Contacts of the strand formed by residues 23 - 29 (chain A) in PDB entry 1HJW
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 LYS 23 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A TYR* 1.3 76.0 - - - +
24A LEU* 1.3 60.9 + - - +
25A VAL* 3.9 11.0 - - + -
52A THR* 3.5 5.8 - - - +
53A HIS* 4.0 24.7 - - + -
199A ASP* 5.1 5.1 + - - -
200A PHE* 4.1 34.8 - - + -
252A SER 5.1 4.0 + - - -
255A VAL* 4.4 10.3 - - + -
347A ALA* 2.7 28.1 + - + +
348A GLY* 3.2 3.0 - - - -
349A ALA 3.0 24.0 + - - -
380A LEU* 3.8 4.7 - - - +
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Residues in contact with LEU 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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23A LYS* 1.3 74.1 - - - +
25A VAL* 1.3 59.8 + - - +
26A CYS* 3.9 18.8 - - - -
50A LEU 3.5 22.4 - - - +
51A CYS* 3.1 13.1 - - - +
52A THR* 2.8 41.8 + - + +
53A HIS 3.2 2.6 + - - -
349A ALA* 3.4 10.1 - - + +
351A VAL* 4.0 17.7 - - + -
373A THR* 4.2 8.1 - - + +
376A ILE* 4.1 15.5 - - + -
377A LYS* 3.7 33.7 - - + +
380A LEU* 4.3 6.7 - - + -
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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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23A LYS* 4.3 13.9 - - + -
24A LEU* 1.3 72.7 - - - +
26A CYS* 1.3 57.2 + - - +
27A TYR* 4.3 1.8 - - + -
53A HIS* 3.5 24.7 - - + +
55A ILE* 3.4 36.6 - - + -
200A PHE* 3.9 25.4 - - + -
202A SER* 4.5 0.4 - - - +
255A VAL* 4.3 7.4 - - + -
349A ALA 2.9 12.3 + - - +
350A MET* 3.0 18.3 - - + +
351A VAL* 2.7 32.1 + - - +
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Residues in contact with CYS 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 LEU* 3.7 17.0 - - - -
25A VAL* 1.3 78.6 - - - +
27A TYR* 1.3 57.6 + - - +
51A CYS* 2.1 48.0 - - - -
53A HIS 2.8 9.9 + - - +
54A ILE* 3.1 7.0 - - + +
55A ILE* 2.8 30.6 + - - -
351A VAL* 3.8 9.4 - - + -
354A LEU* 3.4 20.6 - - + -
373A THR* 4.0 10.5 - - - -
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Residues in contact with TYR 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* 4.8 0.4 - - + -
26A CYS* 1.3 75.4 - - - +
28A TYR* 1.3 59.5 + - - +
55A ILE* 3.3 45.2 - - + +
57A SER* 4.0 7.6 - - - +
95A SER* 4.1 5.8 - - - -
136A ASP* 2.6 30.3 + - - -
177A ALA* 3.5 13.5 - - - +
202A SER* 4.5 3.1 + - - -
350A MET* 3.5 40.2 - - + -
351A VAL 3.0 12.5 + - - +
352A TRP* 3.4 38.6 - + + -
353A ALA* 3.7 4.7 - - + -
354A LEU* 2.9 32.7 + - - +
3C NAG 3.4 19.1 - - + -
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Residues in contact with TYR 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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27A TYR* 1.3 73.4 - - - +
29A THR* 1.3 80.5 + - - +
30A SER* 4.0 2.8 + - - -
32A SER* 3.5 15.7 + - - -
33A GLN* 4.3 4.0 - - - +
41A CYS* 2.8 36.3 + - - -
42A PHE* 3.7 0.3 - - - -
43A PRO* 3.5 30.0 - - + +
46A LEU* 3.9 33.9 - - + -
54A ILE* 4.2 11.9 - - + -
55A ILE 3.0 6.4 + - - +
56A TYR* 3.7 36.6 - + + -
57A SER* 2.9 27.2 + - - -
76A LEU* 4.1 10.1 - - + +
80A LEU* 5.8 1.1 - - + -
354A LEU* 4.6 2.2 - - + -
355A ASP* 3.8 8.7 - - + -
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Residues in contact with THR 29 (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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28A TYR* 1.3 84.5 - - - +
30A SER* 1.3 64.7 + - - +
31A TRP* 3.0 48.7 + - + +
32A SER* 2.9 26.9 + - - -
35A ARG* 4.7 0.2 + - - -
57A SER* 3.2 7.9 - - - +
352A TRP* 3.6 19.5 - - + -
353A ALA* 4.4 6.5 - - + -
355A ASP* 2.9 29.8 + - - +
356A LEU* 6.3 0.2 - - + -
4C NAG 5.7 0.4 - - - +
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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