Contacts of the strand formed by residues 321 - 329 (chain B) in PDB entry 1U0C
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 GLY 321 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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316B PHE 3.7 0.6 + - - -
317B VAL* 2.8 31.5 + - - -
319B GLY 3.5 0.4 - - - -
320B ASP* 1.3 80.5 - - - +
322B SER* 1.3 63.9 + - - -
344B GLN 3.1 10.5 - - - -
345B VAL* 4.2 4.0 - - - -
398B LYS* 3.1 20.3 + - - -
565D G 3.5 12.6 - - - +
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Residues in contact with SER 322 (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 VAL* 4.7 2.6 - - - +
321B GLY* 1.3 78.1 - - - -
323B ILE* 1.3 62.0 + - - +
324B ILE* 2.7 28.1 - - - +
342B THR 3.3 4.2 - - - +
343B PHE* 3.6 1.8 - - - -
344B GLN* 2.7 53.3 + - - +
398B LYS* 4.5 0.9 - - - +
565D G 3.5 18.0 - - - +
566D A 2.6 20.8 + - - -
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Residues in contact with ILE 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B VAL* 4.0 15.9 - - + -
322B SER* 1.3 74.9 + - - +
324B ILE* 1.3 60.3 + - - +
342B THR 3.4 7.0 - - - +
343B PHE* 4.6 13.7 - - + -
388B LEU* 4.6 11.2 - - + -
391B LEU* 6.0 0.2 - - + -
395B LEU* 5.1 4.0 - - + -
398B LYS* 3.6 38.7 - - + +
401B GLN* 3.8 23.5 - - + +
402B ALA* 4.2 12.8 - - + +
405B VAL* 3.3 33.9 - - + -
432B ILE* 3.8 5.9 - - + +
436B ASN* 3.1 23.3 + - - +
566D A 4.4 1.8 + - - -
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Residues in contact with ILE 324 (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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322B SER* 2.7 35.7 - - - +
323B ILE* 1.3 80.3 - - - +
325B ALA* 1.3 65.7 + - - +
326B GLN* 3.5 32.3 - - + +
340B SER 4.5 0.4 - - - -
341B LEU* 3.5 7.8 - - - +
342B THR* 2.7 55.6 + - + +
344B GLN* 4.8 5.6 - - + -
405B VAL* 4.4 4.0 - - - +
432B ILE* 4.8 1.3 - - - -
436B ASN* 4.0 4.0 - - - +
566D A 3.5 26.2 - - + -
567D C 4.0 21.8 - - + +
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Residues in contact with ALA 325 (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 ILE* 1.3 76.7 - - - +
326B GLN* 1.3 67.4 + - - +
340B SER 3.6 4.9 - - - -
341B LEU* 3.8 10.8 - - + -
408B ILE* 4.4 1.3 - - + -
429B VAL* 3.6 23.6 - - + +
432B ILE* 3.4 38.9 - - + +
433B ALA* 5.5 0.2 - - - +
441B ARG* 3.9 14.4 + - - -
567D C 4.5 7.5 + - - +
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Residues in contact with GLN 326 (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 ILE* 3.5 22.6 - - + +
325B ALA* 1.3 82.3 - - - +
327B ILE* 1.3 65.8 + - - +
328B LYS* 3.0 38.5 + - + +
338B GLN 3.7 1.0 - - - +
339B LEU* 3.8 2.6 - - - +
340B SER* 3.0 34.1 + - - +
342B THR* 4.2 13.7 + - - -
429B VAL* 4.4 2.2 - - - +
441B ARG* 5.1 2.0 - - - +
567D C 4.0 24.7 - - - +
568D G 3.4 42.4 + - - +
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Residues in contact with ILE 327 (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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326B GLN* 1.3 72.9 - - - +
328B LYS* 1.3 58.5 + - - +
329B PRO* 3.5 0.7 - - - +
337B HIS* 3.8 24.0 - - + -
338B GLN 4.1 2.0 - - - +
339B LEU* 3.2 31.6 - - + -
426B CYS* 3.4 19.1 - - + -
429B VAL* 3.6 29.7 - - + +
441B ARG* 5.2 0.2 - - - +
443B THR* 3.2 46.3 + - + +
444B THR 4.6 8.7 - - - -
445B SER 4.7 0.4 - - - +
448B VAL* 3.7 24.2 - - + -
568D G 4.8 5.0 + - - -
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Residues in contact with LYS 328 (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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326B GLN* 3.0 40.1 - - + +
327B ILE* 1.3 72.9 - - - +
329B PRO* 1.3 73.2 - - + +
330B ASN* 3.1 1.9 + - - +
337B HIS* 3.2 2.0 - - - -
338B GLN* 2.9 58.0 + - + +
340B SER* 3.1 29.9 + - - -
342B THR* 5.4 0.2 + - - -
505C A 5.1 5.6 - - - +
506C A 4.3 9.6 - - - +
568D G 5.4 1.1 + - - +
569D T 2.6 44.9 - - + +
570D T 5.3 7.0 - - + +
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Residues in contact with PRO 329 (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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327B ILE 3.5 8.7 - - - +
328B LYS* 1.3 86.2 - - + +
330B ASN* 1.3 59.5 + - - +
331B GLN* 6.0 0.7 - - - -
336B LYS 3.5 1.3 - - - +
337B HIS* 3.4 23.0 - - + +
443B THR* 3.8 18.4 - - + +
569D T 3.7 27.4 - - + +
570D T 5.3 9.0 - - - +
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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