Contacts of the strand formed by residues 361 - 368 (chain B) in PDB entry 4HXG
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 LEU 361 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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357B LYS* 3.5 5.9 - - - +
358B SER 2.9 30.6 + - - +
359B ILE 3.4 1.5 - - - +
360B ASP* 1.3 97.3 - - - +
362B GLU* 1.3 61.8 + - - +
363B LEU* 3.6 13.0 - - + -
416B ARG* 3.7 27.4 - - + +
425B PHE* 4.0 29.8 - - + -
428B ARG* 3.9 33.0 - - - +
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Residues in contact with GLU 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355B ARG* 3.0 59.6 + - + +
356B PHE 3.5 12.6 - - - +
357B LYS* 4.6 3.6 - - + +
361B LEU* 1.3 74.4 - - - +
363B LEU* 1.3 66.7 + - - +
425B PHE* 5.6 0.5 - - - -
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Residues in contact with LEU 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B ARG* 3.4 16.7 - - - +
356B PHE* 2.9 50.7 + - + +
358B SER* 3.8 13.9 - - - -
361B LEU* 3.6 24.7 - - + -
362B GLU* 1.3 84.2 - - - +
364B ASP* 1.3 61.8 + - - +
414B ASN 4.0 13.7 - - - +
415B PRO* 4.4 5.2 - - + -
416B ARG* 4.8 0.4 - - - +
421B TYR* 6.3 1.1 - - - -
425B PHE* 3.9 19.5 - - + -
440B ASP* 3.3 43.7 - - + +
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Residues in contact with ASP 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281B GLU* 3.8 18.4 - - - +
353B HIS* 2.5 29.8 + - - +
354B PHE 4.0 0.7 - - - -
355B ARG* 3.0 22.6 + - - +
356B PHE* 3.6 4.5 - - - -
363B LEU* 1.3 74.3 - - - +
365B GLY* 1.3 58.4 + - - +
366B TRP* 3.4 18.6 - - + -
413B VAL* 3.5 6.2 - - - +
414B ASN 3.3 25.2 + - - -
421B TYR* 2.9 39.4 + - - +
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Residues in contact with GLY 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353B HIS* 3.3 3.1 - - - -
354B PHE* 2.8 48.1 + - - -
356B PHE* 4.2 0.2 - - - -
364B ASP* 1.3 75.7 - - - +
366B TRP* 1.3 71.3 + - - -
412B TYR 3.6 10.5 - - - -
413B VAL* 3.6 10.1 - - - -
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Residues in contact with TRP 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281B GLU 3.9 20.2 - - - -
282B GLY* 4.4 2.2 - - - -
351B PRO* 4.2 9.2 - - + -
352B ARG 3.3 6.1 - - - +
353B HIS* 3.6 37.0 - + + +
354B PHE* 3.3 4.5 - - - -
364B ASP* 3.4 32.5 - - + -
365B GLY* 1.3 86.4 - - - -
367B TYR* 1.3 66.0 + - - +
392B TYR 4.4 6.7 - - - -
393B GLY* 4.6 3.8 - - - -
394B TYR* 3.0 41.6 + + - -
411B VAL* 3.5 5.0 - - - +
412B TYR* 3.0 76.1 + + + +
413B VAL* 4.7 0.7 - - - -
414B ASN* 3.4 32.3 - - - -
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Residues in contact with TYR 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350B GLU 4.5 0.2 - - - +
351B PRO* 3.5 1.7 - - - +
352B ARG* 2.7 61.4 + - + +
353B HIS 5.7 0.2 - - - -
354B PHE* 3.5 26.9 - + + -
366B TRP* 1.3 76.1 - - - +
368B ILE* 1.3 73.6 + - - +
369B LYS* 4.9 6.7 - - + -
409B TYR* 4.5 2.7 - + - -
410B ILE 2.8 13.7 - - - +
411B VAL* 4.3 0.7 - - + -
412B TYR* 5.1 0.7 - - - -
448B PHE* 3.5 37.9 - + + -
451B LEU* 4.3 19.0 + - + +
452B GLU* 2.8 39.9 + - + +
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Residues in contact with ILE 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349B PHE* 3.4 46.7 - - + +
350B GLU 4.9 2.7 - - - +
351B PRO* 4.0 20.2 - - + -
367B TYR* 1.3 83.8 - - - +
369B LYS* 1.3 65.5 + - - +
370B PRO* 3.6 2.1 - - - +
400B MET* 4.4 23.6 - - + +
401B GLN* 4.0 14.1 - - - +
404B ALA* 3.6 17.0 - - + -
408B TYR 4.3 0.2 - - - +
409B TYR* 3.3 10.6 - - - -
410B ILE* 2.8 39.6 + - + -
412B TYR* 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