Contacts of the strand formed by residues 298 - 305 (chain A) 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 LYS 298 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289A PHE 3.9 0.2 - - - -
290A HIS* 3.0 34.3 + - + +
293A TYR* 3.4 9.1 - - - -
296A ASN* 2.9 37.1 + - - +
297A GLY* 1.3 72.8 - - - +
299A LEU* 1.3 59.7 + - - +
300A TYR* 4.2 10.0 - - + +
323A GLU* 2.7 38.5 + - - +
324A TYR 3.5 3.6 - - - +
325A THR* 2.8 28.4 + - - +
338A THR 5.8 0.2 + - - -
340A ARG* 4.1 2.2 - - - +
617A CYS* 3.1 28.7 + - - +
618A THR 3.8 1.1 - - - -
619A PRO* 3.6 28.3 - - + -
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Residues in contact with LEU 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A TYR* 3.4 44.0 - - + +
266A LEU* 4.7 6.3 - - + -
287A LEU* 4.1 18.8 - - + -
288A ALA 3.7 5.2 - - - -
289A PHE* 4.4 9.4 - - + +
293A TYR* 4.2 1.1 - - + -
297A GLY 4.0 4.0 - - - +
298A LYS* 1.3 72.0 - - - +
300A TYR* 1.3 77.5 + - - +
301A VAL* 4.6 7.0 - - + -
323A GLU* 3.4 4.2 - - - +
324A TYR* 2.8 55.4 + - + +
325A THR* 3.9 4.9 - - - +
326A VAL 3.9 12.8 - - - +
334A VAL* 3.8 12.3 - - + -
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Residues in contact with TYR 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A LEU* 3.3 5.4 - - - +
288A ALA* 2.8 50.5 + - + +
290A HIS* 3.9 14.9 - + - -
298A LYS* 4.2 11.5 - - + +
299A LEU* 1.3 81.7 - - - +
301A VAL* 1.3 62.7 + - - +
321A VAL* 5.3 2.9 - - + -
322A VAL 3.4 4.7 - - - +
323A GLU* 2.8 45.1 + - + -
342A PHE* 3.7 22.4 - + - -
357A LEU* 3.4 18.2 - - + +
359A PHE* 3.6 29.6 - + - -
365A LEU* 4.4 13.7 - - + -
397A VAL* 3.5 25.2 - - + +
619A PRO* 4.0 4.5 - - - +
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Residues in contact with VAL 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A LEU* 4.7 14.6 - - + -
268A ILE* 5.2 2.0 - - + -
284A LEU* 3.4 31.0 - - + -
286A SER 3.4 4.9 - - - +
287A LEU* 4.1 17.3 - - + -
299A LEU* 4.6 9.4 - - + -
300A TYR* 1.3 79.0 - - - +
302A SER* 1.3 61.9 + - - +
303A TYR* 3.8 21.2 + - + -
320A ARG 3.9 0.3 - - - +
321A VAL* 3.3 3.1 - - - +
322A VAL* 2.8 35.1 + - - +
324A TYR* 4.1 24.7 - - + -
357A LEU* 3.8 2.9 - - - -
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Residues in contact with SER 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A LEU* 4.0 2.3 - - - +
285A LEU* 3.0 23.1 + - - +
286A SER* 2.9 23.9 + - - +
301A VAL* 1.3 72.6 - - - +
303A TYR* 1.3 61.8 + - - +
319A LEU* 4.5 7.2 - - - -
320A ARG 3.2 11.4 - - - -
321A VAL* 4.1 6.1 - - - -
355A GLY* 2.6 32.4 + - - -
357A LEU* 3.7 15.2 - - - +
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Residues in contact with TYR 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A ILE* 4.1 20.9 - - + +
271A LEU* 3.9 29.0 - - + +
272A VAL* 3.9 14.8 - - + -
283A GLY 3.9 10.8 - - - +
284A LEU* 4.1 15.3 - - + -
285A LEU* 4.2 6.9 - - - +
301A VAL* 3.8 20.6 - - + -
302A SER* 1.3 73.7 - - - +
304A THR* 1.3 70.9 + - - +
305A THR* 3.8 22.2 - - + -
319A LEU* 3.6 1.7 - - - +
320A ARG* 2.7 69.6 + - + +
322A VAL* 3.6 27.6 - - + +
324A TYR* 4.6 1.7 + - - -
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Residues in contact with THR 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A VAL* 3.2 11.3 - - - +
273A GLN* 2.9 24.4 + - + +
282A ARG* 2.9 41.6 + - + +
283A GLY 3.2 7.4 + - - -
285A LEU* 4.0 8.0 - - - +
303A TYR* 1.3 75.6 + - - +
305A THR* 1.3 62.9 + - - +
317A HIS* 3.1 35.6 + - + +
318A ILE 3.8 3.6 - - - -
319A LEU* 4.6 4.0 - - - +
353A LEU* 3.8 17.2 - - - +
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Residues in contact with THR 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A LEU* 2.9 23.7 + - - +
273A GLN* 4.1 4.0 - - - +
303A TYR* 3.8 8.1 - - - -
304A THR* 1.3 74.8 - - - +
306A ASN* 1.3 85.2 + - - +
317A HIS* 3.4 1.8 - - - +
318A ILE* 3.1 49.9 + - + +
320A ARG* 3.5 44.9 + - + +
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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
------------------------------------------------------------
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