Contacts of the strand formed by residues 317 - 326 (chain B) in PDB entry 3HO5
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 HIS 317 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273B GLN* 5.6 0.7 - - + -
282B ARG* 4.0 13.4 - - + +
304B THR* 3.1 40.2 + - + +
305B THR 3.4 14.6 - - - +
306B ASN* 4.0 6.7 - - - +
315B HIS* 3.7 6.8 - - - +
316B ASP* 1.3 102.8 - - + +
318B ILE* 1.3 73.0 + - - +
319B LEU* 4.8 1.8 - - + -
347B GLU* 2.9 48.6 + - + +
349B HIS 2.7 24.9 + - - -
350B ARG* 4.2 3.2 - - - -
353B LEU* 4.1 13.9 - - + +
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Residues in contact with ILE 318 (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 THR* 3.0 39.8 + - + +
307B GLN 5.0 2.9 - - - +
308B GLU* 3.5 18.4 - - - +
310B TRP* 3.7 36.3 - - + -
315B HIS* 4.0 13.7 - - + +
317B HIS* 1.3 87.8 - - - +
319B LEU* 1.3 60.3 + - - +
320B ARG* 3.6 8.0 + - + +
344B GLU* 3.4 37.9 - - + +
345B VAL 3.4 10.3 - - - +
346B ALA* 3.9 13.9 - - - -
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Residues in contact with LEU 319 (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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285B LEU* 3.8 30.1 - - + -
302B SER* 4.6 6.3 - - - -
303B TYR 3.6 6.5 - - - +
304B THR* 4.4 7.0 - - - +
317B HIS* 4.3 3.5 + - + +
318B ILE* 1.3 70.1 - - - +
320B ARG* 1.3 74.8 + - - +
321B VAL* 4.3 12.1 - - + -
343B LEU 3.9 0.2 - - - +
344B GLU* 3.6 2.1 - - - -
345B VAL* 2.8 51.1 + - + +
347B GLU* 4.3 12.7 + - - +
353B LEU* 4.2 20.2 - - + +
355B GLY* 4.6 3.8 - - - -
369B LEU* 3.7 33.0 - - + -
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Residues in contact with ARG 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B LEU* 3.5 20.6 - - - +
301B VAL 3.6 0.7 - - - +
302B SER* 3.0 8.3 - - - -
303B TYR* 2.8 70.6 + - + +
305B THR* 3.5 26.8 + - + +
308B GLU* 3.3 34.0 + - - +
318B ILE* 3.6 2.7 + - + -
319B LEU* 1.3 75.2 - - - +
321B VAL* 1.3 63.2 + - - +
322B VAL* 3.8 17.2 - - + +
341B VAL* 4.5 15.9 - - + +
343B LEU 3.4 9.6 - - - +
344B GLU* 3.6 24.2 + - + -
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Residues in contact with VAL 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B TYR* 5.1 4.5 - - + -
301B VAL 3.4 5.4 - - - +
302B SER* 4.3 6.3 - - - -
319B LEU* 4.3 12.1 - - + -
320B ARG* 1.3 75.5 - - - +
322B VAL* 1.3 67.6 + - - +
342B PHE* 2.8 34.7 + - + +
343B LEU* 3.1 41.0 + - + +
345B VAL* 5.8 0.7 - - + -
357B LEU* 4.0 21.1 - - + -
365B LEU* 4.8 11.2 - - + -
367B ILE* 4.2 24.2 - - + -
395B LEU* 6.0 0.4 - - + -
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Residues in contact with VAL 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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300B TYR* 3.4 5.4 - - - -
301B VAL* 2.7 43.5 + - + +
303B TYR* 4.1 17.3 - - + +
320B ARG* 3.8 28.7 - - + +
321B VAL* 1.3 82.0 - - - +
323B GLU* 1.3 77.0 + - - +
324B TYR* 3.8 21.3 + - + -
339B ALA* 4.0 7.2 - - + -
340B ARG 3.6 16.4 - - - +
341B VAL* 4.0 16.4 - - + +
342B PHE* 4.4 0.7 - - - +
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Residues in contact with GLU 323 (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 LYS* 2.9 31.9 + - + +
299B LEU 3.4 11.0 - - - +
300B TYR* 3.0 42.5 + - + -
322B VAL* 1.3 73.7 - - - +
324B TYR* 1.3 64.1 + - - +
325B THR* 4.1 2.8 + - - -
338B THR 3.5 2.8 - - - +
339B ALA* 3.2 7.6 - - - -
340B ARG* 2.6 79.0 + - + +
342B PHE* 3.6 15.8 - - + -
619B PRO* 3.8 3.8 - - - +
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Residues in contact with TYR 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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266B LEU* 4.8 5.2 - - + -
268B ILE* 3.1 37.3 - - + +
271B LEU* 3.6 16.1 - - - +
298B LYS* 3.5 4.0 - - - -
299B LEU* 2.9 51.0 + - + +
301B VAL* 4.5 14.6 - - + -
303B TYR* 4.7 2.1 + + - -
322B VAL* 3.8 21.4 + - + +
323B GLU* 1.3 80.1 - - - +
325B THR* 1.3 65.2 + - - +
334B VAL* 3.9 17.5 - - + -
335B ASP 3.9 10.3 - - - -
336B LEU* 3.6 28.7 + - + +
338B THR* 3.9 4.9 - - - -
339B ALA* 3.5 26.4 - - + +
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Residues in contact with THR 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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296B ASN 4.0 10.8 - - - +
297B GLY 3.4 11.9 - - - +
298B LYS* 2.8 30.0 + - - +
299B LEU* 4.0 4.0 - - - -
323B GLU* 4.1 1.7 + - - -
324B TYR* 1.3 74.4 - - - +
326B VAL* 1.3 73.2 + - - +
328B ARG* 6.4 1.8 - - - -
334B VAL* 3.7 2.0 - - - +
335B ASP* 2.9 24.4 + - - +
338B THR* 2.9 32.7 + - + +
604B LEU* 4.2 9.4 - - + -
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Residues in contact with VAL 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B TYR* 3.1 27.6 - - + +
293B TYR* 2.7 31.4 - - + +
297B GLY* 3.0 31.1 + - - +
299B LEU* 3.9 1.8 - - - +
325B THR* 1.3 83.6 - - - +
327B SER* 1.3 71.6 + - - +
328B ARG* 3.4 3.1 + - - +
330B ASN 4.8 0.7 - - - +
331B PRO* 4.2 12.1 - - + +
333B GLN 3.8 7.0 - - - +
334B VAL* 3.8 2.9 - - - +
335B ASP* 4.5 2.0 - - - +
338B THR* 5.6 0.5 - - - +
604B LEU* 3.8 23.5 - - + +
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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