Contacts of the strand formed by residues 361 - 374 (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 CYS 361 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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296B CYS* 2.1 52.7 - - + -
297B LYS 3.9 0.4 - - - -
325B CYS* 3.8 14.8 - - - +
326B HIS* 3.5 27.1 - - - -
327B GLY 3.1 24.7 + - - +
329B CYS* 3.9 4.6 - - - -
360B CYS* 1.3 78.7 - - - +
362B VAL* 1.3 64.9 + - - +
394B GLY 3.3 5.2 - - - -
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Residues in contact with VAL 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B CYS* 3.4 7.4 - - - -
360B CYS* 3.9 20.4 - - + +
361B CYS* 1.3 80.5 - - - +
363B PRO* 1.3 84.0 - - + +
364B THR* 3.5 1.1 - - + +
393B CYS* 3.3 2.1 - - - -
394B GLY 2.9 33.4 + - - +
396B ARG* 3.6 34.5 - - + -
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Residues in contact with PRO 363 (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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324B TYR* 5.6 0.4 - - - -
325B CYS* 3.5 14.1 - - + +
362B VAL* 1.3 97.5 - - + +
364B THR* 1.3 60.5 + - - +
366B LEU* 4.1 27.5 - - + +
390B VAL* 3.7 33.0 - - + -
392B GLY 3.4 9.2 - - - +
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Residues in contact with THR 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B ASN* 2.6 33.3 + - - +
362B VAL* 3.5 6.1 - - + +
363B PRO* 1.3 73.9 - - - +
365B GLU* 1.3 64.4 + - - +
366B LEU* 4.7 3.1 - - - -
392B GLY* 3.0 14.8 + - - -
393B CYS 3.5 0.6 + - - -
394B GLY* 3.1 38.8 - - - +
396B ARG* 3.7 26.0 + - - +
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Residues in contact with GLU 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B ASN* 5.4 1.6 - - - +
363B PRO 3.7 0.2 - - - -
364B THR* 1.3 86.3 + - - +
366B LEU* 1.3 73.3 + - - +
390B VAL* 3.8 1.2 - - - +
391B GLU* 2.8 47.2 + - + +
392B GLY* 3.1 14.1 + - - +
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Residues in contact with LEU 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B PRO* 4.1 32.3 - - + +
364B THR 4.7 1.6 - - - -
365B GLU* 1.3 90.4 - - - +
367B SER* 1.3 59.6 + - - +
387B ASP* 3.7 50.4 - - + +
388B MET 4.9 1.8 - - - +
389B VAL 3.2 13.0 - - - +
390B VAL* 4.4 9.4 - - + -
391B GLU* 4.2 4.7 - - - +
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Residues in contact with SER 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B LEU* 1.3 74.0 - - - +
368B ALA* 1.3 61.5 + - - +
369B ILE* 5.2 0.2 - - - +
387B ASP 4.1 4.5 - - - -
388B MET 2.7 32.2 + - - -
389B VAL* 2.7 39.8 + - - +
391B GLU* 3.3 25.9 + - - +
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Residues in contact with ALA 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B SER* 1.3 81.6 + - - +
369B ILE* 1.3 68.4 + - - +
384B ASN* 3.7 14.6 - - - +
385B TYR 3.2 17.7 - - - +
386B GLN* 3.4 31.2 - - - +
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Residues in contact with ILE 369 (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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317B PRO* 5.3 2.7 - - + -
320B TYR* 3.5 38.6 - - + -
367B SER* 4.3 0.4 + - - +
368B ALA* 1.3 79.1 - - - +
370B SER* 1.3 64.2 + - - +
371B MET* 3.9 27.4 - - + -
384B ASN* 3.3 7.0 - - - -
385B TYR* 2.9 27.3 + - + +
388B MET* 3.8 19.7 - - + -
389B VAL* 3.6 23.3 - - + -
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Residues in contact with SER 370 (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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317B PRO* 4.1 1.7 - - - +
369B ILE* 1.3 79.5 - - - +
371B MET* 1.3 65.9 + - - +
382B LEU* 3.9 27.1 - - - +
383B LYS 3.4 7.6 - - - -
384B ASN* 3.4 17.1 + - - +
1400B ACT 3.3 33.6 - - - +
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Residues in contact with MET 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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305B PHE* 3.6 35.4 - - + -
310B TRP* 5.0 0.9 - - + -
313B TRP* 4.5 2.9 - - + -
314B ILE* 4.0 22.0 - - + -
316B ALA 3.5 7.6 - - - +
317B PRO* 3.9 8.3 - - + -
369B ILE* 3.9 17.7 + - + -
370B SER* 1.3 79.7 - - - +
372B LEU* 1.3 66.4 + - - +
373B TYR* 5.3 0.9 - - + -
381B VAL 3.7 0.9 - - - +
382B LEU* 3.4 3.8 - - - +
383B LYS* 2.9 32.6 + - - +
385B TYR* 3.7 40.4 - - + +
388B MET* 4.4 8.3 - - + -
1400B ACT 5.3 1.3 - - - -
103C LEU* 4.2 15.9 - - + -
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Residues in contact with LEU 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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314B ILE* 3.5 6.8 - - - +
315B VAL* 2.8 36.2 + - + -
316B ALA* 2.8 39.5 + - + +
370B SER* 6.3 0.2 - - - -
371B MET* 1.3 82.1 - - - +
373B TYR* 1.3 64.8 + - - +
380B VAL* 4.4 20.4 - - + -
381B VAL 3.3 3.4 - - - +
382B LEU* 3.7 36.1 - - + +
1400B ACT 5.8 9.0 - - + +
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Residues in contact with TYR 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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313B TRP* 3.2 35.7 - + + +
315B VAL* 4.0 5.4 - - - -
371B MET* 5.0 1.1 - - + -
372B LEU* 1.3 75.6 - - - +
374B LEU* 1.3 82.3 + - - +
375B ASP* 4.7 1.3 - - - -
380B VAL* 3.5 3.8 - - - +
381B VAL* 2.7 73.3 + - + +
383B LYS* 4.0 13.6 - - + +
385B TYR* 3.8 18.2 - + - -
100C ARG* 3.9 18.9 - - + +
101C GLY* 3.4 32.2 + - - -
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Residues in contact with LEU 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
896A LEU* 3.3 38.6 - - + +
897A SER* 4.8 4.5 - - - -
313B TRP 4.5 2.4 + - - -
315B VAL* 3.7 19.7 - - + +
373B TYR* 1.3 89.5 - - - +
375B ASP* 1.3 64.1 + - - +
378B GLU* 3.7 28.9 - - - +
379B LYS 3.3 3.1 - - - +
380B VAL* 3.6 30.3 - - + -
100C ARG* 2.9 31.6 + - - +
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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