Contacts of the strand formed by residues 370 - 377 (chain B) in PDB entry 1HQR
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 VAL 370 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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332B PHE 4.5 0.2 - - - +
334B ASN* 3.5 37.3 + - - +
369B GLU* 1.3 85.8 + - - +
371B TYR* 1.3 61.8 + - - +
372B THR* 4.1 14.9 + - - +
387B GLU* 4.2 11.9 - - + -
388B TRP 3.9 18.2 - - - +
389B ARG* 5.2 2.9 - - - +
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Residues in contact with TYR 371 (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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313B ASN* 5.1 0.7 - - - +
331B TRP* 4.3 17.5 - + + -
332B PHE 3.2 15.9 - - - +
333B ARG* 3.7 28.3 - - + +
361B LEU* 5.3 5.6 - - + -
363B THR* 3.1 30.1 + - + -
364B VAL 3.2 6.5 + - - -
365B PRO* 2.7 37.9 - - - +
369B GLU* 3.2 17.5 - - - -
370B VAL* 1.3 74.8 - - - +
372B THR* 1.3 68.4 + - - +
388B TRP* 3.2 63.6 + + - +
390B ALA* 3.7 9.6 - - + -
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Residues in contact with THR 372 (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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301B VAL* 5.9 0.2 - - - -
330B ARG 3.7 0.2 - - - +
331B TRP* 3.2 11.0 - - - -
332B PHE* 3.0 37.1 + - - +
370B VAL* 4.1 5.2 + - - +
371B TYR* 1.3 76.4 + - - +
373B CYS* 1.3 76.4 + - - +
374B GLN* 3.9 0.6 + - + -
385B THR* 4.5 9.2 - - + -
386B VAL 2.7 36.3 - - - +
387B GLU* 2.8 28.4 - - + +
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Residues in contact with CYS 373 (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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299B VAL* 4.3 7.6 - - + +
301B VAL* 4.7 4.3 - - + -
317B CYS* 2.0 52.9 - - + -
329B VAL* 3.5 22.9 - - - -
330B ARG 3.4 4.7 - - - -
331B TRP* 3.8 10.8 - - + -
359B VAL* 4.6 0.9 - - - -
372B THR* 1.3 87.8 - - - +
374B GLN* 1.3 61.9 + - - +
375B VAL* 4.0 8.0 + - - +
385B THR* 3.5 4.7 - - - -
386B VAL* 3.3 19.8 + - - +
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Residues in contact with GLN 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B GLU 4.2 0.7 - - - +
329B VAL* 3.7 0.5 - - - -
330B ARG* 2.8 50.8 + - + +
332B PHE* 4.8 17.0 - - + -
372B THR* 3.9 0.9 + - + +
373B CYS* 1.3 73.8 - - - +
375B VAL* 1.3 63.5 + - - +
376B GLU 4.3 0.2 + - - -
383B PRO* 5.4 7.0 - - + -
384B LEU 3.5 6.7 - - - +
385B THR* 4.3 9.9 - - + -
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Residues in contact with VAL 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B PRO* 4.8 7.4 - - + -
299B VAL* 3.3 36.3 - - + -
319B VAL* 4.2 7.9 - - + -
327B ILE* 3.9 27.1 - - + -
328B GLU 3.8 6.1 - - - +
329B VAL* 4.2 7.2 - - + -
373B CYS* 4.0 19.7 - - - +
374B GLN* 1.3 78.9 - - - +
376B GLU* 1.3 63.1 + - - +
377B HIS* 4.3 0.4 - - + -
380B VAL* 6.1 0.2 - - - +
383B PRO* 3.4 3.4 - - - +
384B LEU* 2.7 54.3 + - + +
385B THR* 6.0 0.2 - - - -
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Residues in contact with GLU 376 (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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327B ILE* 3.4 2.0 - - - +
328B GLU* 3.2 40.5 + - + +
374B GLN 4.3 0.2 - - - -
375B VAL* 1.3 73.6 - - - +
377B HIS* 1.3 60.4 + - - +
380B VAL* 5.0 4.3 - - - +
381B THR 5.8 1.6 - - - +
383B PRO* 4.4 18.2 - - + -
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Residues in contact with HIS 377 (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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295B VAL 3.7 4.0 - - - -
297B PRO* 4.0 14.3 - - + +
322B PHE* 3.4 23.8 - + + -
323B TYR 2.8 48.0 + - - -
324B PRO 3.2 8.8 + - - -
326B SER 3.7 1.1 - - - -
327B ILE* 3.4 20.9 - - + -
375B VAL* 4.3 1.1 - - + -
376B GLU* 1.3 74.5 - - - +
378B PRO* 1.3 74.6 - - + +
379B SER* 2.5 56.9 + - - +
380B VAL* 2.9 24.1 + - + +
384B LEU* 6.2 1.9 - - + +
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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