Contacts of the strand formed by residues 380 - 395 (chain B) in PDB entry 4UI2
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 380 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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315B VAL* 5.1 6.3 - - + -
372B LEU* 4.4 27.4 - - + -
373B TYR 3.5 4.9 - - - +
374B LEU* 3.6 19.5 - - + -
379B LYS* 1.3 77.7 - - - +
381B VAL* 1.3 77.0 + - - +
382B LEU* 4.3 4.3 - - + +
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Residues in contact with VAL 381 (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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371B MET 3.7 1.0 - - - +
372B LEU* 3.3 6.1 - - - +
373B TYR* 2.7 79.2 + - + +
375B ASP* 4.2 24.5 - - + +
379B LYS 4.3 0.4 - - - +
380B VAL* 1.3 81.8 - - - +
382B LEU* 1.3 69.4 + - - +
383B LYS* 4.3 4.3 - - + -
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Residues in contact with LEU 382 (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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370B SER* 3.9 26.2 - - - +
371B MET 3.4 5.6 - - - +
372B LEU* 3.7 22.0 - - + -
380B VAL* 4.2 4.5 - - + +
381B VAL* 1.3 76.2 - - - +
383B LYS* 1.3 64.3 + - - +
384B ASN* 5.2 1.8 - - + +
1400B ACT 5.8 5.6 - - + -
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Residues in contact with LYS 383 (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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370B SER* 3.4 3.6 - - - -
371B MET 2.9 30.7 + - - +
373B TYR* 4.0 20.4 - - + +
381B VAL* 4.3 3.6 - - + -
382B LEU* 1.3 77.5 - - - +
384B ASN* 1.3 67.1 + - - +
385B TYR* 3.2 37.0 - - + +
1399B SRT 3.3 56.5 + - - -
101C GLY 4.7 1.8 - - - +
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Residues in contact with ASN 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B ALA* 3.7 11.6 - - - +
369B ILE* 3.3 23.1 - - - +
370B SER* 3.4 12.8 + - - +
382B LEU* 5.2 1.8 - - + +
383B LYS* 1.3 82.6 + - - +
385B TYR* 1.3 61.8 + - - +
386B GLN* 3.6 25.7 + - - +
1399B SRT 3.4 15.2 - - - +
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Residues in contact with TYR 385 (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 TRP* 3.6 12.5 - + - -
368B ALA* 3.2 16.8 - - - -
369B ILE* 2.9 16.7 + - + +
371B MET* 3.7 33.4 - - + -
373B TYR* 3.8 7.1 - - - -
383B LYS* 3.2 38.5 - - + +
384B ASN* 1.3 72.3 + - - +
386B GLN* 1.3 59.5 + - - +
388B MET* 3.0 34.9 - - + +
1399B SRT 3.7 28.7 - - - +
101C GLY 2.6 33.0 + - - -
103C LEU* 4.1 26.7 - - + -
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Residues in contact with GLN 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B ALA* 3.4 27.3 - - - +
384B ASN* 3.6 18.1 + - - +
385B TYR* 1.3 75.0 - - - +
387B ASP* 1.3 85.7 + - - +
388B MET* 3.2 7.6 + - - +
1399B SRT 3.5 27.3 + - - +
103C LEU* 6.0 0.2 - - - +
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Residues in contact with ASP 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B LEU* 3.7 42.9 - - + +
367B SER* 3.6 11.9 + - - +
368B ALA 4.4 0.2 - - - +
386B GLN* 1.3 85.9 - - - +
388B MET* 1.3 62.5 + - - +
389B VAL 3.8 0.2 - - - -
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Residues in contact with MET 388 (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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310B TRP* 5.3 4.5 - - + -
320B TYR* 2.8 57.0 + - + +
322B ALA* 4.0 7.1 - - - +
366B LEU* 4.9 2.3 - - - +
367B SER 2.7 12.9 + - - +
369B ILE* 3.8 22.4 - - + -
371B MET* 4.4 18.4 - - + -
