Contacts of the strand formed by residues 419 - 429 (chain B) in PDB entry 3BEQ
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 ARG 419 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92B CYS* 3.8 10.8 - - - -
411B VAL* 3.2 9.7 - - - +
412B GLN* 3.0 65.9 + - + +
413B THR* 4.9 5.3 - - + +
415B LEU* 3.9 29.4 - - + +
417B CYS 3.6 1.6 + - - -
418B MET* 1.3 71.4 - - - +
420B PRO* 1.4 77.9 - - + +
421B CYS* 3.9 4.9 - - - -
447B CYS* 4.0 16.2 - - - +
448B GLY 3.5 13.8 + - - +
449B VAL* 4.1 21.4 - - - +
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Residues in contact with PRO 420 (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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91B LEU* 4.3 5.6 - - + -
92B CYS* 4.4 9.0 - - + -
94B ILE* 4.1 23.8 - - + -
97B TRP* 3.5 3.2 - - + -
354B PHE* 3.6 37.0 - - + -
356B TYR* 3.3 25.4 - - + +
410B PHE 4.1 2.9 - - - +
411B VAL* 4.5 2.0 - - + -
418B MET 3.5 8.5 - - - +
419B ARG* 1.4 85.6 - - + +
421B CYS* 1.3 59.0 + - - +
448B GLY 2.7 32.4 + - - +
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Residues in contact with CYS 421 (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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97B TRP* 4.2 1.8 - - - -
354B PHE* 3.3 14.3 - - - -
409B SER* 3.6 0.3 - - - -
410B PHE* 2.9 55.7 + - + +
412B GLN* 4.0 9.9 - - - -
419B ARG* 3.9 12.3 - - - -
420B PRO* 1.3 76.9 - - - +
422B PHE* 1.3 64.7 + - - +
446B PHE 3.1 13.5 - - - +
447B CYS* 2.2 43.1 - - - +
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Residues in contact with PHE 422 (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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97B TRP* 3.6 40.8 - + - -
352B PHE* 3.3 38.4 - + + -
374B PHE* 3.7 10.3 - + - -
376B MET* 3.6 22.4 - - + -
397B ILE* 4.1 7.6 - - + -
408B GLY 3.2 12.3 - - - +
410B PHE* 3.7 7.0 - - - -
421B CYS* 1.3 74.1 - - - +
423B TRP* 1.3 61.6 - - - +
424B VAL* 3.6 29.4 - - + -
445B SER* 3.2 4.2 - - - -
446B PHE* 2.9 64.7 + + + +
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Residues in contact with TRP 423 (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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119B GLU* 4.6 7.0 - - - -
120B PRO* 3.9 23.6 - - + +
121B PHE* 3.4 29.3 - - + +
122B ILE* 3.6 25.9 + - + +
227B GLU 3.7 14.8 - - - -
228B SER* 3.9 2.5 - - - -
350B LYS* 3.8 7.9 - - + -
406B TYR* 3.6 34.8 - - + -
407B SER* 3.1 15.6 - - - -
408B GLY* 3.0 54.1 + - - +
409B SER 4.0 6.4 + - - -
410B PHE* 3.9 11.9 - + - -
422B PHE* 1.3 76.8 - - - +
424B VAL* 1.3 68.7 + - - +
425B GLU* 3.8 15.7 - - + -
443B SER* 5.5 1.8 - - - -
444B ILE 3.3 11.4 - - - +
445B SER* 4.0 7.4 - - - -
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Residues in contact with VAL 424 (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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374B PHE* 3.8 39.0 - - + -
397B ILE* 4.6 0.4 - - + -
404B SER* 4.3 7.2 - - - -
405B GLY 4.6 0.9 - - - +
406B TYR 3.6 8.1 - - - +
422B PHE* 3.6 27.1 - - + -
423B TRP* 1.3 83.7 - - - +
425B GLU* 1.3 73.2 + - - +
426B LEU* 3.9 13.3 + - + +
443B SER* 3.3 6.8 - - - -
444B ILE* 2.9 51.2 + - + +
446B PHE* 5.2 0.2 - - + -
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Residues in contact with GLU 425 (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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118B ARG* 2.6 48.8 + - - -
119B GLU 2.8 22.7 + - - -
120B PRO* 3.7 22.4 - - + -
404B SER 3.0 1.0 - - - -
405B GLY* 3.0 26.3 + - - -
406B TYR* 2.8 35.1 + - - +
423B TRP* 3.8 4.9 - - + -
424B VAL* 1.3 75.3 - - - +
426B LEU* 1.3 61.6 + - - +
427B ILE* 3.3 13.2 - - + +
441B GLY* 4.2 9.7 - - - -
442B SER 3.4 4.7 - - - -
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Residues in contact with LEU 426 (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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102B LYS* 4.8 1.6 - - - +
398B VAL* 4.0 19.3 - - + -
403B TRP 3.8 19.1 - - - +
404B SER* 3.8 4.7 - - - -
424B VAL* 4.0 21.1 - - + +
425B GLU* 1.3 76.8 - - - +
427B ILE* 1.3 60.9 + - - +
428B ARG* 3.6 8.9 + - - +
441B GLY* 3.2 4.1 - - - -
442B SER* 2.8 45.7 + - - +
443B SER 4.7 1.6 - - - -
444B ILE* 4.1 18.4 - - + -
458B TRP 3.6 9.4 - - - +
459B PRO 3.6 7.6 - - - +
460B ASP* 3.4 36.1 - - + +
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Residues in contact with ILE 427 (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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118B ARG* 3.4 18.2 - - - +
371B ARG* 4.1 21.5 - - + +
403B TRP* 3.3 25.8 - - - +
404B SER* 2.9 15.5 + - - +
405B GLY* 3.7 16.2 - - - -
406B TYR 4.3 0.4 - - - +
425B GLU* 3.3 36.3 - - + +
426B LEU* 1.3 70.3 - - - +
428B ARG* 1.3 65.1 + - - +
429B GLY 5.8 0.2 - - - +
430B GLN 4.6 4.9 - - - +
431B PRO* 6.1 0.9 - - + -
433B GLU* 4.4 0.2 - - - +
439B THR* 3.8 28.7 - - + -
440B SER 3.4 6.7 - - - +
441B GLY* 4.1 0.4 - - - -
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Residues in contact with ARG 428 (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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106B ILE* 3.7 19.1 - - + -
403B TRP* 3.8 17.6 - - - -
426B LEU* 4.1 2.2 - - - +
427B ILE* 1.3 85.1 - - - +
429B GLY* 1.3 61.6 + - - +
433B GLU* 2.8 37.9 + - - -
438B TRP* 3.6 6.3 - - + -
439B THR* 3.4 5.5 - - - +
440B SER 2.7 35.0 + - - -
460B ASP* 2.8 56.8 + - + +
461B GLY 4.1 2.0 - - - +
462B ALA* 2.9 30.3 + - - +
464B LEU* 3.7 25.2 - - + +
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Residues in contact with GLY 429 (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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427B ILE* 5.8 0.2 - - - +
428B ARG* 1.3 74.2 - - - +
430B GLN* 1.3 67.0 + - - +
432B LYS* 3.3 4.0 + - - +
433B GLU* 2.8 45.6 + - - +
436B THR* 3.1 20.2 - - - -
438B TRP* 3.3 4.0 - - - -
464B LEU* 3.6 5.5 - - - +
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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