + -
26A GLU* 1.3 79.5 - - - +
28A GLN* 1.3 63.1 + - - +
29A ASP 3.2 24.6 + - - +
31A GLU 3.7 3.4 - - - -
32A MET* 4.7 0.9 - - - +
94A ILE* 3.9 47.5 + - + +
96A ASN* 6.2 3.2 - - + +
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Residues in contact with GLN 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A GLU* 2.7 33.5 + - + +
27A GLN* 1.3 76.3 - - - +
29A ASP* 1.3 73.8 + - - +
31A GLU* 2.9 27.1 + - - +
33A VAL* 3.4 20.9 - - + +
35A TYR* 4.3 8.1 + - - -
56A ARG* 2.8 40.4 + - - +
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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