Contacts of the strand formed by residues 370 - 380 (chain A) in PDB entry 5VLR
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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328A ILE* 3.9 7.0 - - + +
329A GLN* 3.7 20.6 - - + +
363A VAL* 3.7 23.1 - - - +
368A GLU 3.8 8.3 - - - +
369A PRO* 1.3 78.0 - - - +
371A TRP* 1.3 63.7 + - - +
372A LYS* 3.8 32.1 - - + +
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Residues in contact with TRP 371 (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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327A LEU* 3.6 34.5 - - + +
328A ILE 2.8 9.1 + - - -
329A GLN 4.0 10.5 - - - -
330A GLY* 3.7 15.9 - - - -
333A VAL* 5.8 0.9 - - + -
341A LEU* 3.8 29.9 + - + -
342A VAL 4.7 7.2 - - - -
343A VAL* 4.8 6.1 - - + -
360A SER* 3.5 18.5 + - - -
361A SER* 3.2 31.4 + - - -
363A VAL* 3.6 21.4 - - + +
369A PRO* 3.4 46.2 - - + -
370A VAL* 1.3 73.9 - - - +
372A LYS* 1.4 68.0 + - - +
373A GLN* 2.9 15.3 + - + +
394A LEU* 5.1 10.1 - - + -
471A LEU* 5.2 4.0 - - + -
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Residues in contact with LYS 372 (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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326A GLU* 5.2 5.8 - - - -
327A LEU 3.1 5.1 + - - -
328A ILE* 2.8 40.0 + - + +
370A VAL* 3.8 22.2 - - + -
371A TRP* 1.4 70.4 - - - +
373A GLN* 1.4 55.3 + - - +
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Residues in contact with GLN 373 (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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326A GLU* 3.7 4.2 - - - -
327A LEU* 2.9 37.1 + - + +
359A SER 4.1 6.9 + - - -
360A SER* 3.9 13.7 - - - +
361A SER* 3.0 44.2 + - - +
371A TRP* 3.5 19.6 - - + +
372A LYS* 1.4 75.6 - - - +
374A ARG* 1.3 74.1 + - - +
375A LEU* 3.8 6.3 + - + +
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Residues in contact with ARG 374 (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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324A ARG* 6.0 6.7 - - + -
325A ILE 3.7 5.8 - - - +
326A GLU* 4.4 12.9 - - + +
372A LYS 4.5 0.4 + - - -
373A GLN* 1.3 83.4 + - - +
375A LEU* 1.3 65.7 + - - +
376A GLU* 4.2 1.0 + - - -
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Residues in contact with LEU 375 (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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323A PHE 3.9 0.5 - - - +
324A ARG* 3.5 4.5 - - - +
325A ILE* 2.7 59.6 + - + +
327A LEU* 4.3 22.7 - - + -
343A VAL 5.0 2.7 - - - +
345A ALA* 4.3 23.6 - - + -
358A VAL* 3.9 16.8 - - + +
359A SER 3.5 32.8 - - - +
360A SER* 4.4 2.7 - - - +
373A GLN* 4.5 12.6 - - - +
374A ARG* 1.3 78.3 - - - +
376A GLU* 1.3 60.0 + - - +
377A PHE* 4.1 9.1 - - + -
392A PHE* 5.4 2.5 - - + -
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Residues in contact with GLU 376 (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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322A PRO* 3.7 33.0 - - + +
323A PHE 3.5 5.4 - - - +
324A ARG* 3.0 38.4 + - + +
358A VAL* 3.7 15.1 - - - +
374A ARG 4.2 1.2 + - - -
375A LEU* 1.3 74.6 - - - +
377A PHE* 1.3 67.8 + - - +
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Residues in contact with PHE 377 (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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322A PRO* 3.6 14.7 - - - +
323A PHE* 3.0 47.5 + + + +
325A ILE* 4.2 10.5 - - + -
345A ALA* 3.6 43.5 - - + -
346A GLY* 4.3 6.7 - - - -
347A LEU* 4.4 7.2 - - + -
355A CYS* 3.8 17.0 - - - -
356A LYS 3.9 16.2 - - - -
358A VAL* 3.8 15.5 - - + -
375A LEU* 4.1 16.8 - - + -
376A GLU* 1.3 79.3 - - - +
378A ASP* 1.4 52.3 + - - +
379A ILE* 2.7 32.8 + - + +
390A LEU* 4.5 8.5 - - + -
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Residues in contact with ASP 378 (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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354A LEU 4.9 0.3 - - - +
355A CYS* 3.5 23.0 - - + +
356A LYS* 5.0 13.0 + - + +
377A PHE* 1.4 67.2 - - - +
379A ILE* 1.4 58.5 + - - +
380A ASN* 5.5 4.7 + - - -
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Residues in contact with ILE 379 (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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322A PRO* 3.6 1.0 - - - +
323A PHE* 2.9 31.2 + - + +
347A LEU* 4.7 5.8 - - + -
354A LEU* 4.6 13.0 - - + +
355A CYS* 3.7 24.9 - - + -
377A PHE* 2.7 20.5 + - + +
378A ASP* 1.4 74.3 - - - +
380A ASN* 1.3 65.5 + - - +
381A ILE 3.8 0.2 - - - -
383A ASP* 4.0 20.4 - - + -
384A LEU* 3.8 33.9 - - + +
556A ASN* 4.4 11.2 - - + +
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Residues in contact with ASN 380 (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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319A LEU 4.0 0.7 - - - -
320A GLU* 2.8 35.8 - - + +
321A GLN* 3.5 12.6 - - - +
322A PRO* 3.7 8.9 - - - +
378A ASP* 5.5 3.4 + - - -
379A ILE* 1.3 76.0 - - - +
381A ILE* 1.4 50.3 + - - +
382A CYS* 2.7 21.1 + - - -
383A ASP* 2.7 38.2 + - - +
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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