Contacts of the strand formed by residues 416 - 424 (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 CYS 416 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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395A TYR* 3.1 8.1 - - - -
396A ALA* 2.9 55.9 + - + +
414A ALA 3.4 4.6 + - - -
415A ASP* 1.4 67.7 - - - +
417A PRO* 1.4 73.0 - - - +
418A ILE* 3.4 3.0 + - - -
564B ASN* 3.1 42.8 - - - +
567B LYS* 4.2 3.8 - - - -
568B PRO* 3.8 25.6 - - + -
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Residues in contact with PRO 417 (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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394A LEU 4.1 1.6 - - - +
395A TYR* 3.6 26.9 - - + +
415A ASP 3.5 8.0 - - - +
416A CYS* 1.4 80.2 - - - +
418A ILE* 1.3 55.3 + - - +
444A SER* 3.6 21.2 - - - +
445A VAL 5.3 1.1 - - - +
446A PRO* 4.9 8.7 - - + -
450A GLY 5.7 4.0 - - - +
564B ASN* 4.0 0.5 - - - +
567B LYS* 2.7 45.3 + - + +
571B ILE* 3.6 25.6 - - + -
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Residues in contact with ILE 418 (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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333A VAL* 4.5 20.6 - - + -
334A ASN 5.4 0.4 - - - +
335A ALA* 5.0 5.6 - - + -
341A LEU* 5.7 1.3 - - + -
394A LEU* 2.8 31.1 + - + +
395A TYR 3.9 2.2 - - - -
396A ALA* 3.7 32.5 - - + +
416A CYS* 3.9 8.3 - - - +
417A PRO* 1.3 70.4 - - - +
419A ALA* 1.3 66.7 + - + +
441A MET* 5.9 0.7 - - + -
443A PRO* 3.5 5.5 - - - +
444A SER 3.0 16.5 + - - -
469A ALA* 5.9 4.5 - - + -
560B ASP* 5.1 5.2 - - - +
564B ASN* 3.5 30.3 + - - +
567B LYS* 3.4 9.7 + - - -
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Residues in contact with ALA 419 (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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393A ALA* 3.3 3.3 - - - +
394A LEU* 2.8 26.7 + - + +
418A ILE* 1.3 85.8 - - + +
420A TRP* 1.3 61.7 + - - +
441A MET* 3.7 34.3 - - + -
442A TRP 3.1 18.6 - - - +
443A PRO* 4.3 1.1 - - + -
444A SER* 3.4 8.8 + - - -
469A ALA* 5.1 4.9 - - + -
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Residues in contact with TRP 420 (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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392A PHE 3.1 15.3 - - - +
393A ALA* 4.4 5.4 - - + -
419A ALA* 1.3 74.1 - - - +
421A ALA* 1.3 77.8 + - - +
422A ASN* 3.3 33.7 - - - +
441A MET* 3.4 5.7 - - - +
442A TRP* 2.8 81.5 + + + +
443A PRO 3.2 20.8 + - - -
444A SER* 3.5 17.2 - - - +
445A VAL 5.3 0.2 - - - +
454A ASN* 3.4 35.1 - - + +
457A GLY* 3.6 4.9 - - - -
458A THR* 3.5 32.3 - - + -
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Residues in contact with ALA 421 (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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391A CYS 3.7 0.2 - - - -
392A PHE* 2.8 42.0 + - + +
420A TRP* 1.3 82.8 - - - +
422A ASN* 1.3 62.6 + - - +
439A LEU* 4.2 25.4 - - + -
440A TYR 4.9 2.9 - - - +
441A MET* 3.8 23.3 - - + -
442A TRP* 4.8 3.4 - - + -
471A LEU* 6.1 0.9 - - + -
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Residues in contact with ASN 422 (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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389A ARG* 3.9 6.3 - - - +
390A LEU 3.3 6.5 - - - +
391A CYS* 3.2 29.3 - - - +
392A PHE 4.1 1.4 + - - +
420A TRP* 3.3 9.8 - - - -
421A ALA* 1.3 84.0 - - - +
423A LEU* 1.3 62.1 + - - +
439A LEU* 4.9 5.0 - - - +
454A ASN 2.8 28.2 + - - +
457A GLY 3.0 27.7 + - - +
458A THR 3.8 11.5 + - - +
459A VAL* 3.4 33.7 - - + +
460A ARG 5.4 0.3 - - - +
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Residues in contact with LEU 423 (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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389A ARG* 3.2 3.1 - - - -
390A LEU* 2.7 63.4 + - + +
392A PHE* 4.8 2.7 - - + -
422A ASN* 1.3 78.1 - - - +
424A MET* 1.3 68.2 + - - +
425A LEU* 3.6 2.9 + - + +
433A LYS* 3.9 25.8 - - + +
437A ARG* 4.5 17.0 - - + -
439A LEU* 3.5 40.6 - - + -
459A VAL* 4.3 9.2 - - - +
473A ILE* 5.0 4.0 - - + -
475A LEU* 4.8 16.6 - - + -
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Residues in contact with MET 424 (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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386A ARG 4.5 0.4 - - - +
387A MET* 3.6 36.6 - - - +
388A ALA 3.9 2.5 - - - +
389A ARG* 4.1 16.4 - - - -
423A LEU* 1.3 77.1 - - - +
425A LEU* 1.4 62.1 + - - +
426A PHE 3.4 15.5 - - - +
433A LYS* 2.8 34.8 + - - +
459A VAL* 3.7 34.1 - - + +
623A SER* 3.6 27.1 - - - +
624A TYR* 3.4 30.1 - - + +
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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