Contacts of the strand formed by residues 348 - 352 (chain D) in PDB entry 1HJX
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 GLY 348 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22D TYR* 4.1 6.7 - - - -
23D LYS 3.3 11.4 - - - -
254D LEU 3.8 1.9 + - - +
255D VAL* 3.4 6.3 - - - +
256D MET* 2.9 22.0 + - - +
341D LEU* 3.8 26.0 - - - +
346D LEU* 3.2 4.2 - - - +
347D ALA* 1.3 81.1 - - - +
349D ALA* 1.3 59.3 + - - -
380D LEU* 4.7 0.9 - - - -
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Residues in contact with ALA 349 (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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23D LYS 3.0 7.1 + - - +
24D LEU* 3.5 9.3 - - + +
25D VAL 2.9 24.8 + - - -
255D VAL* 3.1 10.1 - - - +
256D MET 3.4 8.3 - - - +
258D ILE* 3.9 22.2 - - + -
341D LEU* 4.0 9.4 - - + -
348D GLY* 1.3 72.8 - - - -
350D MET* 1.3 59.1 + - - +
351D VAL* 5.1 0.7 - - + -
376D ILE* 4.0 19.5 - - + -
380D LEU* 4.5 5.0 - - + +
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Residues in contact with MET 350 (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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25D VAL* 3.1 10.5 - - + +
27D TYR* 3.7 31.6 - - + -
177D ALA* 5.5 0.9 - - + -
202D SER* 3.7 31.9 - - - +
203D ILE 4.1 2.7 - - - +
204D MET* 4.0 14.6 - - + -
206D TYR* 3.3 35.0 - - + +
255D VAL* 3.3 17.9 - - + +
256D MET 2.9 5.7 + - - +
257D GLY* 3.3 16.1 - - - +
258D ILE* 2.7 34.3 + - - +
349D ALA* 1.3 73.4 - - - +
351D VAL* 1.3 70.1 + - - +
352D TRP 4.0 1.1 - - - -
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Residues in contact with VAL 351 (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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24D LEU* 3.9 22.0 - - + -
25D VAL 2.7 12.2 + - - +
26D CYS* 4.2 10.5 - - - -
27D TYR* 3.1 29.1 + - - +
258D ILE 3.4 4.7 - - - +
260D THR* 3.6 28.5 - - + -
349D ALA* 5.1 0.2 - - + -
350D MET* 1.3 81.8 - - - +
352D TRP* 1.3 63.9 + - - +
353D ALA* 3.7 8.0 - - - +
354D LEU* 4.6 2.0 - - + +
373D THR* 3.9 17.5 - - + +
376D ILE* 3.6 28.9 - - + -
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Residues in contact with TRP 352 (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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27D TYR* 3.5 47.6 - + + -
29D THR* 3.6 29.7 - - + +
31D TRP* 4.0 6.0 - + - -
57D SER* 4.5 1.8 - - - -
58D PHE* 3.7 15.7 - + - -
99D TRP* 3.4 42.9 - + - -
204D MET* 5.9 2.0 - - + -
206D TYR* 3.4 38.4 - + + +
258D ILE 3.1 8.3 + - - -
259D PRO* 3.4 1.9 - - - +
260D THR* 3.0 24.7 + - - -
261D PHE* 3.3 25.2 - + - -
350D MET* 4.0 2.8 - - + -
351D VAL* 1.3 72.6 - - - +
353D ALA* 1.3 56.6 + - + +
356D LEU* 3.9 14.2 - - + +
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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