385B TYR* 3.0 37.7 - - + +
386B GLN 3.6 6.3 - - - +
387B ASP* 1.3 79.8 - - - +
389B VAL* 1.3 59.7 + - - +
390B VAL* 4.1 0.9 + - - +
103C LEU* 3.8 29.4 - - + -
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Residues in contact with VAL 389 (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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298B ARG* 5.0 0.2 - - - +
320B TYR* 4.0 6.1 - - + -
321B HIS 3.4 24.2 - - - +
322B ALA* 3.8 3.1 - - - +
323B PHE* 3.7 18.6 - - + -
366B LEU* 3.2 6.2 - - - -
367B SER* 2.7 48.1 + - - +
369B ILE* 3.6 30.3 - - + -
388B MET* 1.3 79.9 - - - +
390B VAL* 1.3 68.3 + - - +
391B GLU* 4.5 8.5 - - - +
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Residues in contact with VAL 390 (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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298B ARG* 2.6 44.0 + - + -
322B ALA 3.1 19.1 + - - +
323B PHE* 4.0 17.9 - - + +
324B TYR* 4.4 3.8 - - - -
325B CYS* 3.8 16.4 - - - +
363B PRO* 3.7 28.0 - - + -
365B GLU 3.8 3.8 - - - +
366B LEU* 4.4 7.6 - - + -
388B MET 5.4 1.1 - - - +
389B VAL* 1.3 72.3 - - - +
391B GLU* 1.3 55.2 - - - +
392B GLY 3.5 24.0 - - - +
393B CYS* 4.0 0.4 - - - -
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Residues in contact with GLU 391 (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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298B ARG* 3.9 17.8 + - - +
365B GLU* 2.8 38.4 + - + +
366B LEU 4.2 0.7 - - - -
367B SER* 3.3 41.4 + - - +
389B VAL* 3.4 7.0 + - - +
390B VAL* 1.3 77.2 - - - +
392B GLY* 1.3 57.8 + - - +
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Residues in contact with GLY 392 (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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298B ARG* 5.3 2.5 - - - -
363B PRO* 3.4 5.9 - - - +
364B THR* 3.0 29.0 + - - -
365B GLU* 3.1 12.8 + - - -
390B VAL* 3.5 5.2 - - - +
391B GLU* 1.3 81.6 - - - +
393B CYS* 1.3 66.5 + - - -
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Residues in contact with CYS 393 (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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296B CYS* 4.0 14.6 - - - +
297B LYS* 3.4 20.9 - - - +
298B ARG* 3.5 19.5 - - - +
325B CYS* 2.0 50.0 - - + -
337B LEU 5.6 0.2 - - - +
338B ASN* 3.3 14.0 - - - +
362B VAL 3.3 4.5 - - - -
364B THR* 3.5 5.8 + - - -
390B VAL* 4.0 1.8 - - - -
392B GLY* 1.3 75.9 - - - -
394B GLY* 1.3 58.9 + - - +
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Residues in contact with GLY 394 (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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296B CYS* 3.9 4.9 - - - -
337B LEU 5.8 0.7 - - - -
338B ASN* 3.7 10.3 - - - -
360B CYS 3.4 0.5 - - - +
361B CYS* 3.3 4.9 - - - -
362B VAL* 2.9 32.0 + - - +
364B THR* 3.1 16.7 - - - +
393B CYS* 1.3 76.0 - - - +
395B CYS* 1.3 66.2 + - - -
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Residues in contact with CYS 395 (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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296B CYS* 4.1 10.8 - - - -
329B CYS* 2.0 53.4 - - + -
333B LEU* 5.2 4.9 - - - -
334B ALA* 4.4 16.2 - - + -
338B ASN 3.6 6.1 + - - -
339B SER* 3.6 22.3 + - - +
343B ALA* 3.7 6.1 - - + +
359B ALA* 3.9 8.1 - - + -
360B CYS 3.3 3.8 - - - -
394B GLY* 1.3 76.7 - - - -
396B ARG* 1.3 73.9 + - - +
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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